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Conserved domains on  [gi|379056383|ref|NP_001243808|]
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DNA polymerase delta subunit 2 [Homo sapiens]

Protein Classification

DNA polymerase delta 2/small subunit family protein( domain architecture ID 16058311)

DNA polymerase delta 2/small subunit family protein similar to human DNA polymerase delta subunit 2, an accessory component of both the DNA polymerase delta complex and the DNA polymerase zeta complex, that plays a regulatory role and serves as a scaffold for complex assembly

CATH:  3.60.21.10
Gene Ontology:  GO:0043625|GO:0003677|GO:0006261|GO:0006281
PubMed:  19296856

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MPP_PolD2_C cd07387
PolD2 (DNA polymerase delta, subunit 2), C-terminal domain; PolD2 (DNA polymerase delta, ...
 215-452 7.59e-149

PolD2 (DNA polymerase delta, subunit 2), C-terminal domain; PolD2 (DNA polymerase delta, subunit 2) is an auxiliary subunit of the eukaryotic DNA polymerase delta (PolD) complex thought to play a regulatory role and to serve as a scaffold for PolD assembly by interacting simultaneously with all of the other three subunits. PolD2 is catalytically inactive and lacks the active site residues required for phosphoesterase activity in other members of this superfamily. PolD2 is also involved in the recruitment of several proteins regulating DNA metabolism, including p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3), and p12(PolD4). PolD is one of three major replicases in eukaryotes. PolD also plays an essential role in translesion DNA synthesis, homologous recombination, and DNA repair. Within the PolD complex, PolD2 tightly associates with PolD3. PolD2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


:

Pssm-ID: 277333  Cd Length: 257  Bit Score: 424.36  E-value: 7.59e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 215 TQLLVDVVTGQLGDEGEQCSAAHVSRVILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDV 294
Cdd:cd07387   20 LQLLVDWLTGQLGDESEQLSASSIVRLIIAGNSLAKSEQGKDSQSKARYLTKKSSAASVEAVKELDEFLSQLASSVPVDV 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 295 MPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHI 374
Cdd:cd07387  100 MPGENDPANFMLPQQPLHRCMFPKSRSYSTLNLVTNPYEFSVDGVRVLGTSGQNVSDILKYSSKESRLDALESTLRWRHI 179

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 379056383 375 SPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNTPSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSLACQPISF 452
Cdd:cd07387  180 APTAPDTLWCYPFTDRDPFILEECPHVYFAGNQPKFGTKLVEGENGQRVLLVCVPSFSKTGSAVLVNLRTLECEPINF 257
DNA_pol_D_N pfam18018
DNA polymerase delta subunit OB-fold domain; The eukaryotic DNA polymerase delta (Pol delta) ...
 49-176 2.89e-60

DNA polymerase delta subunit OB-fold domain; The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance. Human Pol delta consists of four subunits: p125, p50, p66 and p12. The first three subunits correspond to the three subunits of S. cerevisiae Pol delta. p50 serves as a scaffold for the assembly of Pol delta by interacting simultaneously with all of the other three subunits. This entry corresponds to the OB fold domain found in the p50 subunit.


:

Pssm-ID: 436215  Cd Length: 129  Bit Score: 193.18  E-value: 2.89e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383   49 QYAHIYATRLIQMRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREVSEEHNLLPQPPRSKYIH 128
Cdd:pfam18018   1 QYAHIYFARLEALRPRLLEAAKKKWGDVIPVNKILDLKEGEECIIIGTLYKEMKLKPSILDEYSEENQLAPQPPRTKYTS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 379056383  129 PDDELVLEDELQRIKLKG-TIDVSKLVTGTVLAVFGSVRDDGKFLVEDY 176
Cdd:pfam18018  81 DDDELFLEDESGRIKLIGdKIDVDELVTGVVVAVLGRENEDGDFEVEDI 129
 
Name Accession Description Interval E-value
MPP_PolD2_C cd07387
PolD2 (DNA polymerase delta, subunit 2), C-terminal domain; PolD2 (DNA polymerase delta, ...
 215-452 7.59e-149

