3osp

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (16:57, 1 November 2023) (edit) (undo)
 
(5 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3osp.jpg|left|200px]]
 
-
<!--
+
==Structure of rev1==
-
The line below this paragraph, containing "STRUCTURE_3osp", creates the "Structure Box" on the page.
+
<StructureSection load='3osp' size='340' side='right'caption='[[3osp]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3osp]] 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=3OSP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OSP FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <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></td></tr>
-
{{STRUCTURE_3osp| PDB=3osp | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3osp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3osp OCA], [https://pdbe.org/3osp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3osp RCSB], [https://www.ebi.ac.uk/pdbsum/3osp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3osp 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>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Abasic (apurinic/apyrimidinic) sites are among the most abundant DNA lesions in humans, and they present a strong block to replication. They are also highly mutagenic because when replicative DNA polymerases manage to insert a nucleotide opposite the lesion, they prefer to insert an A. Rev1, a member of Y-family DNA polymerases, does not obey the A-rule. This enzyme inserts a C opposite an abasic lesion with much greater catalytic efficiency than an A, G, or T. We present here the structure of yeast Rev1 in ternary complex with DNA containing an abasic lesion and with dCTP as the incoming nucleotide. The structure reveals a mechanism of synthesis across an abasic lesion that differs from that in other polymerases. The lesion is driven to an extrahelical position, and the incorporation of a C is mediated by an arginine (Arg324) that is conserved in all known orthologs of Rev1, including humans. The hydrophobic cavity that normally accommodates the unmodified G is instead filled with water molecules. Since Gs are especially prone to depurination through a spontaneous hydrolysis of the glycosidic bond, the ability of Rev1 to stabilize an abasic lesion in its active site and employ a surrogate arginine to incorporate a C provides a unique means for the "error-free" bypass of this noninstructional lesion.
-
===Structure of rev1===
+
DNA synthesis across an abasic lesion by yeast REV1 DNA polymerase.,Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK J Mol Biol. 2011 Feb 11;406(1):18-28. Epub 2010 Dec 15. PMID:21167175<ref>PMID:21167175</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3osp" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_21167175}}, adds the Publication Abstract to the page
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 21167175 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_21167175}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
[[3osp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OSP OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:21167175</ref><references group="xtra"/>
+
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Aggarwal, A K.]]
+
[[Category: Aggarwal AK]]
-
[[Category: Nair, D T.]]
+
[[Category: Nair DT]]

Current revision

Structure of rev1

PDB ID 3osp

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3osp"
Personal tools