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Conserved domains on  [gi|418487886|ref|YP_007002117|]
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3'-5' exonuclease [Brucella phage Pr]

Protein Classification

3'-5' exonuclease family protein( domain architecture ID 1085)

3'-5' exonuclease family protein may cleave nucleotides one at a time from the end (exo) of a polynucleotide chain

CATH:  3.30.420.10
Gene Ontology:  GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DnaQ_like_exo super family cl10012
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 5-202 2.77e-36

DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer.


The actual alignment was detected with superfamily member cd05782:

Pssm-ID: 447876 [Multi-domain]  Cd Length: 208  Bit Score: 126.20  E-value: 2.77e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886   5 YFDVETIPDQSEGALERAKESVKVPanyknpdtiaayieENAQEAWERTALDG-------WKGHVACI--VMNDMKW--- 72
Cdd:cd05782    3 VFDIETVPDVDLGRRLYLLLELDDL--------------EVLEKRFAQRLEKSgsdflplPFHKVVSIsaLYRDDDGgfl 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  73 MVQET--WREKEMLQDFFNRLNES--TLVGHNIIGFDIPFLTKRALVLGVKLPP----EHIWPRNLKPWDNRVFDTM--L 142
Cdd:cd05782   69 KVRTLdgADEKELLEDFFQLIEKKnpRLVSFNGRGFDLPVLHLRALIHGVSAPAyfdlGNKDWNYRNRYSERHLDLMdlL 148

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886 143 QLGNGKEFISLDNLARNLGTKGKGNTTGAQVHYMWQNGLHDEIAEYCANDVRIVREIHER 202
Cdd:cd05782  149 AFYGARARASLDLLAKLLGIPGKMDVDGSQVWELYAEGKLDEIAEYCETDVLNTYLLYLR 208
 
Name Accession Description Interval E-value
DNA_polB_like1_exo cd05782
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ...
 5-202 2.77e-36

Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.


Pssm-ID: 99825 [Multi-domain]  Cd Length: 208  Bit Score: 126.20  E-value: 2.77e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886   5 YFDVETIPDQSEGALERAKESVKVPanyknpdtiaayieENAQEAWERTALDG-------WKGHVACI--VMNDMKW--- 72
Cdd:cd05782    3 VFDIETVPDVDLGRRLYLLLELDDL--------------EVLEKRFAQRLEKSgsdflplPFHKVVSIsaLYRDDDGgfl 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  73 MVQET--WREKEMLQDFFNRLNES--TLVGHNIIGFDIPFLTKRALVLGVKLPP----EHIWPRNLKPWDNRVFDTM--L 142
Cdd:cd05782   69 KVRTLdgADEKELLEDFFQLIEKKnpRLVSFNGRGFDLPVLHLRALIHGVSAPAyfdlGNKDWNYRNRYSERHLDLMdlL 148

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886 143 QLGNGKEFISLDNLARNLGTKGKGNTTGAQVHYMWQNGLHDEIAEYCANDVRIVREIHER 202
Cdd:cd05782  149 AFYGARARASLDLLAKLLGIPGKMDVDGSQVWELYAEGKLDEIAEYCETDVLNTYLLYLR 208
DNA_pol_B_exo2 pfam10108
Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in ...
 79-193 7.80e-20

Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins.


Pssm-ID: 462958 [Multi-domain]  Cd Length: 210  Bit Score: 83.43  E-value: 7.80e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886   79 REKEMLQDFFNRLNEST--LVGHNIIGFDIPFLTKRALVLGVKLPPEHIWPRNLKPWDN-------RVFDTM--LQLGNG 147
Cdd:pfam10108  36 SEKELIQRFFDGVEKYTpqLVSFNGRGFDLPVLHYRALKHGVSAPRYWDTGDGDFKWNNyfnryhtRHLDLMdlLAGYGG 115

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 418487886  148 KEFISLDNLARNLGTKGKGNTTGAQVHYMWQNGLHDEIAEYCANDV 193
Cdd:pfam10108 116 RANAPLDEVAKLLGFPGKMGMDGSKVWELYQAGRLDEIRDYCETDV 161
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
80-199 9.66e-15

DNA polymerase B elongation subunit [Replication, recombination and repair];


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 72.17  E-value: 9.66e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  80 EKEMLQDFFNRLNE---STLVGHNIIGFDIPFLTKRALVLGVKL-------PPEHIWPRNLKPWD--NRV-FDT------ 140
Cdd:COG0417  216 EKALLEAFFEIIREydpDIIIGWNVDNFDLPYLQKRAERLGIPLdlgrdgsEPSWREHGGQGFASipGRVvIDLydalks 295

