PDBsum entry 4dtu

Transferase/DNA

PDB id: 4dtu

Contents

Protein chain

901 a.a.

DNA/RNA

Ligands

DGT

Metals

_CA ×6

Waters ×814

PDB id:

4dtu

Name:

Transferase/DNA

Title:

Rb69 DNA polymerase ternary complex with dgtp opposite an abasic site and ddc/dg as the penultimate base-pair

Structure:

DNA polymerase. Chain: a. Synonym: gp43. Engineered: yes. Mutation: yes. DNA tempalte. Chain: t. Engineered: yes. DNA primer.

Source:

Enterobacteria phage rb69. Organism_taxid: 12353. Gene: 43. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Resolution:

1.86Å R-factor: 0.171 R-free: 0.201

Authors:

S.Xia,J.Wang,W.H.Konigsberg

Key ref:

S.Xia et al. (2012). Contribution of partial charge interactions and base stacking to the efficiency of primer extension at and beyond abasic sites in DNA. Biochemistry, 51, 4922-4931. PubMed id: 22630605

Date:

21-Feb-12 Release date: 06-Jun-12

Protein chain

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

Seq: 903 a.a.

Struc: 901 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DNA/RNA chains

T-C-G-3DR-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 1: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: E.C.3.1.11.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

Biochemistry 51:4922-4931 (2012)

PubMed id: 22630605

Contribution of partial charge interactions and base stacking to the efficiency of primer extension at and beyond abasic sites in DNA.

S.Xia, A.Vashishtha, D.Bulkley, S.H.Eom, J.Wang, W.H.Konigsberg.

ABSTRACT

No abstract given.