4yn4: Difference between revisions

Revision as of 11:35, 10 August 2016

Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable dTTP WITH MANGANESE IN THE ACTIVE SITEStructure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable dTTP WITH MANGANESE IN THE ACTIVE SITE

Structural highlights

4yn4 is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Related:	4ymm, 4ymn, 4ymo
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

↑ 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
↑ 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
↑ 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
↑ 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

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OCA

[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

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-==Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITE==
+==Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable dTTP WITH MANGANESE IN THE ACTIVE SITE==
 <StructureSection load='4yn4' size='340' side='right' caption='[[4yn4]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
 == Structural highlights ==
@@ Line 7: / Line 7: @@
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=7BG:2-AMINO-7-BENZYL-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-6-OXO-6,9-DIHYDRO-1H-PURIN-7-IUM'>7BG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ymm|4ymm]], [[4ymn|4ymn]], [[4ymo|4ymo]]</td></tr>
-<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=4yn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yn4 OCA], [http://pdbe.org/4yn4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yn4 RCSB], [http://www.ebi.ac.uk/pdbsum/4yn4 PDBsum]</span></td></tr>
+<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=4yn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yn4 OCA], [http://pdbe.org/4yn4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yn4 RCSB], [http://www.ebi.ac.uk/pdbsum/4yn4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yn4 ProSAT]</span></td></tr>
 </table>
 == Function ==

4yn4: Difference between revisions

Revision as of 11:35, 10 August 2016

Structural highlights

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4yn4: Difference between revisions

Revision as of 11:35, 10 August 2016

Structural highlights

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