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[[ | ==DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated primer with an incoming deoxynucleotide (dCTP)== | ||
<StructureSection load='3rh5' size='340' side='right' caption='[[3rh5]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3rh5]] 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=3RH5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RH5 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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3rh4|3rh4]], [[3rh6|3rh6]]</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='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=3rh5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rh5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rh5 RCSB], [http://www.ebi.ac.uk/pdbsum/3rh5 PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
DNA polymerases can misinsert ribonucleotides that lead to genomic instability. DNA polymerase beta discourages ribonucleotide insertion with the backbone carbonyl of Tyr-271; alanine substitution of Tyr-271, but not Phe-272, resulted in a > 10-fold loss in discrimination. The Y271A mutant also inserted ribonucleotides more efficiently than wild type on a variety of rNMP-containing DNA substrates. Substituting Mn(2+) for Mg(2+) decreased sugar discrimination for both wild-type and mutant enzymes primarily by increasing the affinity for rCTP. This facilitated crystallization of ternary substrate complexes of both the wild-type and Y271A mutant enzymes. Crystallographic structures of Y271A- and wild type-substrate complexes indicate that rCTP is well accommodated in the active site, but that O2' of rCTP and the carbonyl oxygen of Tyr-271 or Ala-271 are unusually close (~2.5 and 2.6 A, respectively). Structure-based modeling indicates that the local energetic cost of positioning these closely spaced oxygens is ~2.2 kcal/mol for the wild-type enzyme. Since the side chain of Tyr-271 also hydrogen bonds with the primer terminus, loss of this interaction affects its catalytic positioning. Our results support a model where DNA polymerase beta utilizes two strategies, steric and geometric, with a single protein residue to deter ribonucleotide insertion. | |||
Molecular insights into DNA polymerase deterrents for Ribonucleotide insertion.,Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen LG, Wilson SH J Biol Chem. 2011 Jul 6. PMID:21733843<ref>PMID:21733843</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[DNA polymerase|DNA polymerase]] | *[[DNA polymerase|DNA polymerase]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Batra, V K | [[Category: Batra, V K]] | ||
[[Category: Beard, W A | [[Category: Beard, W A]] | ||
[[Category: Cavanaugh, N A | [[Category: Cavanaugh, N A]] | ||
[[Category: Pedersen, L G | [[Category: Pedersen, L G]] | ||
[[Category: Perera, L | [[Category: Perera, L]] | ||
[[Category: Wilson, S H | [[Category: Wilson, S H]] | ||
[[Category: Dctp]] | [[Category: Dctp]] | ||
[[Category: Dna polymerase beta mutant]] | [[Category: Dna polymerase beta mutant]] | ||
Revision as of 16:43, 9 December 2014
DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated primer with an incoming deoxynucleotide (dCTP)DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated primer with an incoming deoxynucleotide (dCTP)
Structural highlights
Publication Abstract from PubMedDNA polymerases can misinsert ribonucleotides that lead to genomic instability. DNA polymerase beta discourages ribonucleotide insertion with the backbone carbonyl of Tyr-271; alanine substitution of Tyr-271, but not Phe-272, resulted in a > 10-fold loss in discrimination. The Y271A mutant also inserted ribonucleotides more efficiently than wild type on a variety of rNMP-containing DNA substrates. Substituting Mn(2+) for Mg(2+) decreased sugar discrimination for both wild-type and mutant enzymes primarily by increasing the affinity for rCTP. This facilitated crystallization of ternary substrate complexes of both the wild-type and Y271A mutant enzymes. Crystallographic structures of Y271A- and wild type-substrate complexes indicate that rCTP is well accommodated in the active site, but that O2' of rCTP and the carbonyl oxygen of Tyr-271 or Ala-271 are unusually close (~2.5 and 2.6 A, respectively). Structure-based modeling indicates that the local energetic cost of positioning these closely spaced oxygens is ~2.2 kcal/mol for the wild-type enzyme. Since the side chain of Tyr-271 also hydrogen bonds with the primer terminus, loss of this interaction affects its catalytic positioning. Our results support a model where DNA polymerase beta utilizes two strategies, steric and geometric, with a single protein residue to deter ribonucleotide insertion. Molecular insights into DNA polymerase deterrents for Ribonucleotide insertion.,Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen LG, Wilson SH J Biol Chem. 2011 Jul 6. PMID:21733843[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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