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Conserved domains on  [gi|1958802260|ref|XP_038939462|]
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DNA polymerase eta isoform X2 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PolY super family cl28996
Y-family of DNA polymerases; Y-family DNA polymerases are a specialized subset of polymerases ...
 1-179 3.39e-67

Y-family of DNA polymerases; Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.


The actual alignment was detected with superfamily member cd01702:

Pssm-ID: 452909 [Multi-domain]  Cd Length: 359  Bit Score: 218.34  E-value: 3.39e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802260   1 MPIRKIRSLGGKLGASVIDVLGVEYMGDLTQF--TEAQLQSHFGEKNGSWLYAMCRGIEHEPVKPRQLPKTIGCSKNFPG 78
Cdd:cd01702   182 LPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFrsSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFPG 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802260  79 KTALATrEQVQWWLLQLALELEERLTKDRTDNGRVATQLVVSIRVEGDKrlSSLRRCCALTRYDAHKMSQDAFATIRNCN 158
Cdd:cd01702   262 KTALST-EDVQHWLLVLASELNSRLEDDRYENNRRPKTLVLSLRQRGDG--VRRSRSCALPRYDAQKIVKDAFKLIKAIN 338

                         170       180
                  ....*....|....*....|.
gi 1958802260 159 TSGVQTEWSPPLTMLFLCATK 179
Cdd:cd01702   339 EEGLGLAWNYPLTLLSLSFTK 359
zf_UBZ pfam18439
Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA ...
 360-390 1.95e-11

Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA polymerase eta (EC:2.7.7.7). It is important in the recruitment of the polymerase to the stalled replication machinery in translesion synthesis. The UBZ domain adopts a classical C2H2 zinc-finger structure characterized by a beta-beta-alpha fold.


:

Pssm-ID: 465769  Cd Length: 32  Bit Score: 58.29  E-value: 1.95e-11
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958802260 360 DQVLCEKCDSLVPVWDMPEHLDYHFALELQK 390
Cdd:pfam18439   1 DTYVCPRCGKEIPESELPEHEDWHFAKDLQR 31
 
Name Accession Description Interval E-value
PolY_Pol_eta cd01702
DNA Polymerase eta; Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. ...
 1-179 3.39e-67

DNA Polymerase eta; Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.


Pssm-ID: 176456 [Multi-domain]  Cd Length: 359  Bit Score: 218.34  E-value: 3.39e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802260   1 MPIRKIRSLGGKLGASVIDVLGVEYMGDLTQF--TEAQLQSHFGEKNGSWLYAMCRGIEHEPVKPRQLPKTIGCSKNFPG 78
Cdd:cd01702   182 LPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFrsSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFPG 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802260  79 KTALATrEQVQWWLLQLALELEERLTKDRTDNGRVATQLVVSIRVEGDKrlSSLRRCCALTRYDAHKMSQDAFATIRNCN 158
Cdd:cd01702   262 KTALST-EDVQHWLLVLASELNSRLEDDRYENNRRPKTLVLSLRQRGDG--VRRSRSCALPRYDAQKIVKDAFKLIKAIN 338

                         170       180
                  ....*....|....*....|.
gi 1958802260 159 TSGVQTEWSPPLTMLFLCATK 179
Cdd:cd01702   339 EEGLGLAWNYPLTLLSLSFTK 359
DinP COG0389
Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination ...
 1-89 5.25e-12

Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination and repair];


Pssm-ID: 440158 [Multi-domain]  Cd Length: 336  Bit Score: 66.71  E-value: 5.25e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802260   1 MPIRKIRSLGGKLGASVIDvLGVEYMGDLTQFTEAQLQSHFGeKNGSWLYAMCRGIEHEPVKPRQLPKTIGCSKNFPgkT 80
Cdd:COG0389   174 LPVEKLWGVGPKTAEKLAR-LGIRTIGDLAALPRAELRRRFG-KVGERLYRLARGIDPRPVEPRRPRKSIGVERTFG--E 249


                  ....*....
gi 1958802260  81 ALATREQVQ 89
Cdd:COG0389   250 DLTDLEELE 258
zf_UBZ pfam18439
Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA ...
 360-390 1.95e-11

Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA polymerase eta (EC:2.7.7.7). It is important in the recruitment of the polymerase to the stalled replication machinery in translesion synthesis. The UBZ domain adopts a classical C2H2 zinc-finger structure characterized by a beta-beta-alpha fold.


