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3bjy

From Proteopedia

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Current revision

Catalytic core of Rev1 in complex with DNA (modified template guanine) and incoming nucleotide

Structural highlights

3bjy is a 3 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.41Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

REV1_YEAST 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. Involved in mitochondrial DNA mutagenesis.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Acrolein is generated as the end product of lipid peroxidation and is also a ubiquitous environmental pollutant. Its reaction with the N2 of guanine leads to a cyclic gamma-HOPdG adduct that presents a block to normal replication. We show here that yeast Rev1 incorporates the correct nucleotide C opposite a permanently ring-closed form of gamma-HOPdG (PdG) with nearly the same efficiency as opposite an undamaged G. The structural basis of this action lies in the eviction of the PdG adduct from the Rev1 active site, and the pairing of incoming dCTP with a "surrogate" arginine residue. We also show that yeast Polzeta can carry out the subsequent extension reaction. Together, our studies reveal how the exocyclic PdG adduct is accommodated in a DNA polymerase active site, and they show that the combined action of Rev1 and Polzeta provides for accurate and efficient synthesis through this potentially carcinogenic DNA lesion.

Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase.,Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK Structure. 2008 Feb;16(2):239-45. PMID:18275815^[4]

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

References

↑ Nelson JR, Lawrence CW, Hinkle DC. Deoxycytidyl transferase activity of yeast REV1 protein. Nature. 1996 Aug 22;382(6593):729-31. PMID:8751446 doi:10.1038/382729a0
↑ Haracska L, Unk I, Johnson RE, Johansson E, Burgers PM, Prakash S, Prakash L. Roles of yeast DNA polymerases delta and zeta and of Rev1 in the bypass of abasic sites. Genes Dev. 2001 Apr 15;15(8):945-54. PMID:11316789 doi:10.1101/gad.882301
↑ Zhang H, Chatterjee A, Singh KK. Saccharomyces cerevisiae polymerase zeta functions in mitochondria. Genetics. 2006 Apr;172(4):2683-8. Epub 2006 Feb 1. PMID:16452144 doi:genetics.105.051029
↑ Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase. Structure. 2008 Feb;16(2):239-45. PMID:18275815 doi:10.1016/j.str.2007.12.009

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3bjy"

@@ Line 3: / Line 3: @@
 <StructureSection load='3bjy' size='340' side='right'caption='[[3bjy]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bjy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BJY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bjy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BJY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.41&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=P:2-DEOXY-N1,N2-PROPANO+GUANOSINE+MONOPHOSPHATE'>P</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P:2-DEOXY-N1,N2-PROPANO+GUANOSINE+MONOPHOSPHATE'>P</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2aq4|2aq4]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">REV1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3bjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bjy OCA], [https://pdbe.org/3bjy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bjy RCSB], [https://www.ebi.ac.uk/pdbsum/3bjy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bjy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/REV1_YEAST REV1_YEAST]] 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. Involved in mitochondrial DNA mutagenesis.<ref>PMID:8751446</ref> <ref>PMID:11316789</ref> <ref>PMID:16452144</ref>
+[https://www.uniprot.org/uniprot/REV1_YEAST REV1_YEAST] 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. Involved in mitochondrial DNA mutagenesis.<ref>PMID:8751446</ref> <ref>PMID:11316789</ref> <ref>PMID:16452144</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 29: @@
 </div>
 <div class="pdbe-citations 3bjy" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: Aggarwal, A K]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Johnson, R E]]
+[[Category: Aggarwal AK]]
-[[Category: Nair, D T]]
+[[Category: Johnson RE]]
-[[Category: Prakash, L]]
+[[Category: Nair DT]]
-[[Category: Prakash, S]]
+[[Category: Prakash L]]
-[[Category: Adduct]]
+[[Category: Prakash S]]
-[[Category: Bypass]]
-[[Category: Dna damage]]
-[[Category: Dna polymerase]]
-[[Category: Dna repair]]
-[[Category: Dna synthesis]]
-[[Category: Dna-binding]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Nucleus]]
-[[Category: Protein-dna complex]]
-[[Category: Transferase]]
-[[Category: Transferase-dna complex]]

3bjy

From Proteopedia

Current revision

Catalytic core of Rev1 in complex with DNA (modified template guanine) and incoming nucleotide

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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