4rt2

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'''Unreleased structure'''
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==Ternary complex crystal structure of DNA polymerase Beta with (alpha,beta)-CH2-(beta,gamma)-NH-dTTP==
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<StructureSection load='4rt2' size='340' side='right' caption='[[4rt2]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4rt2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RT2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RT2 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=N6T:2-DEOXY-5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]METHYL}PHOSPHORYL]-3,4-DIHYDROTHYMIDINE'>N6T</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4rt3|4rt3]]</td></tr>
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<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=4rt2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rt2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rt2 RCSB], [http://www.ebi.ac.uk/pdbsum/4rt2 PDBsum]</span></td></tr>
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</table>
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== Function ==
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[[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Novel alpha,beta-CH2 and beta,gamma-NH (1a) or alpha,beta-NH and beta,gamma-CH2 (1b) "Met-Im" dTTPs were synthesized via monodemethylation of triethyl-dimethyl phosphorimido-bisphosphonate synthons (4a, 4b), formed via a base-induced [1,3]-rearrangement of precursors (3a, 3b) in a reaction with dimethyl or diethyl phosphochloridate. Anomerization during final bromotrimethylsilane (BTMS) deprotection after Mitsunobu conjugation with dT was avoided by microwave conditions. 1a was 9-fold more potent in inhibiting DNA polymerase beta, attributed to an NH-group interaction with R183 in the active site.
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The entry 4rt2 is ON HOLD until Paper Publication
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Two Scaffolds from Two Flips: (alpha,beta)/(beta,gamma) CH2/NH "Met-Im" Analogues of dTTP.,Kadina AP, Kashemirov BA, Oertell K, Batra VK, Wilson SH, Goodman MF, McKenna CE Org Lett. 2015 Jun 5;17(11):2586-9. doi: 10.1021/acs.orglett.5b00799. Epub 2015, May 13. PMID:25970636<ref>PMID:25970636</ref>
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Authors: Batra, V.K., Wilson, S.H.
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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Description: Ternary complex crystal structure of DNA polymerase Beta with (alpha,beta)-CH2-(beta,gamma)-NH-dTTP
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== References ==
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[[Category: Unreleased Structures]]
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<references/>
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[[Category: Wilson, S.H]]
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__TOC__
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[[Category: Batra, V.K]]
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</StructureSection>
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[[Category: Batra, V K]]
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[[Category: Wilson, S H]]
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[[Category: Conformational change]]
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[[Category: Dna polymerase beta]]
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[[Category: Enzyme mechanism]]
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[[Category: Transferase-dna complex]]

Revision as of 12:11, 1 July 2015

Ternary complex crystal structure of DNA polymerase Beta with (alpha,beta)-CH2-(beta,gamma)-NH-dTTP

4rt2, resolution 1.92Å

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