PDBsum entry 3spy

Transferase/DNA

PDB id: 3spy

Contents

Protein chain

901 a.a.

DNA/RNA

Ligands

UPC

Metals

_MG ×5

Waters ×496

PDB id:

3spy

Name:

Transferase/DNA

Title:

Rb69 DNA polymerase(l415a/l561a/s565g/y567a) ternary complex with dupcpp opposite da

Structure:

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

Source:

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

Resolution:

2.14Å R-factor: 0.194 R-free: 0.242

Authors:

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

Key ref:

S.Xia et al. (2011). Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase. Biochemistry, 50, 9114-9124. PubMed id: 21923197

Date:

04-Jul-11 Release date: 12-Oct-11

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 6 residue positions (black crosses)

DNA/RNA chains

T-C-G-A-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-C 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 50:9114-9124 (2011)

PubMed id: 21923197

Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase.

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

ABSTRACT

No abstract given.