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Conserved domains on  [gi|19112314|ref|NP_595522|]
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AP-endonuclease Apn2 [Schizosaccharomyces pombe]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-302 1.24e-157

Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


:

Pssm-ID: 197322 [Multi-domain]  Cd Length: 309  Bit Score: 451.00  E-value: 1.24e-157
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   2 RILSWNVNGIQNPFNYFPWNKKNSYKEIFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFPKIRKGYSGVGFYVK 81
Cdd:cd09088   1 RIVTWNVNGIRTRLQYQPWNKENSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGVATYCR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  82 KDVAIPVKAEEGITGILPVRGQKYsysEAPEHEKIGFFPKDID---RKTANWIDSEGRCILLDFQMFILIGVYCPVNSG- 157
Cdd:cd09088  81 DSAATPVAAEEGLTGVLSSPNQKN---ELSENDDIGCYGEMLEftdSKELLELDSEGRCVLTDHGTFVLINVYCPRADPe 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 158 -ENRLEYRRAFYKALRERIERLIKEGnRKIILVGDVNILCNPIDTADQKDIIRESL-IPSIMESRQWIR------DLLLP 229
Cdd:cd09088 158 kEERLEFKLDFYRLLEERVEALLKAG-RRVILVGDVNVSHRPIDHCDPDDSEDFGGeSFEDNPSRQWLDqllgdsGEGGG 236

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19112314 230 SRLGLLLDIGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLDL 302
Cdd:cd09088 237 SPGGLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
zf-GRF super family cl46396
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 456-513 4.31e-04

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


The actual alignment was detected with superfamily member pfam06839:

Pssm-ID: 480736  Cd Length: 45  Bit Score: 38.15  E-value: 4.31e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 19112314   456 PLCEgHKEPCKYLTVRKPGINYGRKFWICarPVGEliknsnavseedtqPFQCRFFIW 513
Cdd:pfam06839   1 PLCP-CGQRAVLLTVRKTGPNPGRQFYKC--PVGR--------------EKQCGFFQW 41
 
Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-302 1.24e-157

Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197322 [Multi-domain]  Cd Length: 309  Bit Score: 451.00  E-value: 1.24e-157
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   2 RILSWNVNGIQNPFNYFPWNKKNSYKEIFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFPKIRKGYSGVGFYVK 81
Cdd:cd09088   1 RIVTWNVNGIRTRLQYQPWNKENSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGVATYCR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  82 KDVAIPVKAEEGITGILPVRGQKYsysEAPEHEKIGFFPKDID---RKTANWIDSEGRCILLDFQMFILIGVYCPVNSG- 157
Cdd:cd09088  81 DSAATPVAAEEGLTGVLSSPNQKN---ELSENDDIGCYGEMLEftdSKELLELDSEGRCVLTDHGTFVLINVYCPRADPe 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 158 -ENRLEYRRAFYKALRERIERLIKEGnRKIILVGDVNILCNPIDTADQKDIIRESL-IPSIMESRQWIR------DLLLP 229
Cdd:cd09088 158 kEERLEFKLDFYRLLEERVEALLKAG-RRVILVGDVNVSHRPIDHCDPDDSEDFGGeSFEDNPSRQWLDqllgdsGEGGG 236

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19112314 230 SRLGLLLDIGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLDL 302
Cdd:cd09088 237 SPGGLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-303 2.71e-46

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 162.17  E-value: 2.71e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   1 MRILSWNVNGI---QNPFnyFPWnkknsykeiFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFpkiRKGYSGVG 77
Cdd:COG0708   1 MKIASWNVNGIrarLPKL--LDW---------LAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHG---QKGYNGVA 66

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  78 FYVKkdvaipvkaeegitgilpvrgqkysysEAPEHEKIGFfPKDIDrktanwiDSEGRCILLDFQMFILIGVYCPvnSG 157
Cdd:COG0708  67 ILSR---------------------------LPPEDVRRGL-GGDEF-------DAEGRYIEADFGGVRVVSLYVP--NG 109

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 158 EN----RLEYRRAFYKALRERIERLIKEGnRKIILVGDVNILCNPIDTADQKDIIRESLI-PsimESRQWIRDLLLPSRL 232
Cdd:COG0708 110 GSvgseKFDYKLRFLDALRAYLAELLAPG-RPLILCGDFNIAPTEIDVKNPKANLKNAGFlP---EERAWFDRLLELGLV 185