PolD2 (DNA polymerase delta, subunit 2), C-terminal domain; PolD2 (DNA polymerase delta, subunit 2) is an auxiliary subunit of the eukaryotic DNA polymerase delta (PolD) complex thought to play a regulatory role and to serve as a scaffold for PolD assembly by interacting simultaneously with all of the other three subunits. PolD2 is catalytically inactive and lacks the active site residues required for phosphoesterase activity in other members of this superfamily. PolD2 is also involved in the recruitment of several proteins regulating DNA metabolism, including p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3), and p12(PolD4). PolD is one of three major replicases in eukaryotes. PolD also plays an essential role in translesion DNA synthesis, homologous recombination, and DNA repair. Within the PolD complex, PolD2 tightly associates with PolD3. PolD2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277333  Cd Length: 257  Bit Score: 424.36  E-value: 7.59e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 215 TQLLVDVVTGQLGDEGEQCSAAHVSRVILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDV 294
Cdd:cd07387   20 LQLLVDWLTGQLGDESEQLSASSIVRLIIAGNSLAKSEQGKDSQSKARYLTKKSSAASVEAVKELDEFLSQLASSVPVDV 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 295 MPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHI 374
Cdd:cd07387  100 MPGENDPANFMLPQQPLHRCMFPKSRSYSTLNLVTNPYEFSVDGVRVLGTSGQNVSDILKYSSKESRLDALESTLRWRHI 179

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 379056383 375 SPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNTPSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSLACQPISF 452
Cdd:cd07387  180 APTAPDTLWCYPFTDRDPFILEECPHVYFAGNQPKFGTKLVEGENGQRVLLVCVPSFSKTGSAVLVNLRTLECEPINF 257
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 216-412 8.11e-63

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


Pssm-ID: 461142  Cd Length: 210  Bit Score: 202.92  E-value: 8.11e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383  216 QLLVDVVTGQLgdegeqcSAAHVSRVILAGNLLSHSTQSRDSINKAKyltkKTQAASVEAVKMLDEILLQLSASVPVDVM 295
Cdd:pfam04042  17 EALRDLLDGYN-------EDSPPDRLILAGPFLDSKHNLIASGAVAG----DTLTYNFLFLKLLLSILEQLLEKTPVILV 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383  296 PGEFDPTN-YTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDH------LEILEWT 368
Cdd:pfam04042  86 PGPNDPANsTVLPQPPFPRCLLPRIKKNNSLIFVTNPCRFSINGVEVVVTSGDNVSDLLRYELKFSSsdvdrfLRLVETI 165

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 379056383  369 LRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNT-PSFGS 412
Cdd:pfam04042 166 LRQRHLAPLAPDTLRPYPYDKDDAFVLYPLPDVLILGSElPSFAK 210
DNA_pol_D_N pfam18018
DNA polymerase delta subunit OB-fold domain; The eukaryotic DNA polymerase delta (Pol delta) ...
 49-176 2.89e-60

DNA polymerase delta subunit OB-fold domain; The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance. Human Pol delta consists of four subunits: p125, p50, p66 and p12. The first three subunits correspond to the three subunits of S. cerevisiae Pol delta. p50 serves as a scaffold for the assembly of Pol delta by interacting simultaneously with all of the other three subunits. This entry corresponds to the OB fold domain found in the p50 subunit.


Pssm-ID: 436215  Cd Length: 129  Bit Score: 193.18  E-value: 2.89e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383   49 QYAHIYATRLIQMRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREVSEEHNLLPQPPRSKYIH 128
Cdd:pfam18018   1 QYAHIYFARLEALRPRLLEAAKKKWGDVIPVNKILDLKEGEECIIIGTLYKEMKLKPSILDEYSEENQLAPQPPRTKYTS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 379056383  129 PDDELVLEDELQRIKLKG-TIDVSKLVTGTVLAVFGSVRDDGKFLVEDY 176
Cdd:pfam18018  81 DDDELFLEDESGRIKLIGdKIDVDELVTGVVVAVLGRENEDGDFEVEDI 129
PRK04036 PRK04036
DNA-directed DNA polymerase II small subunit;
50-426 1.62e-04

DNA-directed DNA polymerase II small subunit;


Pssm-ID: 235208 [Multi-domain]  Cd Length: 504  Bit Score: 44.17  E-value: 1.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383  50 YAHIYATRLIQMRPFLENRAQqhwgsGVGVKKLCEL-QPEEKCCVVGTLfkamplqpSILREVSEEHNLLpqpprskyih 128
Cdd:PRK04036 119 FVAYFRDRYEKLSKIIRGRVN-----HRPIESLKKLkRGGEEVSIIGMV--------SDIRSTKNGHKIV---------- 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 129 pddelVLEDELQRIK---LKGTID----VSKLVTGTVLAVFGSVRDDGK-FLVEDYCFADLAPQKPAPPLDTDrfvllvs 200
Cdd:PRK04036 176 -----ELEDTTGTFPvliMKDREDlaelADELLLDEVIGVEGTLSGDGGlIFADEIIRPDVPRTKEPPTKDEK------- 243

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 201 glglgggggeslLGTQLLVDVVTG----------------QLGDEGEQCSAAHVSRVILAGNLLshstqsrDSI----NK 260
Cdd:PRK04036 244 ------------VYAVFISDVHVGskefledafekfidwlNGEVGNEEEIASRVKYLIIAGDLV-------DGIgiypGQ 304

