1bpx
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DNA POLYMERASE BETA/DNA COMPLEX
OverviewOverview
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.
About this StructureAbout this Structure
1BPX is a Single protein structure of sequence from Homo sapiens with NA as ligand. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.
ReferenceReference
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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