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19112314 233 glllDIGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIM----AEVMGSDHCPVYLDLK 303
Cdd:COG0708 186 ----DAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDreprGDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-303 4.64e-43

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 153.59  E-value: 4.64e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314     1 MRILSWNVNGIQNpfnyfpWNKKNSYkEIFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFPKirKGYSGVGFYV 80
Cdd:TIGR00633   1 MKIISWNVNGLRA------RLHKLFL-DWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAK--KGYSGVAILS 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314    81 KkdvaipvkaeegitgilpvrgqkysysEAPEHEKIGFfpkDIDRKtanwiDSEGRCILLDFQMFILIGVYCPvNSGE-- 158
Cdd:TIGR00633  72 K---------------------------VEPLDVRYGF---GGEPH-----DEEGRVITAEFDGFTVVNVYVP-NGGSrd 115

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   159 -NRLEYRRAFYKALRERIERLIKEGNrKIILVGDVNILCNPIDTADQKDIiRESLIPSIMEsRQWIRDLLLPSRLglllD 237
Cdd:TIGR00633 116 lERLEYKLQFWDALFQYLEKELDAGK-PVVICGDMNVAHTEIDLGNPKEN-KGNAGFTPEE-REWFDELLEAGFV----D 188

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19112314   238 IGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLDLK 303
Cdd:TIGR00633 189 TFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDSEIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-302 1.03e-25

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 105.93  E-value: 1.03e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314    1 MRILSWNVNGIQNPFNyfpwnkkNSYKEIFQELQADVICVQELKMQkdsfpQQYAVVEgFDSYFTF--PKIRKGYSGVGF 78
Cdd:PRK13911   1 MKLISWNVNGLRACMT-------KGFMDFFNSVDADVFCIQESKMQ-----QEQNTFE-FKGYFDFwnCAIKKGYSGVVT 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   79 YVKKDvaiPVKAEEGITgilpvrgqkysyseAPEHEKigffpkdidrktanwidsEGRCILLDFQMFILIGVYCPvNSGE 158
Cdd:PRK13911  68 FTKKE---PLSVSYGIN--------------IEEHDK------------------EGRVITCEFESFYLVNVYTP-NSQQ 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  159 --NRLEYRRAFYKALRERIERLikEGNRKIILVGDVNILCNPIDTADQKdIIRESLIPSIMEsrqwiRDLLLPSRLGLLL 236
Cdd:PRK13911 112 alSRLSYRMSWEVEFKKFLKAL--ELKKPVIVCGDLNVAHNEIDLENPK-TNRKNAGFSDEE-----RGKFSELLNAGFI 183

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19112314  237 DIGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLDL 302
Cdd:PRK13911 184 DTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGSDHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-198 1.04e-11

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 63.78  E-value: 1.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314     4 LSWNVNGIQNPFNYFPwNKKNSYKEIFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFPKIRKGYSGVGFYVKKD 83
Cdd:pfam03372   1 LTWNVNGGNADAAGDD-RKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRYP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314    84 VaipvkaeegitgilpvrgqkysyseapEHEKIGFFPKDIDRktanwidsEGRCILLDFQMFILIGVYCPVNSGENRLEY 163
Cdd:pfam03372  80 L---------------------------SSVILVDLGEFGDP--------ALRGAIAPFAGVLVVPLVLTLAPHASPRLA 124

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 19112314   164 RRAFYKALRERIERLIKEGNRKIILVGDVN---ILCNP 198
Cdd:pfam03372 125 RDEQRADLLLLLLALLAPRSEPVILAGDFNadyILVSG 162
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 456-513 4.31e-04

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 38.15  E-value: 4.31e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 19112314   456 PLCEgHKEPCKYLTVRKPGINYGRKFWICarPVGEliknsnavseedtqPFQCRFFIW 513
Cdd:pfam06839   1 PLCP-CGQRAVLLTVRKTGPNPGRQFYKC--PVGR--------------EKQCGFFQW 41
 
Name Accession Description Interval E-value
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-302 1.24e-157

Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197322 [Multi-domain]  Cd Length: 309  Bit Score: 451.00  E-value: 1.24e-157
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   2 RILSWNVNGIQNPFNYFPWNKKNSYKEIFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFPKIRKGYSGVGFYVK 81
Cdd:cd09088   1 RIVTWNVNGIRTRLQYQPWNKENSLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRKGYSGVATYCR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  82 KDVAIPVKAEEGITGILPVRGQKYsysEAPEHEKIGFFPKDID---RKTANWIDSEGRCILLDFQMFILIGVYCPVNSG- 157
Cdd:cd09088  81 DSAATPVAAEEGLTGVLSSPNQKN---ELSENDDIGCYGEMLEftdSKELLELDSEGRCVLTDHGTFVLINVYCPRADPe 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 158 -ENRLEYRRAFYKALRERIERLIKEGnRKIILVGDVNILCNPIDTADQKDIIRESL-IPSIMESRQWIR------DLLLP 229
Cdd:cd09088 158 kEERLEFKLDFYRLLEERVEALLKAG-RRVILVGDVNVSHRPIDHCDPDDSEDFGGeSFEDNPSRQWLDqllgdsGEGGG 236

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19112314 230 SRLGLLLDIGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLDL 302
Cdd:cd09088 237 SPGGLLIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-302 2.97e-55

Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197307 [Multi-domain]  Cd Length: 251  Bit Score: 185.95  E-value: 2.97e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   2 RILSWNVNGIQNPFnyfpwnkKNSYKEIFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFPKiRKGYSGVGFYVK 81
Cdd:cd09073   1 KIISWNVNGLRARL-------KKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPAR-KKGYSGVATLSK 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  82 KDvaiPVKAEEGItGILPvrgqkysyseapehekigffpkdidrktanwIDSEGRCILLDFQMFILIGVYCPvNSGEN-- 159
Cdd:cd09073  73 EE---PLDVSYGI-GGEE-------------------------------FDSEGRVITAEFDDFYLINVYFP-NGGRGle 116

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 160 RLEYRRAFYKALRERIERLIKEGnRKIILVGDVNILCNPIDTADQKDIIRESLIPSimESRQWIrdllLPSRLGLLLDIG 239
Cdd:cd09073 117 RLDYKLRFYEAFLEFLEKLRKRG-KPVVICGDFNVAHEEIDLARPKKNEKNAGFTP--EERAWF----DKLLSLGYVDTF 189

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19112314 240 RIQHPtRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLDL 302
Cdd:cd09073 190 RHFHP-EPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILSKVKGSDHAPVTLEL 251
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-302 4.43e-52

Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.


Pssm-ID: 197319 [Multi-domain]  Cd Length: 252  Bit Score: 177.47  E-value: 4.43e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   1 MRILSWNVNGIQNPFnyfpwnKKNsYKEIFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFPKiRKGYSGVGFYV 80
Cdd:cd09085   1 MKIISWNVNGLRAVH------KKG-FLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAE-RKGYSGVALYS 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  81 KKDvaipvkaeegitgilpvrgqkysyseaPEHEKIGFFPKDIDRktanwidsEGRCILLDFQMFILIGVYCPvNSGEN- 159
Cdd:cd09085  73 KIE---------------------------PDSVREGLGVEEFDN--------EGRILIADFDDFTLFNIYFP-NGQMSe 116

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 160 -RLEYRRAFYKALRERIERLIKEGnRKIILVGDVNILCNPIDTADQKDiiRESLIPSIMESRQWIRDLLLPSRLglllDI 238
Cdd:cd09085 117 eRLDYKLEFYDAFLEYLNELRDSG-KNVIICGDFNTAHKEIDLARPKE--NEKVSGFLPEERAWMDKFIENGYV----DT 189

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19112314 239 GRIQHPTRkGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLDL 302
Cdd:cd09085 190 FRMFNKEP-GQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPDVMGSDHCPVSLEL 252
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-302 4.22e-50

Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197321 [Multi-domain]  Cd Length: 253  Bit Score: 172.35  E-value: 4.22e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   1 MRILSWNVNGIQNpfnyfpWNKKNSyKEIFQELQADVICVQELKMQKDSFPQQYA-VVEGFDSYFtFPKIRKGYSGVGFY 79
Cdd:cd09087   1 LKIISWNVNGLRA------LLKKGL-LDYVKKEDPDILCLQETKLQEGDVPKELKeLLKGYHQYW-NAAEKKGYSGTAIL 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  80 VKKDvaiPVKAEEGITGilpvrgqkysyseaPEHekigffpkdidrktanwiDSEGRCILLDFQMFILIGVYCPvNSGEN 159
Cdd:cd09087  73 SKKK---PLSVTYGIGI--------------EEH------------------DQEGRVITAEFENFYLVNTYVP-NSGRG 116

