6nkv: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry 6nkv is ON HOLD until Paper Publication~~

==Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP==

~~Authors: Batra, V.K., Wilson, S.H.~~

== Structural highlights ==

<table><tr><td colspan='2'>[[6nkv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NKV OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NKV FirstGlance].

~~Description:~~ Ternary complex crystal structure of DNA polymerase Beta with ""hot-spot sequence"" with beta-gamma CHF analogue of dGTP

</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GFH:2-DEOXY-5-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE'>GFH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>

[[Category: ~~Unreleased~~ Structures]]

<tr id='NonStdRes'><td class="sblockLbl">[[Non-Standard_Residue|NonStd Res:]]</td><td class="sblockDat"><scene name='pdbligand=2DT:3-DEOXYTHYMIDINE-5-MONOPHOSPHATE'>2DT</scene></td></tr>

[[Category: Wilson, S.H]]

<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </td></tr>

[[Category: ~~Batra, V.K~~]]

<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6nkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nkv OCA], [http://pdbe.org/6nkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nkv RCSB], [http://www.ebi.ac.uk/pdbsum/6nkv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nkv ProSAT]</td></tr>

</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>

== References ==

__TOC__

</StructureSection>

[[Category: DNA-directed DNA polymerase]]

[[Category: Large Structures]]

[[Category: Batra, V K]]

[[Category: Wilson, S H]]

[[Category: Conformational change]]

[[Category: Dna polymerase beta]]

[[Category: Enzyme mechanism]]

[[Category: Transcription]]

[[Category: Transcription-dna complex]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6nkv is ON HOLD  until Paper Publication
+==Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP==
+<StructureSection load='6nkv' size='340' side='right'caption='[[6nkv]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-Authors: Batra, V.K., Wilson, S.H.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6nkv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NKV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NKV FirstGlance]. <br>
-Description: Ternary complex crystal structure of DNA polymerase Beta with ""hot-spot sequence"" with beta-gamma CHF analogue of dGTP
+</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=GFH:2-DEOXY-5-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE'>GFH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-[[Category: Unreleased Structures]]
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DT:3-DEOXYTHYMIDINE-5-MONOPHOSPHATE'>2DT</scene></td></tr>
-[[Category: Wilson, S.H]]
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
-[[Category: Batra, V.K]]
+<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=6nkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nkv OCA], [http://pdbe.org/6nkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nkv RCSB], [http://www.ebi.ac.uk/pdbsum/6nkv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nkv ProSAT]</span></td></tr>
+</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>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: DNA-directed DNA polymerase]]
+[[Category: Large Structures]]
+[[Category: Batra, V K]]
+[[Category: Wilson, S H]]
+[[Category: Conformational change]]
+[[Category: Dna polymerase beta]]
+[[Category: Enzyme mechanism]]
+[[Category: Transcription]]
+[[Category: Transcription-dna complex]]