PDBsum entry 4dqi

Transferase/DNA

PDB id: 4dqi

Contents

Protein chains

579 a.a.

DNA/RNA

Ligands

DCP ×3

SO4 ×2

Metals

_MG ×2

Waters ×1636

PDB id:

4dqi

Name:

Transferase/DNA

Title:

Ternary complex of bacillus DNA polymerase i large fragment, DNA duplex, and dctp (paired with dg of template)

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 (Doc))-3'). Chain: b, e. Engineered: yes. DNA (5'-d( C Ap Tp Gp Gp Gp Ap Gp Tp Cp Ap Gp G)-3').

Source:

Geobacillus kaustophilus. Organism_taxid: 235909. Strain: hta426. Gene: gk2730, gymc61_0787, pola. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

1.69Å R-factor: 0.159 R-free: 0.185

Authors:

W.Wang,L.S.Beese

Key ref:

W.Wang et al. (2012). Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J Biol Chem, 287, 28215-28226. PubMed id: 22648417

Date:

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

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 2 residue positions (black crosses)

DNA/RNA chains

C-C-T-G-A-C-T-C-DOC 9 bases

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

C-C-T-G-A-C-T-C-DOC 9 bases

A-T-G-G-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

J Biol Chem 287:28215-28226 (2012)

PubMed id: 22648417

Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.

W.Wang, E.Y.Wu, H.W.Hellinga, L.S.Beese.

ABSTRACT

No abstract given.