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Conserved domains on  [gi|530387849|ref|XP_005273597|]
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DNA polymerase beta isoform X5 [Homo sapiens]

Protein Classification

nucleotidyltransferase domain-containing protein( domain architecture ID 10065437)

nucleotidyltransferase domain-containing protein of family X DNA polymerases which includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT).

EC:  2.7.7.7
Gene Ontology:  GO:0003887|GO:0003677

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 1-179 4.74e-78

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


:

Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 234.78  E-value: 4.74e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849   1 MLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSestkqPKLLHQVVEQLQKVHFITDTLSKGETK 80
Cdd:cd00141  143 ALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATS-----RGLLEKVVDALVELGFVTEVLSKGDTK 217

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849  81 FMGVCQLPskndeKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPlgvtGVAGEPLPVD 160
Cdd:cd00141  218 ASGILKLP-----GGWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFD----GVDGERLPGE 288

                        170
                 ....*....|....*....
gi 530387849 161 SEKDIFDYIQWKYREPKDR 179
Cdd:cd00141  289 TEEEIFEALGLPYIEPELR 307
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 1-179 4.74e-78

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 234.78  E-value: 4.74e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849   1 MLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSestkqPKLLHQVVEQLQKVHFITDTLSKGETK 80
Cdd:cd00141  143 ALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATS-----RGLLEKVVDALVELGFVTEVLSKGDTK 217

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849  81 FMGVCQLPskndeKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPlgvtGVAGEPLPVD 160
Cdd:cd00141  218 ASGILKLP-----GGWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFD----GVDGERLPGE 288

                        170
                 ....*....|....*....
gi 530387849 161 SEKDIFDYIQWKYREPKDR 179
Cdd:cd00141  289 TEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 1-180 7.24e-66

DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases


Pssm-ID: 214688  Cd Length: 334  Bit Score: 204.91  E-value: 7.24e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849     1 MLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFT---SESTKQPKLLHQVVEQLQKVHFITDTLSKG 77
Cdd:smart00483 147 AFAVEYIVKRAVRKILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAkekELEVLDLLLLESTFEELQLPSIRVATLDHG 226

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849    78 ETKFMGVCQLPSKNDEKEYP--------HRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGfTINEYTIRPLGV 149
Cdd:smart00483 227 QKKFMILKLSPSREDKEKSGkpdekgwkARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKF-KLMLDGHELYDK 305

                          170       180       190
                   ....*....|....*....|....*....|.
gi 530387849   150 TGvaGEPLPVDSEKDIFDYIQWKYREPKDRS 180
Cdd:smart00483 306 TK--EKFLKVESEEDIFDHLGLPYIEPEERN 334
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
 1-107 1.89e-46

DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.


Pssm-ID: 464318  Cd Length: 110  Bit Score: 147.71  E-value: 1.89e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849    1 MLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSEStKQPKLLHQVVEQLQKVHFITDTLS--KGE 78
Cdd:pfam14792   7 VEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSES-ELKGLLDRLVARLKKSGFLTDDLAvdSGG 85

                          90       100
                  ....*....|....*....|....*....
gi 530387849   79 TKFMGVCQLPskndEKEYPHRRIDIRLIP 107
Cdd:pfam14792  86 SKWMGVCRLP----GSERLHRRIDILVVP 110
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
1-169 2.12e-23

DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 96.03  E-value: 2.12e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849   1 MLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLThpsftsesTKQPKllhQVVEQLQKVHFITDTLSKGETK 80
Cdd:COG1796  161 ALPLAEEILAYLRALPGVERVEVAGSLRRRKETVGDIDILVA--------SDDPE---AVMDAFVKLPEVKEVLAKGDTK 229

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849  81 fmgvCQLPSKNDekeyphRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYtirplGVTGVAGEPLPVD 160
Cdd:COG1796  230 ----ASVRLKSG------LQVDLRVVPPESFGAALQYFTGSKEHNVALRQLAKERGLKLNEY-----GLFDVGGERIAGE 294

                        170
                 ....*....|....
gi 530387849 161 SEKDIF-----DYI 169
Cdd:COG1796  295 TEEEVYaalglPYI 308
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
23-181 5.87e-13

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 65.75  E-value: 5.87e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849  23 VCGSFRRGAESSGDMDVLLthpsftseSTKQPkllHQVVEQLQKVHFITDTLSKGETKFmgvcqlpSKNDEKEYPhRRID 102
Cdd:PRK08609 180 RAGSLRRARETVKDLDFII--------ATDEP---EAVREQLLQLPNIVEVIAAGDTKV-------SVELEYEYT-ISVD 240

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849 103 IRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYtirplGVTGV-AGEPLPVDSEKDIFDYIQWKYREP---KD 178
Cdd:PRK08609 241 FRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEY-----GVEQAdTGEVKTFESEEAFFAHFGLPFIPPevrED 315


                 ...
gi 530387849 179 RSE 181
Cdd:PRK08609 316 GSE 318
 
Name Accession Description Interval E-value
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 1-179 4.74e-78