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 261 AKYLTKKTQAASVEAVKMLdeiLLQLSASVPVDVMPGEFDPTNYTLPQQPLHP---CMFPLATAYstlqLVTNPYQATID 337
Cdd:PRK04036 305 EEELEIVDIYEQYEAAAEY---LKQIPEDIKIIISPGNHDAVRQAEPQPAFPEeirSLFPEHNVT----FVSNPALVNLH 377

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 338 GVRFLGTSGQNVSDIFRYS---SMEDHLEILEWTLRVRHISPT-------APDtlgcypfyKTDPFIFPECPHVYFCGNT 407
Cdd:PRK04036 378 GVDVLIYHGRSIDDVISLIpgaSYEKPGKAMEELLKRRHLAPIyggrtpiAPE--------KEDYLVIDEVPDIFHTGHV 449

                        410
                 ....*....|....*....
gi 379056383 408 PSFGSKIIRGpedqtVLLV 426
Cdd:PRK04036 450 HINGYGKYRG-----VLLI 463
 
Name Accession Description Interval E-value
MPP_PolD2_C cd07387
PolD2 (DNA polymerase delta, subunit 2), C-terminal domain; PolD2 (DNA polymerase delta, ...
 215-452 7.59e-149

PolD2 (DNA polymerase delta, subunit 2), C-terminal domain; PolD2 (DNA polymerase delta, subunit 2) is an auxiliary subunit of the eukaryotic DNA polymerase delta (PolD) complex thought to play a regulatory role and to serve as a scaffold for PolD assembly by interacting simultaneously with all of the other three subunits. PolD2 is catalytically inactive and lacks the active site residues required for phosphoesterase activity in other members of this superfamily. PolD2 is also involved in the recruitment of several proteins regulating DNA metabolism, including p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3), and p12(PolD4). PolD is one of three major replicases in eukaryotes. PolD also plays an essential role in translesion DNA synthesis, homologous recombination, and DNA repair. Within the PolD complex, PolD2 tightly associates with PolD3. PolD2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277333  Cd Length: 257  Bit Score: 424.36  E-value: 7.59e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 215 TQLLVDVVTGQLGDEGEQCSAAHVSRVILAGNLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDV 294
Cdd:cd07387   20 LQLLVDWLTGQLGDESEQLSASSIVRLIIAGNSLAKSEQGKDSQSKARYLTKKSSAASVEAVKELDEFLSQLASSVPVDV 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 295 MPGEFDPTNYTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHI 374
Cdd:cd07387  100 MPGENDPANFMLPQQPLHRCMFPKSRSYSTLNLVTNPYEFSVDGVRVLGTSGQNVSDILKYSSKESRLDALESTLRWRHI 179

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 379056383 375 SPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNTPSFGSKIIRGPEDQTVLLVTVPDFSATQTACLVNLRSLACQPISF 452
Cdd:cd07387  180 APTAPDTLWCYPFTDRDPFILEECPHVYFAGNQPKFGTKLVEGENGQRVLLVCVPSFSKTGSAVLVNLRTLECEPINF 257
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 216-412 8.11e-63

DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.


Pssm-ID: 461142  Cd Length: 210  Bit Score: 202.92  E-value: 8.11e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383  216 QLLVDVVTGQLgdegeqcSAAHVSRVILAGNLLSHSTQSRDSINKAKyltkKTQAASVEAVKMLDEILLQLSASVPVDVM 295
Cdd:pfam04042  17 EALRDLLDGYN-------EDSPPDRLILAGPFLDSKHNLIASGAVAG----DTLTYNFLFLKLLLSILEQLLEKTPVILV 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383  296 PGEFDPTN-YTLPQQPLHPCMFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDH------LEILEWT 368
Cdd:pfam04042  86 PGPNDPANsTVLPQPPFPRCLLPRIKKNNSLIFVTNPCRFSINGVEVVVTSGDNVSDLLRYELKFSSsdvdrfLRLVETI 165

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 379056383  369 LRVRHISPTAPDTLGCYPFYKTDPFIFPECPHVYFCGNT-PSFGS 412
Cdd:pfam04042 166 LRQRHLAPLAPDTLRPYPYDKDDAFVLYPLPDVLILGSElPSFAK 210
DNA_pol_D_N pfam18018
DNA polymerase delta subunit OB-fold domain; The eukaryotic DNA polymerase delta (Pol delta) ...
 49-176 2.89e-60

DNA polymerase delta subunit OB-fold domain; The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance. Human Pol delta consists of four subunits: p125, p50, p66 and p12. The first three subunits correspond to the three subunits of S. cerevisiae Pol delta. p50 serves as a scaffold for the assembly of Pol delta by interacting simultaneously with all of the other three subunits. This entry corresponds to the OB fold domain found in the p50 subunit.


