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Conserved domains on  [gi|148233344|ref|NP_001080101|]
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DNA polymerase delta subunit 2 [Xenopus laevis]

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, ...
 222-452 6.31e-145

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: 414.34  E-value: 6.31e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344 222 VTGQAGAEEDQGCAARISRVILAGNLLSENTQGKDSLNKAKYLSKKTQAASVEAVKMLDEILLQMSGSVSVDVMPGAFDP 301
Cdd:cd07387   27 LTGQLGDESEQLSASSIVRLIIAGNSLAKSEQGKDSQSKARYLTKKSSAASVEAVKELDEFLSQLASSVPVDVMPGENDP 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344 302 TNYILPQQPLHRCMFPQSALYSTLQLVTNPYEAEIDGVRFLGTSGQNIGDIYKYSSMQDYLDILEWTLQVGHLCPTAPDT 381
Cdd:cd07387  107 ANFMLPQQPLHRCMFPKSRSYSTLNLVTNPYEFSVDGVRVLGTSGQNVSDILKYSSKESRLDALESTLRWRHIAPTAPDT 186

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148233344 382 LGCYPFYKSDPFILQNCPHVYFCGSAPKFSCKEVTGAEGQRVLLLTVPEFCSTQTACLVNLRTLQCQPISF 452
Cdd:cd07387  187 LWCYPFTDRDPFILEECPHVYFAGNQPKFGTKLVEGENGQRVLLVCVPSFSKTGSAVLVNLRTLECEPINF 257
DNA_pol_D_N pfam18018
DNA polymerase delta subunit OB-fold domain; The eukaryotic DNA polymerase delta (Pol delta) ...
 49-176 5.35e-62

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: 197.42  E-value: 5.35e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344   49 QYAHIYATRLEQMRPLLIKSAKQRWGDDIAVRKLCELQGGEKCCVIGTLFKSMELQPSILREISEEHNLLPQPARQKYIS 128
Cdd:pfam18018   1 QYAHIYFARLEALRPRLLEAAKKKWGDVIPVNKILDLKEGEECIIIGTLYKEMKLKPSILDEYSEENQLAPQPPRTKYTS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 148233344  129 DSDELILEDELQRIKLEGAT-DVQQLVTGAVLAVLGAEEDAGKFVVEDF 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, ...
 222-452 6.31e-145

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: 414.34  E-value: 6.31e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344 222 VTGQAGAEEDQGCAARISRVILAGNLLSENTQGKDSLNKAKYLSKKTQAASVEAVKMLDEILLQMSGSVSVDVMPGAFDP 301
Cdd:cd07387   27 LTGQLGDESEQLSASSIVRLIIAGNSLAKSEQGKDSQSKARYLTKKSSAASVEAVKELDEFLSQLASSVPVDVMPGENDP 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344 302 TNYILPQQPLHRCMFPQSALYSTLQLVTNPYEAEIDGVRFLGTSGQNIGDIYKYSSMQDYLDILEWTLQVGHLCPTAPDT 381
Cdd:cd07387  107 ANFMLPQQPLHRCMFPKSRSYSTLNLVTNPYEFSVDGVRVLGTSGQNVSDILKYSSKESRLDALESTLRWRHIAPTAPDT 186

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148233344 382 LGCYPFYKSDPFILQNCPHVYFCGSAPKFSCKEVTGAEGQRVLLLTVPEFCSTQTACLVNLRTLQCQPISF 452
Cdd:cd07387  187 LWCYPFTDRDPFILEECPHVYFAGNQPKFGTKLVEGENGQRVLLVCVPSFSKTGSAVLVNLRTLECEPINF 257
DNA_pol_D_N pfam18018
DNA polymerase delta subunit OB-fold domain; The eukaryotic DNA polymerase delta (Pol delta) ...
 49-176 5.35e-62

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: 197.42  E-value: 5.35e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344   49 QYAHIYATRLEQMRPLLIKSAKQRWGDDIAVRKLCELQGGEKCCVIGTLFKSMELQPSILREISEEHNLLPQPARQKYIS 128
Cdd:pfam18018   1 QYAHIYFARLEALRPRLLEAAKKKWGDVIPVNKILDLKEGEECIIIGTLYKEMKLKPSILDEYSEENQLAPQPPRTKYTS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 148233344  129 DSDELILEDELQRIKLEGAT-DVQQLVTGAVLAVLGAEEDAGKFVVEDF 176
Cdd:pfam18018  81 DDDELFLEDESGRIKLIGDKiDVDELVTGVVVAVLGRENEDGDFEVEDI 129
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 235-412 8.26e-59

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: 192.14  E-value: 8.26e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344  235 AARISRVILAGNLLSENTQGKDSLNKAKylskKTQAASVEAVKMLDEILLQMSGSVSVDVMPGAFDPTN-YILPQQPLHR 313
Cdd:pfam04042  29 DSPPDRLILAGPFLDSKHNLIASGAVAG----DTLTYNFLFLKLLLSILEQLLEKTPVILVPGPNDPANsTVLPQPPFPR 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344  314 CMFPQSALYSTLQLVTNPYEAEIDGVRFLGTSGQNIGDIYKYSSM------QDYLDILEWTLQVGHLCPTAPDTLGCYPF 387
Cdd:pfam04042 105 CLLPRIKKNNSLIFVTNPCRFSINGVEVVVTSGDNVSDLLRYELKfsssdvDRFLRLVETILRQRHLAPLAPDTLRPYPY 184