Pssm-ID: 465769  Cd Length: 32  Bit Score: 58.29  E-value: 1.95e-11
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958802260 360 DQVLCEKCDSLVPVWDMPEHLDYHFALELQK 390
Cdd:pfam18439   1 DTYVCPRCGKEIPESELPEHEDWHFAKDLQR 31
PRK02406 PRK02406
DNA polymerase IV; Validated
 1-71 4.06e-09

DNA polymerase IV; Validated


Pssm-ID: 235035 [Multi-domain]  Cd Length: 343  Bit Score: 57.82  E-value: 4.06e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958802260   1 MPIRKIRslG-GKLGASVIDVLGVEYMGDLTQFTEAQLQSHFGeKNGSWLYAMCRGIEHEPVKPRQLPKTIG 71
Cdd:PRK02406  168 LPVEKIP--GvGKVTAEKLHALGIYTCADLQKYDLAELIRHFG-KFGRRLYERARGIDERPVKPDRERKSVG 236
 
Name Accession Description Interval E-value
PolY_Pol_eta cd01702
DNA Polymerase eta; Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. ...
 1-179 3.39e-67

DNA Polymerase eta; Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.


Pssm-ID: 176456 [Multi-domain]  Cd Length: 359  Bit Score: 218.34  E-value: 3.39e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802260   1 MPIRKIRSLGGKLGASVIDVLGVEYMGDLTQF--TEAQLQSHFGEKNGSWLYAMCRGIEHEPVKPRQLPKTIGCSKNFPG 78
Cdd:cd01702   182 LPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFrsSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFPG 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802260  79 KTALATrEQVQWWLLQLALELEERLTKDRTDNGRVATQLVVSIRVEGDKrlSSLRRCCALTRYDAHKMSQDAFATIRNCN 158
Cdd:cd01702   262 KTALST-EDVQHWLLVLASELNSRLEDDRYENNRRPKTLVLSLRQRGDG--VRRSRSCALPRYDAQKIVKDAFKLIKAIN 338

                         170       180
                  ....*....|....*....|.
gi 1958802260 159 TSGVQTEWSPPLTMLFLCATK 179
Cdd:cd01702   339 EEGLGLAWNYPLTLLSLSFTK 359
DinP COG0389
Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination ...
 1-89 5.25e-12

Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination and repair];


Pssm-ID: 440158 [Multi-domain]  Cd Length: 336  Bit Score: 66.71  E-value: 5.25e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802260   1 MPIRKIRSLGGKLGASVIDvLGVEYMGDLTQFTEAQLQSHFGeKNGSWLYAMCRGIEHEPVKPRQLPKTIGCSKNFPgkT 80
Cdd:COG0389   174 LPVEKLWGVGPKTAEKLAR-LGIRTIGDLAALPRAELRRRFG-KVGERLYRLARGIDPRPVEPRRPRKSIGVERTFG--E 249


                  ....*....
gi 1958802260  81 ALATREQVQ 89
Cdd:COG0389   250 DLTDLEELE 258
zf_UBZ pfam18439
Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA ...
 360-390 1.95e-11

Ubiquitin-Binding Zinc Finger; This is ubiquitin-binding zinc finger (UBZ) domain found in DNA polymerase eta (EC:2.7.7.7). It is important in the recruitment of the polymerase to the stalled replication machinery in translesion synthesis. The UBZ domain adopts a classical C2H2 zinc-finger structure characterized by a beta-beta-alpha fold.