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 160 --RLEYRRAFYKALRERIERLikEGNRKIILVGDVNILCNPIDTADQK---------DIIRESLiPSIMESRqWIrdlll 228
Cdd:cd09087 117 leRLDRRKEWDVDFRAYLKKL--DSKKPVIWCGDLNVAHEEIDLANPKtnkksagftPEERESF-TELLEAG-FV----- 187

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19112314 229 psrlglllDIGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLDL 302
Cdd:cd09087 188 --------DTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFIRSDIMGSDHCPIGLEL 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-303 2.71e-46

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 162.17  E-value: 2.71e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   1 MRILSWNVNGI---QNPFnyFPWnkknsykeiFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFpkiRKGYSGVG 77
Cdd:COG0708   1 MKIASWNVNGIrarLPKL--LDW---------LAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHG---QKGYNGVA 66

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  78 FYVKkdvaipvkaeegitgilpvrgqkysysEAPEHEKIGFfPKDIDrktanwiDSEGRCILLDFQMFILIGVYCPvnSG 157
Cdd:COG0708  67 ILSR---------------------------LPPEDVRRGL-GGDEF-------DAEGRYIEADFGGVRVVSLYVP--NG 109

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 158 EN----RLEYRRAFYKALRERIERLIKEGnRKIILVGDVNILCNPIDTADQKDIIRESLI-PsimESRQWIRDLLLPSRL 232
Cdd:COG0708 110 GSvgseKFDYKLRFLDALRAYLAELLAPG-RPLILCGDFNIAPTEIDVKNPKANLKNAGFlP---EERAWFDRLLELGLV 185

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19112314 233 glllDIGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIM----AEVMGSDHCPVYLDLK 303
Cdd:COG0708 186 ----DAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDreprGDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-303 4.64e-43

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 153.59  E-value: 4.64e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314     1 MRILSWNVNGIQNpfnyfpWNKKNSYkEIFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFPKirKGYSGVGFYV 80
Cdd:TIGR00633   1 MKIISWNVNGLRA------RLHKLFL-DWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAK--KGYSGVAILS 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314    81 KkdvaipvkaeegitgilpvrgqkysysEAPEHEKIGFfpkDIDRKtanwiDSEGRCILLDFQMFILIGVYCPvNSGE-- 158
Cdd:TIGR00633  72 K---------------------------VEPLDVRYGF---GGEPH-----DEEGRVITAEFDGFTVVNVYVP-NGGSrd 115

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   159 -NRLEYRRAFYKALRERIERLIKEGNrKIILVGDVNILCNPIDTADQKDIiRESLIPSIMEsRQWIRDLLLPSRLglllD 237
Cdd:TIGR00633 116 lERLEYKLQFWDALFQYLEKELDAGK-PVVICGDMNVAHTEIDLGNPKEN-KGNAGFTPEE-REWFDELLEAGFV----D 188

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19112314   238 IGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLDLK 303
Cdd:TIGR00633 189 TFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDSEIRGSDHCPIVLELD 254
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-302 1.32e-37

exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 272954 [Multi-domain]  Cd Length: 254  Bit Score: 139.06  E-value: 1.32e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314     1 MRILSWNVNGIQN-PFNYFPWNKKNsykeifqelQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFpkiRKGYSGVGFY 79
Cdd:TIGR00195   1 MKIISWNVNGLRArPHKGLAWLKEN---------QPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSG---QKGYSGVAIF 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314    80 VKkdvaipvkaeegitgilpvrgqkysysEAPEHEKIGFfpkDIDRKtanwiDSEGRCILLDFQMFILIGVYCPVNS--G 157
Cdd:TIGR00195  69 SK---------------------------EEPISVRRGF---GVEEE-----DAEGRIIMAEFDSFLVINGYFPNGSrdD 113

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   158 ENRLEYRRAFYKALRERIERLIKEGNrKIILVGDVNILCNPIDTADQKDIiRESLIPSIMEsRQWIRDLLLPSRLglllD 237
Cdd:TIGR00195 114 SEKLPYKLQWLEALQNYLEKLVDKDK-PVLICGDMNIAPTEIDLHIPDEN-RNHTGFLPEE-REWLDRLLEAGLV----D 186

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19112314   238 IGRIQHPTrKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMG----SDHCPVYLDL 302
Cdd:TIGR00195 187 TFRKFNPD-EGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDYDIRGsekpSDHCPVVLEF 254
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-301 5.05e-35

Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.


