4doc - Revision history

OCA at 14:40, 14 March 2024

2024-03-14T14:40:35Z

← Older revision		Revision as of 14:40, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4doc]] 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=4DOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DOC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4doc]] 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=4DOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DOC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=G1C:5-O-[(R)-{[(S)-[(S)-CHLORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>G1C</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.949Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=G1C:5-O-[(R)-{[(S)-[(S)-CHLORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>G1C</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=4doc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doc OCA], [https://pdbe.org/4doc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4doc RCSB], [https://www.ebi.ac.uk/pdbsum/4doc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4doc ProSAT]</span></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=4doc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doc OCA], [https://pdbe.org/4doc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4doc RCSB], [https://www.ebi.ac.uk/pdbsum/4doc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4doc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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>		[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 ==~~
	Deoxynucleoside 5'-triphosphate analogues in which the beta,gamma-bridging oxygen has been replaced with a CXY group are useful chemical probes to investigate DNA polymerase catalytic and base-selection mechanisms. A limitation of such probes has been that conventional synthetic methods generate a mixture of diastereomers when the bridging carbon substitution is nonequivalent (X not equal Y). We report here a general solution to this long-standing problem with four examples of beta,gamma-CXY dNTP diastereomers: (S)- and (R)-beta,gamma-CHCl-dGTP (12a-1/12a-2) and (S)- and (R)-beta,gamma-CHF-dGTP (12b-1/12b-2). Central to their preparation was conversion of the prochiral parent bisphosphonic acids to the P,C-dimorpholinamide derivatives 7 of their (R)-mandelic acid monoesters, which provided access to the individual diastereomers 7a-1, 7a-2, 7b-1, and 7b-2 by preparative HPLC. Selective acidic hydrolysis of the P-N bond then afforded "portal" diastereomers, which were readily coupled to morpholine-activated dGMP. Removal of the chiral auxiliary by H(2) (Pd/C) gave the four individual diastereomeric nucleotides 12, which were characterized by (31)P, (1)H, and (19)F NMR spectroscopy and by mass spectrometry. After treatment with Chelex-100 to remove traces of paramagnetic ions, at pH approximately 10 the diastereomer pairs 12a,b exhibit discrete P(alpha) and P(beta)(31)P resonances. The more upfield P(alpha) and more downfield P(beta) resonances (and also the more upfield (19)F NMR resonance in 12b) are assigned to the R configuration at the P(beta)-CHX-P(gamma) carbons on the basis of the absolute configurations of the individual diastereomers as determined from the X-ray crystallographic structures of their ternary complexes with DNA and polymerase beta.

	beta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases.,Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE J Am Chem Soc. 2012 May 30;134(21):8734-7. Epub 2012 May 18. PMID:22397499<ref>PMID:22397499</ref>		==See Also==
			*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class~~=~~"pdbe-citations 4doc" style~~=~~"background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:31, 21 September 2022

2022-09-21T08:31:52Z

← Older revision		Revision as of 08:31, 21 September 2022
Line 1:		Line 1:

	==Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer==		==Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer==
	<StructureSection load='4doc' size='340' side='right' caption='[[4doc]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='4doc' size='340' side='right'caption='[[4doc]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4doc]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DOC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4doc]] 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=4DOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DOC FirstGlance]. <br>
	</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=G1C:5-O-[(R)-{[(S)-[(S)-CHLORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>G1C</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=G1C:5-O-[(R)-{[(S)-[(S)-CHLORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>G1C</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	~~<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>~~		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4doc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doc OCA], [https://pdbe.org/4doc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4doc RCSB], [https://www.ebi.ac.uk/pdbsum/4doc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4doc ProSAT]</span></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4do9\|4do9]], [[4doa\|4doa]], [[4dob\|4dob]]</td></tr>~~
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=4doc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doc OCA], [~~http~~://pdbe.org/4doc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4doc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4doc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4doc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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>		[[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4doc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4doc" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA polymerase\|DNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: ~~Batra, V K~~]]		[[Category: Large Structures]]
	[[Category: ~~Dna polymerase]]~~		[[Category: Batra VK]]
	~~[[Category: Polymerase]]~~
	~~[[Category: Stereoselectivity]]~~
	~~[[Category: Transferase-dna complex~~]]

OCA at 13:04, 5 August 2016

2016-08-05T13:04:04Z

← Older revision		Revision as of 13:04, 5 August 2016
Line 1:		Line 1:

	==Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer==		==Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer==
	<StructureSection load='4doc' size='340' side='right' caption='[[4doc]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='4doc' size='340' side='right' caption='[[4doc]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4doc]] 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=4DOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DOC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4doc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DOC FirstGlance]. <br>
	</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=G1C:5-O-[(R)-{[(S)-[(S)-CHLORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>G1C</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</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=G1C:5-O-[(R)-{[(S)-[(S)-CHLORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>G1C</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<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>		<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>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4do9\|4do9]], [[4doa\|4doa]], [[4dob\|4dob]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4do9\|4do9]], [[4doa\|4doa]], [[4dob\|4dob]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4doc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4doc RCSB], [http://www.ebi.ac.uk/pdbsum/4doc 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=4doc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doc OCA], [http://pdbe.org/4doc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4doc RCSB], [http://www.ebi.ac.uk/pdbsum/4doc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4doc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 4doc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Batra, V K]]		[[Category: Batra, V K]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]

OCA at 19:04, 25 December 2014

2014-12-25T19:04:14Z

← Older revision		Revision as of 19:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4doc]] 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=4DOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DOC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4doc]] 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=4DOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DOC FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G1C:5-O-[(R)-{[(S)-[(S)-CHLORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>G1C</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>		</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=G1C:5-O-[(R)-{[(S)-[(S)-CHLORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>G1C</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr><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>		<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>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4do9\|4do9]], [[4doa\|4doa]], [[4dob\|4dob]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4do9\|4do9]], [[4doa\|4doa]], [[4dob\|4dob]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4doc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4doc RCSB], [http://www.ebi.ac.uk/pdbsum/4doc 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=4doc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4doc RCSB], [http://www.ebi.ac.uk/pdbsum/4doc PDBsum]</span></td></tr>
	<table>		</table>
			== 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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	beta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases.,Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE J Am Chem Soc. 2012 May 30;134(21):8734-7. Epub 2012 May 18. PMID:22397499<ref>PMID:22397499</ref>		beta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases.,Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE J Am Chem Soc. 2012 May 30;134(21):8734-7. Epub 2012 May 18. PMID:22397499<ref>PMID:22397499</ref>

	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>

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	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Batra, V K.]]		[[Category: Batra, V K]]
	[[Category: Dna polymerase]]		[[Category: Dna polymerase]]
	[[Category: Polymerase]]		[[Category: Polymerase]]
	[[Category: Stereoselectivity]]		[[Category: Stereoselectivity]]
	[[Category: Transferase-dna complex]]		[[Category: Transferase-dna complex]]

OCA at 07:18, 5 June 2014

2014-06-05T07:18:40Z

← Older revision		Revision as of 07:18, 5 June 2014
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	[[~~Image~~:~~4doc~~.~~jpg~~\|~~left~~\|~~200px~~]]		==Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer==
			<StructureSection load='4doc' size='340' side='right' caption='[[4doc]], [[Resolution\|resolution]] 1.95Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4doc]] 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=4DOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DOC FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G1C:5-O-[(R)-{[(S)-[(S)-CHLORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-2-DEOXYGUANOSINE'>G1C</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
			<tr><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>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4do9\|4do9]], [[4doa\|4doa]], [[4dob\|4dob]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4doc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4doc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4doc RCSB], [http://www.ebi.ac.uk/pdbsum/4doc PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Deoxynucleoside 5'-triphosphate analogues in which the beta,gamma-bridging oxygen has been replaced with a CXY group are useful chemical probes to investigate DNA polymerase catalytic and base-selection mechanisms. A limitation of such probes has been that conventional synthetic methods generate a mixture of diastereomers when the bridging carbon substitution is nonequivalent (X not equal Y). We report here a general solution to this long-standing problem with four examples of beta,gamma-CXY dNTP diastereomers: (S)- and (R)-beta,gamma-CHCl-dGTP (12a-1/12a-2) and (S)- and (R)-beta,gamma-CHF-dGTP (12b-1/12b-2). Central to their preparation was conversion of the prochiral parent bisphosphonic acids to the P,C-dimorpholinamide derivatives 7 of their (R)-mandelic acid monoesters, which provided access to the individual diastereomers 7a-1, 7a-2, 7b-1, and 7b-2 by preparative HPLC. Selective acidic hydrolysis of the P-N bond then afforded "portal" diastereomers, which were readily coupled to morpholine-activated dGMP. Removal of the chiral auxiliary by H(2) (Pd/C) gave the four individual diastereomeric nucleotides 12, which were characterized by (31)P, (1)H, and (19)F NMR spectroscopy and by mass spectrometry. After treatment with Chelex-100 to remove traces of paramagnetic ions, at pH approximately 10 the diastereomer pairs 12a,b exhibit discrete P(alpha) and P(beta)(31)P resonances. The more upfield P(alpha) and more downfield P(beta) resonances (and also the more upfield (19)F NMR resonance in 12b) are assigned to the R configuration at the P(beta)-CHX-P(gamma) carbons on the basis of the absolute configurations of the individual diastereomers as determined from the X-ray crystallographic structures of their ternary complexes with DNA and polymerase beta.