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886 141 -MLQLgngKEFiSLDNLARNLGTKGKGNTTGAQVHYMWQNGLhDEIAEYCANDVRIVREI 199
Cdd:COG0417  296 aTYKF---KSY-SLDAVAEELLGEGKLIVDGGEIERLWDDDK-PALAEYNLRDAELTLRI 350
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
 80-199 3.22e-11

DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases


Pssm-ID: 214691 [Multi-domain]  Cd Length: 474  Bit Score: 61.78  E-value: 3.22e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886    80 EKEMLQDFFN---RLNESTLVGHNIIGFDIPFLTKRALVLGV-------KLPPEHIWPRNLKPWDNRVFDTMLQLGNGKE 149
Cdd:smart00486  69 EKELLLAFFEfikKYDPDIIYGHNISNFDLPYIISRLEKLKIdplskigRLKIGLRIPNKKPLFGSKSFGLSDIKVYIKG 148

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 418487886   150 FI-----------------SLDNLARNLGTKGKGNTTGAQV--HYMWQNGLHDEIAEYCANDVRIVREI 199
Cdd:smart00486 149 RLvidlyrlyknklklpsyKLDTVAEYLLGKEKDDLPYKDIpeLYNGNYEERDELLRYCIQDAVLTLKL 217
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
 79-128 1.19e-05

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 45.40  E-value: 1.19e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 418487886   79 REKEML---QDFFNRLNESTLVGHNIIGFDIPFLTKRALVLgvKLPPEHIWPR 128
Cdd:PTZ00166  329 TEKELLlawAEFVIAVDPDFLTGYNIINFDLPYLLNRAKAL--KLNDFKYLGR 379
 
Name Accession Description Interval E-value
DNA_polB_like1_exo cd05782
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ...
 5-202 2.77e-36

Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.


Pssm-ID: 99825 [Multi-domain]  Cd Length: 208  Bit Score: 126.20  E-value: 2.77e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886   5 YFDVETIPDQSEGALERAKESVKVPanyknpdtiaayieENAQEAWERTALDG-------WKGHVACI--VMNDMKW--- 72
Cdd:cd05782    3 VFDIETVPDVDLGRRLYLLLELDDL--------------EVLEKRFAQRLEKSgsdflplPFHKVVSIsaLYRDDDGgfl 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  73 MVQET--WREKEMLQDFFNRLNES--TLVGHNIIGFDIPFLTKRALVLGVKLPP----EHIWPRNLKPWDNRVFDTM--L 142
Cdd:cd05782   69 KVRTLdgADEKELLEDFFQLIEKKnpRLVSFNGRGFDLPVLHLRALIHGVSAPAyfdlGNKDWNYRNRYSERHLDLMdlL 148

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886 143 QLGNGKEFISLDNLARNLGTKGKGNTTGAQVHYMWQNGLHDEIAEYCANDVRIVREIHER 202
Cdd:cd05782  149 AFYGARARASLDLLAKLLGIPGKMDVDGSQVWELYAEGKLDEIAEYCETDVLNTYLLYLR 208
DNA_pol_B_exo2 pfam10108
Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in ...
 79-193 7.80e-20

Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins.


Pssm-ID: 462958 [Multi-domain]  Cd Length: 210  Bit Score: 83.43  E-value: 7.80e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886   79 REKEMLQDFFNRLNEST--LVGHNIIGFDIPFLTKRALVLGVKLPPEHIWPRNLKPWDN-------RVFDTM--LQLGNG 147
Cdd:pfam10108  36 SEKELIQRFFDGVEKYTpqLVSFNGRGFDLPVLHYRALKHGVSAPRYWDTGDGDFKWNNyfnryhtRHLDLMdlLAGYGG 115

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 418487886  148 KEFISLDNLARNLGTKGKGNTTGAQVHYMWQNGLHDEIAEYCANDV 193
Cdd:pfam10108 116 RANAPLDEVAKLLGFPGKMGMDGSKVWELYQAGRLDEIRDYCETDV 161
PolB COG0417
DNA polymerase B elongation subunit [Replication, recombination and repair];
80-199 9.66e-15

DNA polymerase B elongation subunit [Replication, recombination and repair];


