PDBsum entry 3nci

Transferase/DNA

PDB id: 3nci

Contents

Protein chain

903 a.a. *

DNA/RNA

Ligands

DCP

Metals

_CA ×3

Waters ×1373

* Residue conservation analysis

PDB id:

3nci

Name:

Transferase/DNA

Title:

Rb69 DNA polymerase ternary complex with dctp opposite dg at 1.8 angstrom resolution

Structure:

DNA polymerase. Chain: a. Fragment: DNA polymerase. Synonym: gp43. Engineered: yes. Mutation: yes. DNA (5'- d( Tp Cp Ap Gp Gp Tp Ap Ap Gp Cp Ap Gp Tp Cp Cp Gp Cp G)-3'). Chain: t.

Source:

Enterobacteria phage rb69. Bacteriophage rb69. Organism_taxid: 12353. Gene: 43, gp43. Expressed in: escherichia coli. Expression_system_taxid: 511693. Synthetic: yes. Synthetic: yes

Resolution:

1.79Å R-factor: 0.176 R-free: 0.201

Authors:

M.Wang,G.Blaha,T.A.Steitz,W.H.Konigsberg,J.Wang

Key ref:

M.Wang et al. (2011). Insights into base selectivity from the 1.8 Å resolution structure of an RB69 DNA polymerase ternary complex. Biochemistry, 50, 581-590. PubMed id: 21158418

Date:

04-Jun-10 Release date: 02-Feb-11

Protein chain

Q38087  (DPOL_BPR69) -  DNA-directed DNA polymerase from Escherichia phage RB69

Seq: 903 a.a.

Struc: 903 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

T-C-A-G-G-T-A-A-G-C-A-G-T-C-C-G-C-G 18 bases

G-C-G-G-A-C-T-G-C-T-T-A-DOC 13 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

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

Added reference

Biochemistry 50:581-590 (2011)

PubMed id: 21158418

Insights into base selectivity from the 1.8 Å resolution structure of an RB69 DNA polymerase ternary complex.

M.Wang, S.Xia, G.Blaha, T.A.Steitz, W.H.Konigsberg, J.Wang.

ABSTRACT

Bacteriophage RB69 DNA polymerase (RB69 pol) has served as a model for investigating how B family polymerases achieve a high level of fidelity during DNA replication. We report here the structure of an RB69 pol ternary complex at 1.8 Å resolution, extending the resolution from our previously reported structure at 2.6 Å [Franklin, M. C., et al. (2001) Cell 105, 657-667]. In the structure presented here, a network of five highly ordered, buried water molecules can be seen to interact with the N3 and O2 atoms in the minor groove of the DNA duplex. This structure reveals how the formation of the closed ternary complex eliminates two ordered water molecules, which are responsible for a kink in helix P in the apo structure. In addition, three pairs of polar-nonpolar interactions have been observed between (i) the Cα hydrogen of G568 and the N3 atom of the dG templating base, (ii) the O5' and C5 atoms of the incoming dCTP, and (iii) the OH group of S565 and the aromatic face of the dG templating base. These interactions are optimized in the dehydrated environment that envelops Watson-Crick nascent base pairs and serve to enhance base selectivity in wild-type RB69 pol.