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Conserved domains on  [gi|15230500|ref|NP_187852|]
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Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Arabidopsis thaliana]

Protein Classification

3'-5' exonuclease( domain architecture ID 10150121)

3'-5' exonuclease catalyzes the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction; similar to human exonuclease 3'-5' domain-containing protein 2 that that has both 3'-5' exoribonuclease and exodeoxyribonuclease activities

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 31-238 1.12e-38

DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved 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. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.


:

Pssm-ID: 176653 [Multi-domain]  Cd Length: 170  Bit Score: 132.32  E-value: 1.12e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500  31 TPDPSVIGQWIHdvffhnRLSSHPLVVGVGVQWTPSGYHPASPPVSyrsdsspdsyrsdsppvfyssdppadTLQLCVGN 110
Cdd:cd06141   1 TDSAQDAEEAVK------ELLGKEKVVGFDTEWRPSFRKGKRNKVA--------------------------LLQLATES 48

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500 111 RCIIIQLRYCERVPQVLRNFLADRDNTFVGIWNSQDAGKLERsRHQLEIAELMDLREFVSDSSGRRSmyNYSLEKIVEEN 190
Cdd:cd06141  49 RCLLFQLAHMDKLPPSLKQLLEDPSILKVGVGIKGDARKLAR-DFGIEVRGVVDLSHLAKRVGPRRK--LVSLARLVEEV 125

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
gi 15230500 191 LGYPGVRlDREVSMSDWRVYNLSYDQILQASIDVYACcsLAILDHLWE 238
Cdd:cd06141 126 LGLPLSK-PKKVRCSNWEARPLSKEQILYAATDAYAS--LELYRKLLA 170
 
Name Accession Description Interval E-value
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 31-238 1.12e-38

DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved 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. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.


Pssm-ID: 176653 [Multi-domain]  Cd Length: 170  Bit Score: 132.32  E-value: 1.12e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500  31 TPDPSVIGQWIHdvffhnRLSSHPLVVGVGVQWTPSGYHPASPPVSyrsdsspdsyrsdsppvfyssdppadTLQLCVGN 110
Cdd:cd06141   1 TDSAQDAEEAVK------ELLGKEKVVGFDTEWRPSFRKGKRNKVA--------------------------LLQLATES 48

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500 111 RCIIIQLRYCERVPQVLRNFLADRDNTFVGIWNSQDAGKLERsRHQLEIAELMDLREFVSDSSGRRSmyNYSLEKIVEEN 190
Cdd:cd06141  49 RCLLFQLAHMDKLPPSLKQLLEDPSILKVGVGIKGDARKLAR-DFGIEVRGVVDLSHLAKRVGPRRK--LVSLARLVEEV 125

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
gi 15230500 191 LGYPGVRlDREVSMSDWRVYNLSYDQILQASIDVYACcsLAILDHLWE 238
Cdd:cd06141 126 LGLPLSK-PKKVRCSNWEARPLSKEQILYAATDAYAS--LELYRKLLA 170
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 34-239 6.90e-14

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: 67.38  E-value: 6.90e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500     34 PSVIGQWIHDVFFHNRLSSHPLVVGVGVQWTPSGYHpasppvsyrsdsspdsyrsdsppvfyssDPPADTLQLCV-GNRC 112
Cdd:smart00474   1 VIVVTDSETLEELLEKLRAAGGEVALDTETTGLDSY----------------------------SGKLVLIQISVtGEGA 52

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500    113 IIIQLRYCERVPQVLRNFLADRDNTFVGIWNSQDAGKLERSRHQLEIAELMDLREFVSDSSGRRsmynYSLEKIVEENLg 192
Cdd:smart00474  53 FIIDPLALGDDLEILKDLLEDETITKVGHNAKFDLHVLARFGIELENIFDTMLAAYLLLGGPSK----HGLATLLLGYL- 127

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 15230500    193 ypGVRLDREVSMSDWRVYNLSYDQILQASIDVYACCSLAilDHLWEE 239
Cdd:smart00474 128 --GVELDKEEQKSDWGARPLSEEQLEYAAEDADALLRLY--EKLEKE 170
 
Name Accession Description Interval E-value
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 31-238 1.12e-38

DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved 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. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.


Pssm-ID: 176653 [Multi-domain]  Cd Length: 170  Bit Score: 132.32  E-value: 1.12e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500  31 TPDPSVIGQWIHdvffhnRLSSHPLVVGVGVQWTPSGYHPASPPVSyrsdsspdsyrsdsppvfyssdppadTLQLCVGN 110
Cdd:cd06141   1 TDSAQDAEEAVK------ELLGKEKVVGFDTEWRPSFRKGKRNKVA--------------------------LLQLATES 48

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500 111 RCIIIQLRYCERVPQVLRNFLADRDNTFVGIWNSQDAGKLERsRHQLEIAELMDLREFVSDSSGRRSmyNYSLEKIVEEN 190
Cdd:cd06141  49 RCLLFQLAHMDKLPPSLKQLLEDPSILKVGVGIKGDARKLAR-DFGIEVRGVVDLSHLAKRVGPRRK--LVSLARLVEEV 125

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
gi 15230500 191 LGYPGVRlDREVSMSDWRVYNLSYDQILQASIDVYACcsLAILDHLWE 238
Cdd:cd06141 126 LGLPLSK-PKKVRCSNWEARPLSKEQILYAATDAYAS--LELYRKLLA 170
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 34-239 6.90e-14

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: 67.38  E-value: 6.90e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500     34 PSVIGQWIHDVFFHNRLSSHPLVVGVGVQWTPSGYHpasppvsyrsdsspdsyrsdsppvfyssDPPADTLQLCV-GNRC 112
Cdd:smart00474   1 VIVVTDSETLEELLEKLRAAGGEVALDTETTGLDSY----------------------------SGKLVLIQISVtGEGA 52

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500    113 IIIQLRYCERVPQVLRNFLADRDNTFVGIWNSQDAGKLERSRHQLEIAELMDLREFVSDSSGRRsmynYSLEKIVEENLg 192
Cdd:smart00474  53 FIIDPLALGDDLEILKDLLEDETITKVGHNAKFDLHVLARFGIELENIFDTMLAAYLLLGGPSK----HGLATLLLGYL- 127

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 15230500    193 ypGVRLDREVSMSDWRVYNLSYDQILQASIDVYACCSLAilDHLWEE 239
Cdd:smart00474 128 --GVELDKEEQKSDWGARPLSEEQLEYAAEDADALLRLY--EKLEKE 170
RNaseD_like cd06129
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
 104-226 1.46e-05

DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved 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. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Egl is a component of an mRNA-binding complex which is required for oocyte specification. The Egl subfamily does not possess a completely conserved YX(3)D pattern at the ExoIII motif.


Pssm-ID: 176650 [Multi-domain]  Cd Length: 161  Bit Score: 44.04  E-value: 1.46e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230500 104 LQLCV-GNRCIIIQLRYCERVPQVLRNFLADRDNTFVGIWNSQDAGKLERSrHQLEIAELMDLrEFVSDSSGRRSmyNYS 182
Cdd:cd06129  35 IQLCVsEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDLWKLLRD-FGEKLQRLFDT-TIAANLKGLPE--RWS 110

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 15230500 183 LEKIVEEnlgYPGVRLDREVSMSDWRVYNLSYDQILQASIDVYA 226
Cdd:cd06129 111 LASLVEH---FLGKTLDKSISCADWSYRPLTEDQKLYAAADVYA 151
 
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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