PDBsum entry: 3cq8

Transferase/DNA

PDB id: 3cq8

Contents

Protein chain

902 a.a. *

DNA/RNA

Ligands

GOL ×3

TTP

Metals

_CA ×6

_NA ×3

Waters ×433

* Residue conservation analysis

PDB id:

3cq8

Name:

Transferase/DNA

Title:

Ternary complex of the l415f mutant rb69 exo(-)polymerase

Structure:

DNA polymerase. Chain: a. Fragment: rb69 polymerase. Synonym: gp43. Engineered: yes. Mutation: yes. DNA (5'- d( Dap Dcp Dap Dgp Dgp Dtp Dap Dap Dgp Dcp Dap Dgp Dtp Dcp P Dg)-3').

Source:

Enterobacteria phage. Organism_taxid: 12353. Strain: rb69. Gene: 43. Expressed in: escherichia coli. Synthetic: yes. Synthetic: yes

Resolution:

2.50Å R-factor: 0.212 R-free: 0.281

Authors:

X.Zhong,L.C.Pedersen,T.A.Kunkel

Key ref:

X.Zhong et al. (2008). Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity. Nucleic Acids Res, 36, 3892-3904. PubMed id: 18503083 DOI: 10.1093/nar/gkn312

Date:

02-Apr-08 Release date: 02-Sep-08

Protein chain

Q38087  (DPOL_BPR69) -  DNA polymerase

Seq: 903 a.a.

Struc: 902 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)

Deoxynucleoside triphosphate (Bound ligand (Het Group name = TTP) matches with 66.67% similarity) + DNA(n) = diphosphate + DNA(n+1)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (2 terms)
• Biochemical function: nucleotide binding (9 terms)

reference

DOI no: 10.1093/nar/gkn312

Nucleic Acids Res 36:3892-3904 (2008)

PubMed id: 18503083

Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity.

X.Zhong, L.C.Pedersen, T.A.Kunkel.

ABSTRACT

Changing a highly conserved amino acid in motif A of any of the four yeast family B DNA polymerases, DNA polymerase alpha, delta, epsilon or zeta, results in yeast strains with elevated mutation rates. In order to better understand this phenotype, we have performed structure-function studies of homologous mutants of RB69 DNA polymerase (RB69 pol), a structural model for family B members. When Leu415 in RB69 pol is replaced with phenylalanine or glycine, the mutant polymerases retain high-catalytic efficiency for correct nucleotide incorporation, yet have increased error rates due to increased misinsertion, increased mismatch extension and inefficient proofreading. The Leu415Phe mutant also has increased dNTP insertion efficiency opposite a template 8-oxoG and opposite an abasic site. The 2.5 A crystal structure of a ternary complex of RB69 L415F pol with a correctly base-paired incoming dTTP reveals that the phenylalanine ring is accommodated within a cavity seen in the wild-type enzyme, without steric clash or major change in active site geometry, consistent with retention of high-catalytic efficiency for correct incorporation. In addition, slight structural differences were observed that could be relevant to the reduced fidelity of L415F RB69 pol.