Pssm-ID: 197336 [Multi-domain]  Cd Length: 253  Bit Score: 131.58  E-value: 5.05e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   1 MRILSWNVNGIQNPFnyfpwnkKNSYKEIFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFtFPKIRKGYSGVGFYV 80
Cdd:cd10281   1 MRVISVNVNGIRAAA-------KKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYF-FDAEKKGYAGVAIYS 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  81 KKDvaipvkaeegitgilpvrgqkysyseapehekigffPKDIDRK-TANWIDSEGRCILLDFQMFILIGVYCPV-NSGE 158
Cdd:cd10281  73 RTQ------------------------------------PKAVIYGlGFEEFDDEGRYIEADFDNVSVASLYVPSgSSGD 116

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 159 NRLEYRRAFYKALRERIERLIKEGnRKIILVGDVNILCNPIDTADQKDIIRES-LIPsimESRQWIRDLLLPSRLGlllD 237
Cdd:cd10281 117 ERQEAKMAFLDAFLEHLKELRRKR-REFIVCGDFNIAHTEIDIKNWKANQKNSgFLP---EERAWLDQVFGELGYV---D 189

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19112314 238 IGRIQHPTrKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLD 301
Cdd:cd10281 190 AFRELNPD-EGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYREERFSDHAPLIVD 252
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-302 8.83e-28

Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and 3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197320 [Multi-domain]  Cd Length: 254  Bit Score: 111.84  E-value: 8.83e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   1 MRILSWNVNGIqnpfnyfpwnkkNSYKEIFQEL----QADVICVQELKMQKDSFPqqYAVVE--GFDSYFtfpKIRKGYS 74
Cdd:cd09086   1 MKIATWNVNSI------------RARLEQVLDWlkeeDPDVLCLQETKVEDDQFP--ADAFEalGYHVAV---HGQKAYN 63

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  75 GVgfyvkkdvAIPVKaeegitgilpvrgqkysysEAPEHEKIGFFpkdidrktANWIDSEGRCILLDFQMFILIGVYCP- 153
Cdd:cd09086  64 GV--------AILSR-------------------LPLEDVRTGFP--------GDPDDDQARLIAARVGGVRVINLYVPn 108

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 154 -VNSGENRLEYRRAFYKALRERIERLIKEGNrKIILVGDVNILCNPIDTAD----QKDIireSLIPsimESRQWIRDLLL 228
Cdd:cd09086 109 gGDIGSPKFAYKLDWLDRLIRYLQKLLKPDD-PLVLVGDFNIAPEDIDVWDpkqlLGKV---LFTP---EEREALRALLD 181

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19112314 229 PSRLglllDIGRIQHPTrKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMG----SDHCPVYLDL 302
Cdd:cd09086 182 LGFV----DAFRALHPD-EKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGIDREPRGwekpSDHAPVVAEL 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-302 1.03e-25

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 105.93  E-value: 1.03e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314    1 MRILSWNVNGIQNPFNyfpwnkkNSYKEIFQELQADVICVQELKMQkdsfpQQYAVVEgFDSYFTF--PKIRKGYSGVGF 78
Cdd:PRK13911   1 MKLISWNVNGLRACMT-------KGFMDFFNSVDADVFCIQESKMQ-----QEQNTFE-FKGYFDFwnCAIKKGYSGVVT 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   79 YVKKDvaiPVKAEEGITgilpvrgqkysyseAPEHEKigffpkdidrktanwidsEGRCILLDFQMFILIGVYCPvNSGE 158
Cdd:PRK13911  68 FTKKE---PLSVSYGIN--------------IEEHDK------------------EGRVITCEFESFYLVNVYTP-NSQQ 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  159 --NRLEYRRAFYKALRERIERLikEGNRKIILVGDVNILCNPIDTADQKdIIRESLIPSIMEsrqwiRDLLLPSRLGLLL 236
Cdd:PRK13911 112 alSRLSYRMSWEVEFKKFLKAL--ELKKPVIVCGDLNVAHNEIDLENPK-TNRKNAGFSDEE-----RGKFSELLNAGFI 183