Pssm-ID: 440186 [Multi-domain]  Cd Length: 794  Bit Score: 72.17  E-value: 9.66e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  80 EKEMLQDFFNRLNE---STLVGHNIIGFDIPFLTKRALVLGVKL-------PPEHIWPRNLKPWD--NRV-FDT------ 140
Cdd:COG0417  216 EKALLEAFFEIIREydpDIIIGWNVDNFDLPYLQKRAERLGIPLdlgrdgsEPSWREHGGQGFASipGRVvIDLydalks 295

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886 141 -MLQLgngKEFiSLDNLARNLGTKGKGNTTGAQVHYMWQNGLhDEIAEYCANDVRIVREI 199
Cdd:COG0417  296 aTYKF---KSY-SLDAVAEELLGEGKLIVDGGEIERLWDDDK-PALAEYNLRDAELTLRI 350
DEDDy_DNA_polB_exo cd05160
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ...
 80-199 1.31e-11

DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.


Pssm-ID: 176646 [Multi-domain]  Cd Length: 199  Bit Score: 60.83  E-value: 1.31e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  80 EKEMLQDFFNRLNEST---LVGHNIIGFDIPFLTKRALVLGVKLPPEHIW-PRNLKPWDNR---------VFDTmlqLGN 146
Cdd:cd05160   63 EKELLKRFFDIIREYDpdiLTGYNIDDFDLPYLLKRAEALGIKLTDGIYRrSGGEKSSGSTeriavkgrvVFDL---LAA 139

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 418487886 147 GKEFI-----SLDNLARNLGTKGKGNTTGAQV-HYMWQNGLHDeIAEYCANDVRIVREI 199
Cdd:cd05160  140 YKRDFklksyTLDAVAEELLGEGKEKVDGEIIeDAEWEEDPER-LIEYNLKDAELTLQI 197
POLBc smart00486
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ...
 80-199 3.22e-11

DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases


Pssm-ID: 214691 [Multi-domain]  Cd Length: 474  Bit Score: 61.78  E-value: 3.22e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886    80 EKEMLQDFFN---RLNESTLVGHNIIGFDIPFLTKRALVLGV-------KLPPEHIWPRNLKPWDNRVFDTMLQLGNGKE 149
Cdd:smart00486  69 EKELLLAFFEfikKYDPDIIYGHNISNFDLPYIISRLEKLKIdplskigRLKIGLRIPNKKPLFGSKSFGLSDIKVYIKG 148

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 418487886   150 FI-----------------SLDNLARNLGTKGKGNTTGAQV--HYMWQNGLHDEIAEYCANDVRIVREI 199
Cdd:smart00486 149 RLvidlyrlyknklklpsyKLDTVAEYLLGKEKDDLPYKDIpeLYNGNYEERDELLRYCIQDAVLTLKL 217
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 73-161 2.09e-07

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 48.64  E-value: 2.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  73 MVQETWREKEMLQDFFNRLNESTLVGHNiIGFDIPFLTKRALVLGVKLPPehiwprnlkpwdNRVFDTML---QLGNGKE 149
Cdd:COG0847   60 DVADAPPFAEVLPELLEFLGGAVLVAHN-AAFDLGFLNAELRRAGLPLPP------------FPVLDTLRlarRLLPGLP 126

                         90
                 ....*....|..
gi 418487886 150 FISLDNLARNLG 161
Cdd:COG0847  127 SYSLDALCERLG 138
DNA_polB_delta_exo cd05777
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ...
 79-119 7.30e-07

DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues necessary for metal binding and catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation.


Pssm-ID: 99820 [Multi-domain]  Cd Length: 230  Bit Score: 47.96  E-value: 7.30e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 418487886  79 REKEML---QDFFNRLNESTLVGHNIIGFDIPFLTKRALVLGVK 119
Cdd:cd05777   70 TEEELLlawRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLN 113
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 80-141 3.02e-06

DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 45.37  E-value: 3.02e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 418487886  80 EKEMLQDFFNRLNESTLVGHNiIGFDIPFLTKRALVLGvklppehiwprnLKPWDNRVFDTM 141
Cdd:cd06127   66 FEEVLPEFLEFLGGRVLVAHN-ASFDLRFLNRELRRLG------------GPPLPNPWIDTL 114
DNA_polB_like2_exo cd05785
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA ...
 80-120 1.19e-05

Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.


