1zjm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:09, 23 August 2023) (edit) (undo)
 
(4 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1zjm.png|left|200px]]
 
-
{{STRUCTURE_1zjm| PDB=1zjm | SCENE= }}
+
==Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus==
 +
<StructureSection load='1zjm' size='340' side='right'caption='[[1zjm]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1zjm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZJM FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=1zjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zjm OCA], [https://pdbe.org/1zjm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zjm RCSB], [https://www.ebi.ac.uk/pdbsum/1zjm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zjm ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</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/zj/1zjm_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=1zjm ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
DNA polymerases occasionally insert the wrong nucleotide. For this error to become a mutation, the mispair must be extended. We report a structure of DNA polymerase beta (pol beta) with a DNA mismatch at the boundary of the polymerase active site. The structure of this complex indicates that the templating adenine of the mispair stacks with the primer terminus adenine while the templating (coding) cytosine is flipped out of the DNA helix. Soaking the crystals of the binary complex with dGTP resulted in crystals of a ternary substrate complex. In this case, the templating cytosine is observed within the DNA helix and forms Watson-Crick hydrogen bonds with the incoming dGTP. The adenine at the primer terminus has rotated into a syn-conformation to interact with the opposite adenine in a planar configuration. Yet, the 3'-hydroxyl on the primer terminus is out of position for efficient nucleotide insertion.
-
===Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus===
+
Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate.,Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH Structure. 2005 Aug;13(8):1225-33. PMID:16084394<ref>PMID:16084394</ref>
-
{{ABSTRACT_PUBMED_16084394}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 1zjm" style="background-color:#fffaf0;"></div>
-
[[1zjm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZJM OCA].
+
==See Also==
==See Also==
-
*[[DNA polymerase|DNA polymerase]]
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:016084394</ref><references group="xtra"/>
+
__TOC__
 +
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Batra, V K.]]
+
[[Category: Large Structures]]
-
[[Category: Beard, W A.]]
+
[[Category: Batra VK]]
-
[[Category: Pedersen, L C.]]
+
[[Category: Beard WA]]
-
[[Category: Shock, D D.]]
+
[[Category: Pedersen LC]]
-
[[Category: Wilson, S H.]]
+
[[Category: Shock DD]]
-
[[Category: Base excision repair]]
+
[[Category: Wilson SH]]
-
[[Category: Dna mismatch]]
+
-
[[Category: Dna repair]]
+
-
[[Category: Dna-lyase-transferase complex]]
+
-
[[Category: Nucleotidyltransferase]]
+

Current revision

Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus

PDB ID 1zjm

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/1zjm"
Personal tools