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1bpy

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{{STRUCTURE_1bpy| PDB=1bpy | SCENE= }}
{{STRUCTURE_1bpy| PDB=1bpy | SCENE= }}
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'''HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP'''
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===HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP===
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==Overview==
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DNA polymerase beta (pol beta) fills single nucleotide (nt) gaps in DNA produced by the base excision repair pathway of mammalian cells. Crystal structures have been determined representing intermediates in the 1 nt gap-filling reaction of pol beta: the binary complex with a gapped DNA substrate (2.4 A resolution), the ternary complex including ddCTP (2.2 A), and the binary product complex containing only nicked DNA (2.6 A). Upon binding ddCTP to the binary gap complex, the thumb subdomain rotates into the closed conformation to contact the otherwise solvent-exposed ddCTP-template base pair. Thumb movement triggers further conformational changes which poise catalytic residue Asp192, dNTP, and template for nucleotidyl transfer, effectively assembling the active site. In the product nicked DNA complex, the thumb returns to the open conformation as in the gapped binary DNA complex, facilitating dissociation of the product. These findings suggest that pol beta may enhance fidelity by an induced fit mechanism in which correct base pairing between template and incoming dNTP induces alignment of catalytic groups for catalysis (via thumb closure), but incorrect base pairing will not. The structures also reveal that pol beta binds both gapped and nicked DNA with a 90 degrees kink occurring precisely at the 5'-phosphodiester linkage of the templating residue. If the DNA were not kinked in this way, contact between the thumb and dNTP-template base pair, presumably important for the checking mechanism, would be impossible, especially when the gap is but a single nucleotide. Such a 90 degrees kink may be a mechanistic feature employed by any polymerase involved in filling gaps to completion.
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(as it appears on PubMed at http://www.pubmed.gov), where 9287163 is the PubMed ID number.
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==About this Structure==
==About this Structure==
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[[Category: Dna repair]]
[[Category: Dna repair]]
[[Category: Nucleotidyltransferase]]
[[Category: Nucleotidyltransferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 19:30:46 2008''

Revision as of 16:30, 30 June 2008

Image:1bpy.png

Template:STRUCTURE 1bpy

HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP

Template:ABSTRACT PUBMED 9287163

About this Structure

1BPY is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.

Reference

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism., Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H, Biochemistry. 1997 Sep 16;36(37):11205-15. PMID:9287163

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