Pssm-ID: 99828 [Multi-domain]  Cd Length: 207  Bit Score: 44.32  E-value: 1.19e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 418487886  80 EKEMLQDFFNRLNE---STLVGHNIIGFDIPFLTKRALVLGVKL 120
Cdd:cd05785   58 EKELLEELVAIIRErdpDVIEGHNIFRFDLPYLRRRCRRHGVPL 101
PTZ00166 PTZ00166
DNA polymerase delta catalytic subunit; Provisional
 79-128 1.19e-05

DNA polymerase delta catalytic subunit; Provisional


Pssm-ID: 240301 [Multi-domain]  Cd Length: 1054  Bit Score: 45.40  E-value: 1.19e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 418487886   79 REKEML---QDFFNRLNESTLVGHNIIGFDIPFLTKRALVLgvKLPPEHIWPR 128
Cdd:PTZ00166  329 TEKELLlawAEFVIAVDPDFLTGYNIINFDLPYLLNRAKAL--KLNDFKYLGR 379
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
 80-113 1.20e-05

DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.


Pssm-ID: 397292  Cd Length: 333  Bit Score: 45.10  E-value: 1.20e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 418487886   80 EKEMLQDFFNRLNEST---LVGHNIIGFDIPFLTKRA 113
Cdd:pfam03104 234 EKELLRRFFEFIRQYDpdiITGYNGDNFDWPYILNRA 270
PRK05762 PRK05762
DNA polymerase II; Reviewed
 80-120 4.04e-05

DNA polymerase II; Reviewed


Pssm-ID: 235595 [Multi-domain]  Cd Length: 786  Bit Score: 43.69  E-value: 4.04e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 418487886  80 EKEMLQ---DFFNRLNESTLVGHNIIGFDIPFLTKRALVLGVKL 120
Cdd:PRK05762 203 EKALLEkfnAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL 246
DNA_polB_Kod1_like_exo cd05780
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ...
 80-203 4.06e-05

DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family-B DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.


Pssm-ID: 99823 [Multi-domain]  Cd Length: 195  Bit Score: 42.73  E-value: 4.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  80 EKEMLQDFFNRLNEST---LVGHNIIGFDIPFLTKRALVLGVKLP---PEHIwPRNLKPWDN-------RV-FD---TML 142
Cdd:cd05780   56 EKEMIKRFIEIVKEKDpdvIYTYNGDNFDFPYLKKRAEKLGIELDlgrDGSE-IKIQRGGFNnaseikgRIhVDlypVAR 134

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 418487886 143 QLGNGKEFiSLDNLARNLGTKGKGNTTGAQVHYMWQNG-LHDEIAEYCANDVRIVREIHERF 203
Cdd:cd05780  135 RTLNLTRY-TLERVYEELFGIEKEDVPGEEIAEAWDSGeNLERLFRYSMEDAKYTYEIGKEF 195
DNA_polB_B1_exo cd05783
DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar ...
 80-195 1.39e-04

DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthesis. This is an additional safeguard mechanism against increased levels of deaminated bases during genome duplication at high temperatures. S. solfataricus B1 also interacts with DNA polymerase Y and may contribute to genome stability mechanisms.


Pssm-ID: 99826 [Multi-domain]  Cd Length: 204  Bit Score: 41.15  E-value: 1.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  80 EKEMLQDFFNRLNESTLV----GHNiigFDIPFLTKRALVLGVklPPEHIwPRNLKP----------------WDNRVFD 139
Cdd:cd05783   73 EKELIREAFKIISEYPIVltfnGDN---FDLPYLYNRALKLGI--PKEEI-PIYLKRdyatlkhgihidlykfFSNRAIQ 146

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 418487886 140 TMLQLGNGKEFiSLDNLARNLGTKGKGNtTGAQVHYMWQNglhdEIAEYCANDVRI 195
Cdd:cd05783  147 VYAFGNKYREY-TLDAVAKALLGEGKVE-LEKNISELNLY----ELAEYNYRDAEL 196
DNA_polB_B3_exo cd05781
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ...
 80-120 2.29e-04

DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.


