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2n1g

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Revision as of 15:25, 2 June 2021

Structure of C-terminal domain of human polymerase Rev1 in complex with PolD3 RIR-motif

Structural highlights

2n1g is a 2 chain structure with sequence from Human. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	REV1, REV1L (HUMAN), KIAA0039, POLD3 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[REV1_HUMAN] Deoxycytidyl transferase involved in DNA repair. Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents.^[1] ^[2] ^[3] ^[4] ^[5] [DPOD3_HUMAN] Required for optimal DNA polymerase delta activity.^[6] ^[7] ^[8]

Publication Abstract from PubMed

Translesion synthesis (TLS) is a mutagenic branch of cellular DNA damage tolerance that enables bypass replication over DNA lesions carried out by specialized low-fidelity DNA polymerases. The replicative bypass of most types of DNA damage is performed in a two-step process of Rev1/Polzeta-dependent TLS. In the first step, a Y-family TLS enzyme, typically Poleta, Poliota, or Polkappa, inserts a nucleotide across a DNA lesion. In the second step, a four-subunit B-family DNA polymerase Polzeta (Rev3/Rev7/PolD2/PolD3 complex) extends the distorted DNA primer-template. The coordinated action of error-prone TLS enzymes is regulated through their interactions with the two scaffold proteins, the sliding clamp PCNA and the TLS polymerase Rev1. Rev1 interactions with all other TLS enzymes are mediated by its C-terminal domain (Rev1-CT), which can simultaneously bind the Rev7 subunit of Polzeta and Rev1-interacting regions (RIRs) from Poleta, Poliota, or Polkappa. In this work, we identified a previously unknown RIR motif in the C-terminal part of PolD3 subunit of Polzeta whose interaction with the Rev1-CT is among the tightest mediated by RIR motifs. Three-dimensional structure of the Rev1-CT/PolD3-RIR complex determined by NMR spectroscopy revealed a structural basis for the relatively high affinity of this interaction. The unexpected discovery of PolD3-RIR motif suggests a mechanism of "inserter" to "extender" DNA polymerase switch upon Rev1/Polzeta-dependent TLS, in which the PolD3-RIR binding to the Rev1-CT (i) helps displace the "inserter" Poleta, Poliota, or Polkappa from its complex with Rev1, and (ii) facilitates assembly of the four-subunit "extender" Polzeta through simultaneous interaction of Rev1-CT with Rev7 and PolD3 subunits.

Interaction between the Rev1 C-Terminal Domain and the PolD3 Subunit of Polzeta Suggests a Mechanism of Polymerase Exchange upon Rev1/Polzeta-Dependent Translesion Synthesis.,Pustovalova Y, Magalhaes MT, D'Souza S, Rizzo AA, Korza G, Walker GC, Korzhnev DM Biochemistry. 2016 Apr 5;55(13):2043-53. doi: 10.1021/acs.biochem.5b01282. Epub, 2016 Mar 24. PMID:26982350^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lin W, Xin H, Zhang Y, Wu X, Yuan F, Wang Z. The human REV1 gene codes for a DNA template-dependent dCMP transferase. Nucleic Acids Res. 1999 Nov 15;27(22):4468-75. PMID:10536157
↑ Gibbs PE, Wang XD, Li Z, McManus TP, McGregor WG, Lawrence CW, Maher VM. The function of the human homolog of Saccharomyces cerevisiae REV1 is required for mutagenesis induced by UV light. Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):4186-91. PMID:10760286
↑ Masuda Y, Takahashi M, Tsunekuni N, Minami T, Sumii M, Miyagawa K, Kamiya K. Deoxycytidyl transferase activity of the human REV1 protein is closely associated with the conserved polymerase domain. J Biol Chem. 2001 May 4;276(18):15051-8. Epub 2001 Jan 22. PMID:11278384 doi:10.1074/jbc.M008082200
↑ Murakumo Y, Ogura Y, Ishii H, Numata S, Ichihara M, Croce CM, Fishel R, Takahashi M. Interactions in the error-prone postreplication repair proteins hREV1, hREV3, and hREV7. J Biol Chem. 2001 Sep 21;276(38):35644-51. Epub 2001 Aug 2. PMID:11485998 doi:10.1074/jbc.M102051200
↑ Kim H, Yang K, Dejsuphong D, D'Andrea AD. Regulation of Rev1 by the Fanconi anemia core complex. Nat Struct Mol Biol. 2012 Jan 22;19(2):164-70. doi: 10.1038/nsmb.2222. PMID:22266823 doi:10.1038/nsmb.2222
↑ Hughes P, Tratner I, Ducoux M, Piard K, Baldacci G. Isolation and identification of the third subunit of mammalian DNA polymerase delta by PCNA-affinity chromatography of mouse FM3A cell extracts. Nucleic Acids Res. 1999 May 15;27(10):2108-14. PMID:10219083
↑ Mo J, Liu L, Leon A, Mazloum N, Lee MY. Evidence that DNA polymerase delta isolated by immunoaffinity chromatography exhibits high-molecular weight characteristics and is associated with the KIAA0039 protein and RPA. Biochemistry. 2000 Jun 20;39(24):7245-54. PMID:10852724
↑ Li H, Xie B, Zhou Y, Rahmeh A, Trusa S, Zhang S, Gao Y, Lee EY, Lee MY. Functional roles of p12, the fourth subunit of human DNA polymerase delta. J Biol Chem. 2006 May 26;281(21):14748-55. Epub 2006 Feb 28. PMID:16510448 doi:http://dx.doi.org/10.1074/jbc.M600322200
↑ Pustovalova Y, Magalhaes MT, D'Souza S, Rizzo AA, Korza G, Walker GC, Korzhnev DM. Interaction between the Rev1 C-Terminal Domain and the PolD3 Subunit of Polzeta Suggests a Mechanism of Polymerase Exchange upon Rev1/Polzeta-Dependent Translesion Synthesis. Biochemistry. 2016 Apr 5;55(13):2043-53. doi: 10.1021/acs.biochem.5b01282. Epub, 2016 Mar 24. PMID:26982350 doi:http://dx.doi.org/10.1021/acs.biochem.5b01282