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19112314  237 DIGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMGSDHCPVYLDL 302
Cdd:PRK13911 184 DTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKDILGSDHCPVGLEL 249
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-302 3.09e-17

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


Pssm-ID: 197306 [Multi-domain]  Cd Length: 241  Bit Score: 80.99  E-value: 3.09e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   3 ILSWNVNGiqnpFNYFpwNKKNSYKEIFQELQADVICVQElkmQKDSFPQQYAV----VEGFDSYFTFPKIRKGYSGVGF 78
Cdd:cd08372   1 VASYNVNG----LNAA--TRASGIARWVRELDPDIVCLQE---VKDSQYSAVALnqllPEGYHQYQSGPSRKEGYEGVAI 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  79 YVKKDVAIPVKaeegitgilpvrgqKYSYSEAPEHekigffpkdidrktanwiDSEGRCILLDF----QMFILIGVYCPv 154
Cdd:cd08372  72 LSKTPKFKIVE--------------KHQYKFGEGD------------------SGERRAVVVKFdvhdKELCVVNAHLQ- 118

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 155 nSGENRLEYRRAFYKALRERIERLIKEGNRKIILVGDVNilcNPIDTADqkdiireSLIPSIMESRqwirdlllpSRLGL 234
Cdd:cd08372 119 -AGGTRADVRDAQLKEVLEFLKRLRQPNSAPVVICGDFN---VRPSEVD-------SENPSSMLRL---------FVALN 178

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19112314 235 LLDIgriqHPTRKGMFTCWNTRLNTrptnyGTRIDYTLATPDLLPWVQDADIMAEV----MGSDHCPVYLDL 302
Cdd:cd08372 179 LVDS----FETLPHAYTFDTYMHNV-----KSRLDYIFVSKSLLPSVKSSKILSDAararIPSDHYPIEVTL 241
PRK11756 PRK11756
exonuclease III; Provisional
 1-303 2.60e-16

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 79.17  E-value: 2.60e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314    1 MRILSWNVNGIQNpfnyfpwnKKNSYKEIFQELQADVICVQELKMQKDSFPqqYAVVE--GFDSYFTFpkiRKGYSGVGF 78
Cdd:PRK11756   1 MKFVSFNINGLRA--------RPHQLEAIIEKHQPDVIGLQETKVHDEMFP--LEEVEalGYHVFYHG---QKGHYGVAL 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   79 YVKKDvaiPVKAEEGitgilpvrgqkysyseapehekigfFPKDIDrktanwiDSEGRCILLDF-----QMFILIGvYCP 153
Cdd:PRK11756  68 LSKQT---PIAVRKG-------------------------FPTDDE-------EAQRRIIMATIptpngNLTVING-YFP 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  154 vnSGENR-----LEYRRAFYKALRERIERLIKEGNRkIILVGDVNIlcNPIDtadqKDI-IRE------------SLIPs 215
Cdd:PRK11756 112 --QGESRdhptkFPAKRQFYQDLQNYLETELSPDNP-LLIMGDMNI--SPTD----LDIgIGEenrkrwlrtgkcSFLP- 181

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  216 imESRQWIRdlllPSRLGLLLDIGRIQHPTRKGMFTCWNTRLNTRPTNYGTRIDYTLATPDLLPWVQDADIMAEVMG--- 292
Cdd:PRK11756 182 --EEREWLD----RLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAERCVETGIDYDIRGmek 255

                        330
                 ....*....|..
gi 19112314  293 -SDHCPVYLDLK 303
Cdd:PRK11756 256 pSDHAPIWATFK 267
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-302 7.44e-12

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 65.07  E-value: 7.44e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   3 ILSWNVNGIQNPFnyfpwnKKNSYKEIFQELQADVICVQELKMqKDSFPQQYAVVEGFDSYFTFPKIRKGysGVGFYVKK 82
Cdd:cd09076   1 IGTLNVRGLRSPG------KRAQLLEELKRKKLDILGLQETHW-TGEGELKKKREGGTILYSGSDSGKSR--GVAILLSK 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  83 DVAipvkaeegitgilpvrgqkysyseapehekigffPKDIDRKTanwiDSEGRCILLDFQM----FILIGVYCPVNSGE 158
Cdd:cd09076  72 TAA----------------------------------NKLLEYTK----VVSGRIIMVRFKIkgkrLTIINVYAPTARDE 113

