6bem: Difference between revisions
New page: '''Unreleased structure''' The entry 6bem is ON HOLD Authors: Batra, V.K., Wilson, S.H. Description: Ternary complex crystal structure of DNA polymerase Beta with S-isomer of beta-gamm... |
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==Ternary complex crystal structure of DNA polymerase Beta with S-isomer of beta-gamma-CHCL-dCTP== | |||
<StructureSection load='6bem' size='340' side='right'caption='[[6bem]], [[Resolution|resolution]] 1.88Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6bem]] 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=6BEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BEM 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]] 1.88Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2DA:2,3-DIDEOXYADENOSINE-5-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DJJ:5-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxycytidine'>DJJ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=6bem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bem OCA], [https://pdbe.org/6bem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bem RCSB], [https://www.ebi.ac.uk/pdbsum/6bem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bem 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> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We report high-resolution crystal structures of DNA polymerase (pol) beta in ternary complex with a panel of incoming dNTPs carrying acidity-modified 5'-triphosphate groups. These novel dNTP analogues have a variety of halomethylene substitutions replacing the bridging oxygen between Pbeta and Pgamma of the incoming dNTP, whereas other analogues have alkaline substitutions at the bridging oxygen. Use of these analogues allows the first systematic comparison of effects of 5'-triphosphate acidity modification on active site structures and the rate constant of DNA synthesis. These ternary complex structures with incoming dATP, TTP and dCTP analogues reveal the enzyme's active site is not grossly altered by the acidity modifications of the triphosphate group. Yet, with analogues of all three incoming dNTP bases, subtle structural differences are apparent in interactions around the nascent base pair and at the guanidinium groups of active site arginine residues. These results are important in understanding how acidity modification of the incoming dNTP's 5'-triphosphate can influence DNA polymerase activity and the significance of interactions at arginines 183 and 149 in the active site. | |||
Mapping functional substrate-enzyme interactions in the pol beta active site through chemical biology: Structural responses to acidity modification of incoming dNTPs.,Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH Biochemistry. 2018 Jun 6. doi: 10.1021/acs.biochem.8b00418. PMID:29874056<ref>PMID:29874056</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6bem" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
==See Also== | |||
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | |||
[[Category: Batra VK]] | |||
[[Category: Wilson SH]] | |||