                         170       180
                  ....*....|....*....|....*.
gi 148233344  388 YKSDPFILQNCPHVYFCGS-APKFSC 412
Cdd:pfam04042 185 DKDDAFVLYPLPDVLILGSeLPSFAK 210
 
Name Accession Description Interval E-value
MPP_PolD2_C cd07387
PolD2 (DNA polymerase delta, subunit 2), C-terminal domain; PolD2 (DNA polymerase delta, ...
 222-452 6.31e-145

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: 414.34  E-value: 6.31e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344 222 VTGQAGAEEDQGCAARISRVILAGNLLSENTQGKDSLNKAKYLSKKTQAASVEAVKMLDEILLQMSGSVSVDVMPGAFDP 301
Cdd:cd07387   27 LTGQLGDESEQLSASSIVRLIIAGNSLAKSEQGKDSQSKARYLTKKSSAASVEAVKELDEFLSQLASSVPVDVMPGENDP 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344 302 TNYILPQQPLHRCMFPQSALYSTLQLVTNPYEAEIDGVRFLGTSGQNIGDIYKYSSMQDYLDILEWTLQVGHLCPTAPDT 381
Cdd:cd07387  107 ANFMLPQQPLHRCMFPKSRSYSTLNLVTNPYEFSVDGVRVLGTSGQNVSDILKYSSKESRLDALESTLRWRHIAPTAPDT 186

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148233344 382 LGCYPFYKSDPFILQNCPHVYFCGSAPKFSCKEVTGAEGQRVLLLTVPEFCSTQTACLVNLRTLQCQPISF 452
Cdd:cd07387  187 LWCYPFTDRDPFILEECPHVYFAGNQPKFGTKLVEGENGQRVLLVCVPSFSKTGSAVLVNLRTLECEPINF 257
DNA_pol_D_N pfam18018
DNA polymerase delta subunit OB-fold domain; The eukaryotic DNA polymerase delta (Pol delta) ...
 49-176 5.35e-62

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: 197.42  E-value: 5.35e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344   49 QYAHIYATRLEQMRPLLIKSAKQRWGDDIAVRKLCELQGGEKCCVIGTLFKSMELQPSILREISEEHNLLPQPARQKYIS 128
Cdd:pfam18018   1 QYAHIYFARLEALRPRLLEAAKKKWGDVIPVNKILDLKEGEECIIIGTLYKEMKLKPSILDEYSEENQLAPQPPRTKYTS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 148233344  129 DSDELILEDELQRIKLEGAT-DVQQLVTGAVLAVLGAEEDAGKFVVEDF 176
Cdd:pfam18018  81 DDDELFLEDESGRIKLIGDKiDVDELVTGVVVAVLGRENEDGDFEVEDI 129
DNA_pol_E_B pfam04042
DNA polymerase alpha/epsilon subunit B; This family contains a number of DNA polymerase ...
 235-412 8.26e-59

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: 192.14  E-value: 8.26e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344  235 AARISRVILAGNLLSENTQGKDSLNKAKylskKTQAASVEAVKMLDEILLQMSGSVSVDVMPGAFDPTN-YILPQQPLHR 313
Cdd:pfam04042  29 DSPPDRLILAGPFLDSKHNLIASGAVAG----DTLTYNFLFLKLLLSILEQLLEKTPVILVPGPNDPANsTVLPQPPFPR 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344  314 CMFPQSALYSTLQLVTNPYEAEIDGVRFLGTSGQNIGDIYKYSSM------QDYLDILEWTLQVGHLCPTAPDTLGCYPF 387
Cdd:pfam04042 105 CLLPRIKKNNSLIFVTNPCRFSINGVEVVVTSGDNVSDLLRYELKfsssdvDRFLRLVETILRQRHLAPLAPDTLRPYPY 184

                         170       180
                  ....*....|....*....|....*.
gi 148233344  388 YKSDPFILQNCPHVYFCGS-APKFSC 412
Cdd:pfam04042 185 DKDDAFVLYPLPDVLILGSeLPSFAK 210
MPP_DNA_pol_II_small_archeal_C cd07386
archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain; The small ...
 279-405 3.07e-06

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: 48.45  E-value: 3.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148233344 279 LDEILLQMSGSVSVDVMPGAFDPTNYILPQQPL----HRCMFPQSAlystlQLVTNPYEAEIDGVRFLGTSGQNIGDIYK 354
Cdd:cd07386   71 AAEYLSDVPSHIKIIIIPGNHDAVRQAEPQPALpeeiRKLFYPGNV-----EFLSNPALVKIHGVDVLIYHGRSLDDVVG 145

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148233344 355 Y---SSMQDYLDILEWTLQVGHLCPT-------APDtlgcypfyKSDPFILQNCPHVYFCG 405
Cdd:cd07386  146 LipgLSYDKPGKAMEELLKRRHLAPIyggrtpiAPE--------AEDYLVIDEVPDILHTG 198
 
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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