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 234.78  E-value: 4.74e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849   1 MLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSestkqPKLLHQVVEQLQKVHFITDTLSKGETK 80
Cdd:cd00141  143 ALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATS-----RGLLEKVVDALVELGFVTEVLSKGDTK 217

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849  81 FMGVCQLPskndeKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPlgvtGVAGEPLPVD 160
Cdd:cd00141  218 ASGILKLP-----GGWKGRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFD----GVDGERLPGE 288

                        170
                 ....*....|....*....
gi 530387849 161 SEKDIFDYIQWKYREPKDR 179
Cdd:cd00141  289 TEEEIFEALGLPYIEPELR 307
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 1-180 7.24e-66

DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases


Pssm-ID: 214688  Cd Length: 334  Bit Score: 204.91  E-value: 7.24e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849     1 MLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFT---SESTKQPKLLHQVVEQLQKVHFITDTLSKG 77
Cdd:smart00483 147 AFAVEYIVKRAVRKILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAkekELEVLDLLLLESTFEELQLPSIRVATLDHG 226

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849    78 ETKFMGVCQLPSKNDEKEYP--------HRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGfTINEYTIRPLGV 149
Cdd:smart00483 227 QKKFMILKLSPSREDKEKSGkpdekgwkARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKF-KLMLDGHELYDK 305

                          170       180       190
                   ....*....|....*....|....*....|.
gi 530387849   150 TGvaGEPLPVDSEKDIFDYIQWKYREPKDRS 180
Cdd:smart00483 306 TK--EKFLKVESEEDIFDHLGLPYIEPEERN 334
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
 1-107 1.89e-46

DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.


Pssm-ID: 464318  Cd Length: 110  Bit Score: 147.71  E-value: 1.89e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849    1 MLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSEStKQPKLLHQVVEQLQKVHFITDTLS--KGE 78
Cdd:pfam14792   7 VEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSES-ELKGLLDRLVARLKKSGFLTDDLAvdSGG 85

                          90       100
                  ....*....|....*....|....*....
gi 530387849   79 TKFMGVCQLPskndEKEYPHRRIDIRLIP 107
Cdd:pfam14792  86 SKWMGVCRLP----GSERLHRRIDILVVP 110
DNA_pol_B_thumb pfam14791
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
 115-179 9.85e-24

DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain.


Pssm-ID: 464317 [Multi-domain]  Cd Length: 63  Bit Score: 88.58  E-value: 9.85e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530387849  115 VLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLgvtgVAGEPLPVDSEKDIFDYIQWKYREPKDR 179
Cdd:pfam14791   2 LLYFTGSKEFNRDLRLLAKKKGLKLNEYGLFDL----KDGELLEGETEEDIFEALGLPYIPPELR 62
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
1-169 2.12e-23

DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 96.03  E-value: 2.12e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849   1 MLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLThpsftsesTKQPKllhQVVEQLQKVHFITDTLSKGETK 80
Cdd:COG1796  161 ALPLAEEILAYLRALPGVERVEVAGSLRRRKETVGDIDILVA--------SDDPE---AVMDAFVKLPEVKEVLAKGDTK 229

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849  81 fmgvCQLPSKNDekeyphRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYtirplGVTGVAGEPLPVD 160
Cdd:COG1796  230 ----ASVRLKSG------LQVDLRVVPPESFGAALQYFTGSKEHNVALRQLAKERGLKLNEY-----GLFDVGGERIAGE 294

                        170
                 ....*....|....
gi 530387849 161 SEKDIF-----DYI 169
Cdd:COG1796  295 TEEEVYaalglPYI 308
PRK08609 PRK08609
DNA polymerase/3'-5' exonuclease PolX;
23-181 5.87e-13

DNA polymerase/3'-5' exonuclease PolX;


Pssm-ID: 236311 [Multi-domain]  Cd Length: 570  Bit Score: 65.75  E-value: 5.87e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849  23 VCGSFRRGAESSGDMDVLLthpsftseSTKQPkllHQVVEQLQKVHFITDTLSKGETKFmgvcqlpSKNDEKEYPhRRID 102
Cdd:PRK08609 180 RAGSLRRARETVKDLDFII--------ATDEP---EAVREQLLQLPNIVEVIAAGDTKV-------SVELEYEYT-ISVD 240

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530387849 103 IRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYtirplGVTGV-AGEPLPVDSEKDIFDYIQWKYREP---KD 178
Cdd:PRK08609 241 FRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEY-----GVEQAdTGEVKTFESEEAFFAHFGLPFIPPevrED 315


                 ...
gi 530387849 179 RSE 181
Cdd:PRK08609 316 GSE 318
NT_Pol-beta-like cd05397
Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This ...
 2-42 1.04e-06

Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism for Rel-Spo enzymes.


Pssm-ID: 143387 [Multi-domain]  Cd Length: 49  Bit Score: 43.85  E-value: 1.04e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 530387849   2 LQMQDIVLNEVKKVDSEYIATVCGSFRRGAE-SSGDMDVLLT 42
Cdd:cd05397    1 EELLDIIKERLKKLVPGYEIVVYGSLVRGLLkKSSDIDLACV 42
 
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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