Pssm-ID: 436215  Cd Length: 129  Bit Score: 193.18  E-value: 2.89e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383   49 QYAHIYATRLIQMRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREVSEEHNLLPQPPRSKYIH 128
Cdd:pfam18018   1 QYAHIYFARLEALRPRLLEAAKKKWGDVIPVNKILDLKEGEECIIIGTLYKEMKLKPSILDEYSEENQLAPQPPRTKYTS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 379056383  129 PDDELVLEDELQRIKLKG-TIDVSKLVTGTVLAVFGSVRDDGKFLVEDY 176
Cdd:pfam18018  81 DDDELFLEDESGRIKLIGdKIDVDELVTGVVVAVLGRENEDGDFEVEDI 129
MPP_DNA_pol_II_small_archeal_C cd07386
archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small ...
 279-437 1.61e-08

archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small subunit of the archeal DNA polymerase II contains a C-terminal metallophosphatase domain. This domain is thought to be functionally active because the active site residues required for phosphoesterase activity in other members of this superfamily are intact. The archeal replicative DNA polymerases are thought to possess intrinsic phosphatase activity that hydrolyzes the pyrophosphate released during nucleotide polymerization. This domain belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277332  Cd Length: 243  Bit Score: 55.39  E-value: 1.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 279 LDEILLQLSASVPVDVMPGEFDPTNYTLPQQPL---HPCMFPLATAYstlqLVTNPYQATIDGVRFLGTSGQNVSDIF-- 353
Cdd:cd07386   71 AAEYLSDVPSHIKIIIIPGNHDAVRQAEPQPALpeeIRKLFYPGNVE----FLSNPALVKIHGVDVLIYHGRSLDDVVgl 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 354 -RYSSMEDHLEILEWTLRVRHISPT-------APDtlgcypfyKTDPFIFPECPHVYFCGNTPSFGSKIIRGpedqtVLL 425
Cdd:cd07386  147 iPGLSYDKPGKAMEELLKRRHLAPIyggrtpiAPE--------AEDYLVIDEVPDILHTGHVHVYGVGVYRG-----VLL 213

                        170
                 ....*....|....*
gi 379056383 426 VTvpdfSAT---QTA 437
Cdd:cd07386  214 VN----SGTwqsQTE 224
PRK04036 PRK04036
DNA-directed DNA polymerase II small subunit;
50-426 1.62e-04

DNA-directed DNA polymerase II small subunit;


Pssm-ID: 235208 [Multi-domain]  Cd Length: 504  Bit Score: 44.17  E-value: 1.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383  50 YAHIYATRLIQMRPFLENRAQqhwgsGVGVKKLCEL-QPEEKCCVVGTLfkamplqpSILREVSEEHNLLpqpprskyih 128
Cdd:PRK04036 119 FVAYFRDRYEKLSKIIRGRVN-----HRPIESLKKLkRGGEEVSIIGMV--------SDIRSTKNGHKIV---------- 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 129 pddelVLEDELQRIK---LKGTID----VSKLVTGTVLAVFGSVRDDGK-FLVEDYCFADLAPQKPAPPLDTDrfvllvs 200
Cdd:PRK04036 176 -----ELEDTTGTFPvliMKDREDlaelADELLLDEVIGVEGTLSGDGGlIFADEIIRPDVPRTKEPPTKDEK------- 243

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 201 glglgggggeslLGTQLLVDVVTG----------------QLGDEGEQCSAAHVSRVILAGNLLshstqsrDSI----NK 260
Cdd:PRK04036 244 ------------VYAVFISDVHVGskefledafekfidwlNGEVGNEEEIASRVKYLIIAGDLV-------DGIgiypGQ 304

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 261 AKYLTKKTQAASVEAVKMLdeiLLQLSASVPVDVMPGEFDPTNYTLPQQPLHP---CMFPLATAYstlqLVTNPYQATID 337
Cdd:PRK04036 305 EEELEIVDIYEQYEAAAEY---LKQIPEDIKIIISPGNHDAVRQAEPQPAFPEeirSLFPEHNVT----FVSNPALVNLH 377

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379056383 338 GVRFLGTSGQNVSDIFRYS---SMEDHLEILEWTLRVRHISPT-------APDtlgcypfyKTDPFIFPECPHVYFCGNT 407
Cdd:PRK04036 378 GVDVLIYHGRSIDDVISLIpgaSYEKPGKAMEELLKRRHLAPIyggrtpiAPE--------KEDYLVIDEVPDIFHTGHV 449

                        410
                 ....*....|....*....
gi 379056383 408 PSFGSKIIRGpedqtVLLV 426
Cdd:PRK04036 450 HINGYGKYRG-----VLLI 463
 
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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