PDBsum entry 3pv8

Transferase/DNA

PDB id: 3pv8

Contents

Protein chains

579 a.a.

DNA/RNA

Ligands

D3T ×2

SO4 ×3

Metals

_MG ×2

Waters ×1823

PDB id:

3pv8

Name:

Transferase/DNA

Title:

Crystal structure of bacillus DNA polymerase i large fragment bound to DNA and ddttp-da in closed conformation

Structure:

DNA polymerase i. Chain: a, d. Fragment: bacillus fragment (analogous to e. Coli klenow fragment). Engineered: yes. Mutation: yes. DNA (5'-d( Cp Cp Tp Gp Ap Cp Tp Cp (2Dt))-3'). Chain: b, e. Fragment: DNA primer strand. Engineered: yes.

Source:

Geobacillus kaustophilus. Organism_taxid: 1462. Gene: pola, gk2730. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Resolution:

1.52Å R-factor: 0.187 R-free: 0.211

Authors:

W.Wang,L.S.Beese

Key ref:

W.Wang et al. (2011). Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc Natl Acad Sci U S A, 108, 17644-17648. PubMed id: 22006298

Date:

06-Dec-10 Release date: 19-Oct-11

Protein chains

Q5KWC1  (Q5KWC1_GEOKA) -  DNA polymerase I from Geobacillus kaustophilus (strain HTA426)

Seq: 878 a.a.

Struc: 579 a.a.*

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

DNA/RNA chains

C-C-T-G-A-C-T-C-2DT 9 bases

A-T-A-A-G-A-G-T-C-A-G-G 12 bases

C-C-T-G-A-C-T-C-2DT 9 bases

A-T-A-A-G-A-G-T-C-A-G-G 12 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

Proc Natl Acad Sci U S A 108:17644-17648 (2011)

PubMed id: 22006298

Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.

W.Wang, H.W.Hellinga, L.S.Beese.

ABSTRACT

No abstract given.