Pssm-ID: 99824 [Multi-domain]  Cd Length: 188  Bit Score: 40.39  E-value: 2.29e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 418487886  80 EKEMLQDFFNRLNE---STLVGHNIIGFDIPFLTKRALVLGVKL 120
Cdd:cd05781   48 DRKIIREFVKYVKEydpDIIVGYNSNAFDWPYLVERARVLGVKL 91
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 73-161 2.63e-04

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 39.98  E-value: 2.63e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886    73 MVQETWREKEMLQDFFNRLNESTLVGHNIIGFDIPFLTKralvlgvklppEHIWPRNLKPWDNRVFDTM--LQLGNGKEF 150
Cdd:smart00479  60 MLDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKL-----------EHPRLGIKQPPKLPVIDTLklARATNPGLP 128

                           90
                   ....*....|..
gi 418487886   151 -ISLDNLARNLG 161
Cdd:smart00479 129 kYSLKKLAKRLL 140
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 76-205 6.35e-04

3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes


Pssm-ID: 214681 [Multi-domain]  Cd Length: 172  Bit Score: 38.88  E-value: 6.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886    76 ETWREKEMLQDFFNRLNeSTLVGHNIiGFDIPFLTKralvLGVKLPPehiwprnlkpwdnrVFDTML---QLGNGKEFIS 152
Cdd:smart00474  59 ALGDDLEILKDLLEDET-ITKVGHNA-KFDLHVLAR----FGIELEN--------------IFDTMLaayLLLGGPSKHG 118

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 418487886   153 LDNLARNLGTKGKGNTTGAQVhymWQNG-LHDEIAEYCANDVRIVREIHERFLA 205
Cdd:smart00474 119 LATLLLGYLGVELDKEEQKSD---WGARpLSEEQLEYAAEDADALLRLYEKLEK 169
polC PRK00448
DNA polymerase III PolC; Validated
 73-161 1.14e-03

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 39.44  E-value: 1.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886   73 MVQETWREKEMLQDFFNRLNESTLVGHNIIgFDIPFLTKRALVLGvklppehiwprnLKPWDNRVFDTmLQLG-----NG 147
Cdd:PRK00448  479 MVKDAPSIEEVLPKFKEFCGDSILVAHNAS-FDVGFINTNYEKLG------------LEKIKNPVIDT-LELSrflypEL 544

                          90
                  ....*....|....
gi 418487886  148 KEFiSLDNLARNLG 161
Cdd:PRK00448  545 KSH-RLNTLAKKFG 557
DNA_polB_II_exo cd05784
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial ...
 80-201 1.99e-03

DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Pol II is also involved in lagging strand synthesis.


Pssm-ID: 99827 [Multi-domain]  Cd Length: 193  Bit Score: 37.55  E-value: 1.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  80 EKEML---QDFFNRLNESTLVGHNIIGFDIPFLTKRALVLGVKLppehIWPRNLKPWDNRVFDTmlqlgNGKEFI----- 151
Cdd:cd05784   51 EKSLLlalIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPL----RLGRGGSPLNWRQSGK-----PGQGFLslpgr 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886 152 -------------------SLDNLARNLGTKGKgnttgaQVHYMWQNGlhDEI-----------AEYCANDVRIVREIHE 201
Cdd:cd05784  122 vvldgidalktatyhfesfSLENVAQELLGEGK------LIHDVDDRG--AEIerlfredklalARYNLQDCELVWRIFE 193
DNA_polB_alpha_exo cd05776
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA ...
 80-120 3.47e-03

inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis. This explains why in most organisms, that no specific repair role, other than check point control, has been assigned to this enzyme. The exonuclease domain may have a structural role.


Pssm-ID: 99819 [Multi-domain]  Cd Length: 234  Bit Score: 37.21  E-value: 3.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 418487886  80 EKEMLQDFFNRLNES---TLVGHNIIGFDIPFLTKRALVLGVKL 120
Cdd:cd05776   82 ERALLNFFLAKLQKIdpdVLVGHDLEGFDLDVLLSRIQELKVPH 125
PRK05755 PRK05755
DNA polymerase I; Provisional
 81-205 8.42e-03

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 36.61  E-value: 8.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418487886  81 KEMLQDFFNrlNESTL-VGHNIiGFDIPFLTKRalvlGVKLPpehiwprnlkpwdNRVFDTMLQ---LGNGKEFiSLDNL 156
Cdd:PRK05755 359 LAALKPLLE--DPAIKkVGQNL-KYDLHVLARY----GIELR-------------GIAFDTMLAsylLDPGRRH-GLDSL 417

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 418487886 157 A-RNLGTK--------GKGNTTgAQVhymwqngLHDEIAEYCANDVRIVREIHERFLA 205
Cdd:PRK05755 418 AeRYLGHKtisfeevaGKQLTF-AQV-------DLEEAAEYAAEDADVTLRLHEVLKP 467
 
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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