9ics: Difference between revisions

Revision as of 22:54, 4 May 2008

DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2',3'-DIDEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DDCTP AND MNCL2

OverviewOverview

When crystals of human DNA polymerase beta (pol beta) complexed with DNA [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996) Biochemistry 35, 12742-12761] are soaked in the presence of dATP and Mn2+, X-ray structural analysis shows that nucleotidyl transfer to the primer 3'-OH takes place directly in the crystals, even though the DNA is blunt-ended at the active site. Under similar crystal-soaking conditions, there is no evidence for a reaction when Mn2+ is replaced by Mg2+, which is thought to be the divalent metal ion utilized by most polymerases in vivo. These results suggest that one way Mn2+ may manifest its mutagenic effect on polymerases is by promoting greater reactivity than Mg2+ at the catalytic site, thereby allowing the nucleotidyl transfer reaction to take place with little or no regard to instructions from a template. Non-template-directed nucleotidyl transfer is also observed when pol beta-DNA cocrystals are soaked in the presence of dATP and Zn2+, but the reaction products differ in that the sugar moiety of the incorporated nucleotide appears distorted or otherwise cleaved, in agreement with reports that Zn2+ may act as a polymerase inhibitor rather than as a mutagen [Sirover, M. A., & Loeb, L. A. (1976) Science 194, 1434-1436]. Although no reaction is observed when crystals are soaked in the presence of dATP and other metal ions such as Ca2+, Co2+, Cr3+, or Ni2+, X-ray structural analyses show that these metal ions coordinate the triphosphate moiety of the nucleotide in a manner that differs from that observed with Mg2+. In addition, all metal ions tested, with the exception of Mg2+, promote a change in the side-chain position of aspartic acid 192, which is one of three highly conserved active-site carboxylate residues. Soaking experiments with nucleotides other than dATP (namely, dCTP, dGTP, dTTP, ATP, ddATP, ddCTP, AZT-TP, and dATP alpha S) reveal a non-base-specific binding site on pol beta for the triphosphate and sugar moieties of a nucleotide, suggesting a possible mechanism for nucleotide selectivity whereby triphosphate-sugar binding precedes a check for correct base pairing with the template.

About this StructureAbout this Structure

9ICS is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.

ReferenceReference

A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta., Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J, Biochemistry. 1996 Oct 1;35(39):12762-77. PMID:8841119 Page seeded by OCA on Sun May 4 22:54:07 2008

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OCA

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 [[Image:9ics.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 9ics |SIZE=350|CAPTION= <scene name='initialview01'>9ics</scene>, resolution 2.900&Aring;
+The line below this paragraph, containing "STRUCTURE_9ics", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DCT:2&#39;,3&#39;-DIDEOXYCYTIDINE+5&#39;-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY=
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_9ics|  PDB=9ics  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=9ics FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ics OCA], [http://www.ebi.ac.uk/pdbsum/9ics PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=9ics RCSB]</span>
-}}
 '''DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2',3'-DIDEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DDCTP AND MNCL2'''
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 [[Category: Pelletier, H.]]
 [[Category: Sawaya, M R.]]
-[[Category: complex (nucleotidyltransferase/dna)]]
+[[Category: Dna repair]]
-[[Category: dna repair]]
+[[Category: Dna replication]]
-[[Category: dna replication]]
+[[Category: Dna-directed dna polymerase]]
-[[Category: dna-directed dna polymerase]]
+[[Category: Nucleotidyltransferase]]
-[[Category: nucleotidyltransferase]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 22:54:07 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:46:19 2008''