6ph6: Difference between revisions

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'''Unreleased structure'''


The entry 6ph6 is ON HOLD  until Paper Publication
==Ternary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstream==
 
<StructureSection load='6ph6' size='340' side='right'caption='[[6ph6]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
Authors: Batra, V.K., Wilson, S.H.
== Structural highlights ==
 
<table><tr><td colspan='2'>[[6ph6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PH6 FirstGlance]. <br>
Description: Ternary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstream
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
[[Category: Unreleased Structures]]
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ph6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ph6 OCA], [http://pdbe.org/6ph6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ph6 RCSB], [http://www.ebi.ac.uk/pdbsum/6ph6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ph6 ProSAT]</span></td></tr>
[[Category: Wilson, S.H]]
</table>
[[Category: Batra, V.K]]
== Function ==
[[http://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> 
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Batra, V K]]
[[Category: Wilson, S H]]
[[Category: Conformational change]]
[[Category: Dna polymerase beta]]
[[Category: Enzyme mechanism]]
[[Category: Misalignment mutagenesis]]
[[Category: Transcription-dna complex]]

Revision as of 18:12, 11 December 2019

Ternary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstreamTernary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstream

Structural highlights

6ph6 is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.[1] [2] [3] [4]

References

  1. ↑ Bennett RA, Wilson DM 3rd, Wong D, Demple B. Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway. Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7166-9. PMID:9207062
  2. ↑ Matsumoto Y, Kim K, Katz DS, Feng JA. Catalytic center of DNA polymerase beta for excision of deoxyribose phosphate groups. Biochemistry. 1998 May 5;37(18):6456-64. PMID:9572863 doi:10.1021/bi9727545
  3. ↑ DeMott MS, Beyret E, Wong D, Bales BC, Hwang JT, Greenberg MM, Demple B. Covalent trapping of human DNA polymerase beta by the oxidative DNA lesion 2-deoxyribonolactone. J Biol Chem. 2002 Mar 8;277(10):7637-40. Epub 2002 Jan 22. PMID:11805079 doi:10.1074/jbc.C100577200
  4. ↑ Parsons JL, Dianova II, Khoronenkova SV, Edelmann MJ, Kessler BM, Dianov GL. USP47 is a deubiquitylating enzyme that regulates base excision repair by controlling steady-state levels of DNA polymerase beta. Mol Cell. 2011 Mar 4;41(5):609-15. doi: 10.1016/j.molcel.2011.02.016. PMID:21362556 doi:10.1016/j.molcel.2011.02.016

6ph6, resolution 2.60Å

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