PDBsum entry 3ndk

Transferase/DNA

PDB id: 3ndk

Contents

Protein chain

903 a.a. *

DNA/RNA

Ligands

DCP

Metals

_CA ×7

Waters ×875

* Residue conservation analysis

PDB id:

3ndk

Name:

Transferase/DNA

Title:

Rb69 DNA polymerase (y567a) ternary complex with dctp opposite dg

Structure:

DNA polymerase. Chain: a. 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. Engineered: yes.

Source:

Enterobacteria phage rb69. Bacteriophage rb69. Organism_taxid: 12353. Gene: 43, gp43. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes

Resolution:

2.00Å R-factor: 0.189 R-free: 0.229

Authors:

M.Wang,J.Wang,W.H.Konigsberg

Key ref:

S.Xia et al. (2011). Variation in mutation rates caused by RB69pol fidelity mutants can be rationalized on the basis of their kinetic behavior and crystal structures. J Mol Biol, 406, 558-570. PubMed id: 21216248

Date:

07-Jun-10 Release date: 26-Jan-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 3 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

J Mol Biol 406:558-570 (2011)

PubMed id: 21216248

Variation in mutation rates caused by RB69pol fidelity mutants can be rationalized on the basis of their kinetic behavior and crystal structures.

S.Xia, M.Wang, H.R.Lee, A.Sinha, G.Blaha, T.Christian, J.Wang, W.Konigsberg.

ABSTRACT

No abstract given.