PDBsum entry 1bpy

Transferase/DNA

PDB id: 1bpy

Contents

Protein chain

326 a.a. *

DNA/RNA

Ligands

DCT

Metals

_MG ×2

_NA ×2

Waters ×321

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
• Authors: M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, H.Pelletier.
• Ref.: Biochemistry, 1997, 36, 11205-11215. [DOI no: 10.1021/bi9703812]
• PubMed id: 9287163

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.

Abstract

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.

Secondary reference #1

• Title: Characterization of the metal ion binding helix-Hairpin-Helix motifs in human DNA polymerase beta by x-Ray structural analysis.
• Authors: H.Pelletier, M.R.Sawaya.
• Ref.: Biochemistry, 1996, 35, 12778-12787. [DOI no: 10.1021/bi960790i]
• PubMed id: 8841120

Secondary reference #2

• Title: A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
• Authors: H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut.
• Ref.: Biochemistry, 1996, 35, 12762-12777. [DOI no: 10.1021/bi9529566]
• PubMed id: 8841119

Secondary reference #3

• Title: Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, Processivity, And fidelity.
• Authors: H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut.
• Ref.: Biochemistry, 1996, 35, 12742-12761. [DOI no: 10.1021/bi952955d]
• PubMed id: 8841118

Secondary reference #4

• Title: Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.
• Authors: M.R.Sawaya, H.Pelletier, A.Kumar, S.H.Wilson, J.Kraut.
• Ref.: Science, 1994, 264, 1930-1935. [DOI no: 10.1126/science.7516581]
• PubMed id: 7516581

Secondary reference #5

• Title: Structures of ternary complexes of rat DNA polymerase beta, A DNA template-Primer, And ddctp.
• Authors: H.Pelletier, M.R.Sawaya, A.Kumar, S.H.Wilson, J.Kraut.
• Ref.: Science, 1994, 264, 1891-1903. [DOI no: 10.1126/science.7516580]
• PubMed id: 7516580