This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3bjy

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:47, 1 November 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3bjy.png|left|200px]]
 
-
<!--
+
==Catalytic core of Rev1 in complex with DNA (modified template guanine) and incoming nucleotide==
-
The line below this paragraph, containing "STRUCTURE_3bjy", creates the "Structure Box" on the page.
+
<StructureSection load='3bjy' size='340' side='right'caption='[[3bjy]], [[Resolution|resolution]] 2.41&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'>[[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>
-
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]] 2.41&#8491;</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>
-
{{STRUCTURE_3bjy| PDB=3bjy | SCENE= }}
+
<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>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bj/3bjy_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3bjy ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
===Catalytic core of Rev1 in complex with DNA (modified template guanine) and incoming nucleotide===
+
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<ref>PMID:18275815</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3bjy" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18275815}}, 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 18275815 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18275815}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
3BJY is a 3 chains structure of sequences 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=3BJY OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:18275815</ref><references group="xtra"/>
+
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Aggarwal, A K.]]
+
[[Category: Aggarwal AK]]
-
[[Category: Johnson, R E.]]
+
[[Category: Johnson RE]]
-
[[Category: Nair, D T.]]
+
[[Category: Nair DT]]
-
[[Category: Prakash, L.]]
+
[[Category: Prakash L]]
-
[[Category: Prakash, S.]]
+
[[Category: Prakash S]]
-
[[Category: Adduct]]
+
-
[[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]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:44:46 2009''
+

Current revision

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

PDB ID 3bjy

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/3bjy"
Personal tools