Pssm-ID: 465769  Cd Length: 32  Bit Score: 58.29  E-value: 1.95e-11
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958802260 360 DQVLCEKCDSLVPVWDMPEHLDYHFALELQK 390
Cdd:pfam18439   1 DTYVCPRCGKEIPESELPEHEDWHFAKDLQR 31
PolY_Pol_IV_kappa cd03586
DNA Polymerase IV/Kappa; Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion ...
 1-80 3.05e-11

DNA Polymerase IV/Kappa; Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a higher error rate than other Y-family polymerases.


Pssm-ID: 176459 [Multi-domain]  Cd Length: 334  Bit Score: 64.46  E-value: 3.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802260   1 MPIRKIRSLGGKLGASVIDvLGVEYMGDLTQFTEAQLQSHFGeKNGSWLYAMCRGIEHEPVKPRQLPKTIGCSKNFPGKT 80
Cdd:cd03586   171 LPVRKIPGVGKVTAEKLKE-LGIKTIGDLAKLDVELLKKLFG-KSGRRLYELARGIDNRPVEPDRERKSIGVERTFSEDL 248
PRK02406 PRK02406
DNA polymerase IV; Validated
 1-71 4.06e-09

DNA polymerase IV; Validated


Pssm-ID: 235035 [Multi-domain]  Cd Length: 343  Bit Score: 57.82  E-value: 4.06e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958802260   1 MPIRKIRslG-GKLGASVIDVLGVEYMGDLTQFTEAQLQSHFGeKNGSWLYAMCRGIEHEPVKPRQLPKTIG 71
Cdd:PRK02406  168 LPVEKIP--GvGKVTAEKLHALGIYTCADLQKYDLAELIRHFG-KFGRRLYERARGIDERPVKPDRERKSVG 236
PolY_Rev1 cd01701
DNA polymerase Rev1; Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. ...
 7-77 7.56e-06

DNA polymerase Rev1; Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.


Pssm-ID: 176455 [Multi-domain]  Cd Length: 404  Bit Score: 48.08  E-value: 7.56e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958802260   7 RSLGGKLGASVIDVLGVEymgDLTQFTEAQLQSHFGEKNGSWLYAMCRGIEHEPVKPRQLPKTIGCSKNFP 77
Cdd:cd01701   232 SSLAEKLVKLFGDTCGGL---ELRSKTKEKLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKSVSAEINYG 299
PRK03348 PRK03348
DNA polymerase IV; Provisional
 1-88 1.36e-05

DNA polymerase IV; Provisional


Pssm-ID: 235118 [Multi-domain]  Cd Length: 454  Bit Score: 47.24  E-value: 1.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802260   1 MPIRKIRSLG----GKLGAsvidvLGVEYMGDLTQFTEAQLQSHFGEKNGSWLYAMCRGIEHEPVKPRQLPKTIGCSKNF 76
Cdd:PRK03348  180 LPVRRLWGIGpvteEKLHR-----LGIETIGDLAALSEAEVANLLGATVGPALHRLARGIDDRPVAERAEAKQISAESTF 254

                          90
                  ....*....|..
gi 1958802260  77 PgkTALATREQV 88
Cdd:PRK03348  255 A--VDLTTRAQL 264
PRK14133 PRK14133
DNA polymerase IV; Provisional
 1-71 4.54e-03

DNA polymerase IV; Provisional


Pssm-ID: 184529 [Multi-domain]  Cd Length: 347  Bit Score: 38.93  E-value: 4.54e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958802260   1 MPIRKIRSLGGKLGASVIDVlGVEYMGDLTQFTEAQLQSHFGeKNGSWLYAMCRGIEHEPVKPRQLPKTIG 71
Cdd:PRK14133  173 LPISKVHGIGKKSVEKLNNI-GIYTIEDLLKLSREFLIEYFG-KFGVEIYERIRGIDYREVEVSRERKSIG 241
 
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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