	<!--		beta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases.,Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE J Am Chem Soc. 2012 May 30;134(21):8734-7. Epub 2012 May 18. PMID:22397499<ref>PMID:22397499</ref>
	~~The line below this paragraph~~, ~~containing "STRUCTURE_4doc"~~, ~~creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter~~ (~~which sets the initial scene displayed when the page is loaded~~),
	~~or leave the SCENE parameter empty~~ for ~~the default display~~.
	-->
	~~{{STRUCTURE_4doc\| PDB=4doc \| SCENE= }}~~

	~~===Ternary complex of dna polymerase beta with~~ a ~~dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding~~ of S~~-isomer===~~		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
			</div>

			==See Also==
	~~<!--~~		*[[DNA polymerase\|DNA polymerase]]
	~~The line below this paragraph, {{ABSTRACT_PUBMED_22397499}}, adds the Publication Abstract to the page~~		== References ==
	~~(as it appears on PubMed at http://www.pubmed.gov), where 22397499 is the PubMed ID number.~~		<references/>
	~~-->~~		__TOC__
	~~{{ABSTRACT_PUBMED_22397499}}~~		</StructureSection>

	==~~About this Structure~~==
	[[~~4doc]~~] ~~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=4DOC OCA].~~

	==~~Reference~~==
	<~~ref group="xtra">PMID:022397499<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Batra, V K.]]		[[Category: Batra, V K.]]

OCA at 06:12, 13 June 2012

2012-06-13T06:12:14Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:4doc.jpg|left|200px]]
-The entry 4doc is ON HOLD  until sometime in the future
+<!--
-Authors: Batra, V.K.
+===Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer===
-Description: Ternary complex of dna polymerase beta with a dideoxy 2 terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of r-isomer

OCA at 07:30, 22 February 2012

2012-02-22T07:30:52Z

← Older revision		Revision as of 07:30, 22 February 2012
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4doc is ON HOLD		The entry 4doc is ON HOLD until sometime in the future

	Authors: Batra, V.K.		Authors: Batra, V.K.

	Description: ~~TERNARY COMPLEX OF DNA POLYMERASE BETA WITH A DIDEOXY~~ 2 ~~TERMINATED PRIMER AND~~ 2'-~~DEOXYGUANOSINE~~ 5'-~~BETA~~, ~~GAMMA~~-~~MONOCHLOROROMETHYLENE TRIPHOSPHATE~~:binding of R-isomer		Description: Ternary complex of dna polymerase beta with a dideoxy 2 terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of r-isomer

OCA: Protected "4doc" [edit=sysop:move=sysop]

2012-02-15T06:26:34Z

Protected "4doc" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:26, 15 February 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4doc is ON HOLD Authors: Batra, V.K. Description: TERNARY COMPLEX OF DNA POLYMERASE BETA WITH A DIDEOXY 2 TERMINATED PRIMER AND 2'-DEOXYGUANOSINE 5...

2012-02-15T06:26:33Z

New page: '''Unreleased structure''' The entry 4doc is ON HOLD Authors: Batra, V.K. Description: TERNARY COMPLEX OF DNA POLYMERASE BETA WITH A DIDEOXY 2 TERMINATED PRIMER AND 2'-DEOXYGUANOSINE 5...

New page

'''Unreleased structure'''

The entry 4doc is ON HOLD

Authors: Batra, V.K.

Description: TERNARY COMPLEX OF DNA POLYMERASE BETA WITH A DIDEOXY 2 TERMINATED PRIMER AND 2'-DEOXYGUANOSINE 5'-BETA, GAMMA-MONOCHLOROROMETHYLENE TRIPHOSPHATE:binding of R-isomer