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314 159 nrlEYRRAFYKALRERIERLIKEGNrkIILVGDVN-ILCNPIDTADQKDIIRESLIpsimesrqwiRDLLLPSRLGLLLD 237
Cdd:cd09076 114 ---EEKEEFYDQLQDVLDKVPRHDT--LIIGGDFNaVLGPKDDGRKGLDKRNENGE----------RALSALIEEHDLVD 178

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19112314 238 IGRIQHPTRKGmFTcWNTRlntrPTNYGTRIDYTLATPDLLPWVQDADIMAEVmGSDHCPVYLDL 302
Cdd:cd09076 179 VWRENNPKTRE-YT-WRSP----DHGSRSRIDRILVSKRLRVKVKKTKITPGA-GSDHRLVTLKL 236
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-198 1.04e-11

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 63.78  E-value: 1.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314     4 LSWNVNGIQNPFNYFPwNKKNSYKEIFQELQADVICVQELKMQKDSFPQQYAVVEGFDSYFTFPKIRKGYSGVGFYVKKD 83
Cdd:pfam03372   1 LTWNVNGGNADAAGDD-RKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRYP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314    84 VaipvkaeegitgilpvrgqkysyseapEHEKIGFFPKDIDRktanwidsEGRCILLDFQMFILIGVYCPVNSGENRLEY 163
Cdd:pfam03372  80 L---------------------------SSVILVDLGEFGDP--------ALRGAIAPFAGVLVVPLVLTLAPHASPRLA 124

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 19112314   164 RRAFYKALRERIERLIKEGNRKIILVGDVN---ILCNP 198
Cdd:pfam03372 125 RDEQRADLLLLLLALLAPRSEPVILAGDFNadyILVSG 162
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 3-193 3.29e-04

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197318 [Multi-domain]  Cd Length: 246  Bit Score: 42.28  E-value: 3.29e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   3 ILSWNVNGiqnpFNYFPW-NKKNSYKEIFQELQADVICVQE-LKMQKDSFPQQYAVVEGFDSYFTFPKIRKGYSGVGFYV 80
Cdd:cd09084   1 VMSYNVRS----FNRYKWkDDPDKILDFIKKQDPDILCLQEyYGSEGDKDDDLRLLLKGYPYYYVVYKSDSGGTGLAIFS 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314  81 KkdvaIPVKAEEGITGilPVRGQKYSYSeapehekigffpkDIDRKtanwidseGRCILL---DFQ-MFILIGVYCPVNS 156
Cdd:cd09084  77 K----YPILNSGSIDF--PNTNNNAIFA-------------DIRVG--------GDTIRVynvHLEsFRITPSDKELYKE 129

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 19112314 157 GENRLEYRRAFYKALRER----------IERLIKEGNRKIILVGDVN 193
Cdd:cd09084 130 EKKAKELSRNLLRKLAEAfkrraaqadlLAADIAASPYPVIVCGDFN 176
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 456-513 4.31e-04

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 38.15  E-value: 4.31e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 19112314   456 PLCEgHKEPCKYLTVRKPGINYGRKFWICarPVGEliknsnavseedtqPFQCRFFIW 513
Cdd:pfam06839   1 PLCP-CGQRAVLLTVRKTGPNPGRQFYKC--PVGR--------------EKQCGFFQW 41
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 145-299 6.51e-03

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 36.57  E-value: 6.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   145 FILIGVYCPvnsgenrleyRRAFYKALRERIERLI-KEGNRKIILVGDVN---ILCNPIDTADQKDiirESLIpSIMESR 220
Cdd:pfam14529   1 ILIISVYCP----------PSDQLRNLLDTLEDILrSLDRPPIIIGGDFNahhPLWGSNSTDVSRG---EELI-EFLNEH 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19112314   221 QWIRdlllpsrlgllldigrIQHPTRKGmfTCWntrlntrPTNYGTRIDYTLATPDLLP-WVQDADimaEVMGSDHCPVY 299
Cdd:pfam14529  67 GLNL----------------LNLPKSGP--TFI-------SSNGDSTIDLTLTSDPLAVrVLSDLG---PDSGSDHRPIA 118
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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