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2n1g"

@@ Line 1: / Line 1: @@
 ==Structure of C-terminal domain of human polymerase Rev1 in complex with PolD3 RIR-motif==
-<StructureSection load='2n1g' size='340' side='right' caption='[[2n1g]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2n1g' size='340' side='right'caption='[[2n1g]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2n1g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N1G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N1G FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2n1g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N1G FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">REV1, REV1L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), KIAA0039, POLD3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">REV1, REV1L ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), KIAA0039, POLD3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2n1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n1g OCA], [http://pdbe.org/2n1g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2n1g RCSB], [http://www.ebi.ac.uk/pdbsum/2n1g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2n1g ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2n1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n1g OCA], [https://pdbe.org/2n1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n1g RCSB], [https://www.ebi.ac.uk/pdbsum/2n1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n1g ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/REV1_HUMAN REV1_HUMAN]] Deoxycytidyl transferase involved in DNA repair. Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents.<ref>PMID:10536157</ref> <ref>PMID:10760286</ref> <ref>PMID:11278384</ref> <ref>PMID:11485998</ref> <ref>PMID:22266823</ref>  [[http://www.uniprot.org/uniprot/DPOD3_HUMAN DPOD3_HUMAN]] Required for optimal DNA polymerase delta activity.<ref>PMID:10219083</ref> <ref>PMID:10852724</ref> <ref>PMID:16510448</ref>
+[[https://www.uniprot.org/uniprot/REV1_HUMAN REV1_HUMAN]] Deoxycytidyl transferase involved in DNA repair. Transfers a dCMP residue from dCTP to the 3'-end of a DNA primer in a template-dependent reaction. May assist in the first step in the bypass of abasic lesions by the insertion of a nucleotide opposite the lesion. Required for normal induction of mutations by physical and chemical agents.<ref>PMID:10536157</ref> <ref>PMID:10760286</ref> <ref>PMID:11278384</ref> <ref>PMID:11485998</ref> <ref>PMID:22266823</ref>  [[https://www.uniprot.org/uniprot/DPOD3_HUMAN DPOD3_HUMAN]] Required for optimal DNA polymerase delta activity.<ref>PMID:10219083</ref> <ref>PMID:10852724</ref> <ref>PMID:16510448</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 </StructureSection>
 [[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Korzhnev, D]]
 [[Category: Pustovalova, Y]]

2n1g

From Proteopedia

Revision as of 15:25, 2 June 2021

Structure of C-terminal domain of human polymerase Rev1 in complex with PolD3 RIR-motif

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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