PDBsum entry 7k5u

Transferase/DNA

PDB id: 7k5u

Contents

Protein chain

577 a.a.

DNA/RNA

Ligands

SO4 ×3

Waters ×499

PDB id:

7k5u

Name:

Transferase/DNA

Title:

Bst DNA polymerase i time-resolved structure, 48 hr post datp and dctp addition

Structure:

DNA (5'-d(p Cp Gp Ap Tp Cp Ap Cp Gp Tp Ap C)-3'). Chain: p. Engineered: yes. DNA (5'-d(p Cp Gp Tp Ap Cp Gp Tp Gp Ap Tp Cp Gp C)-3'). Chain: t. Engineered: yes. DNA polymerase i. Chain: a. Synonym: bst DNA polymerase i.

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: pola. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.191 R-free: 0.230

Authors:

N.Chim,R.A.Meza,A.M.Trinh,J.C.Chaput

Key ref:

N.Chim et al. (2021). Following replicative DNA synthesis by time-resolved X-ray crystallography. Nat Commun, 12, 2641. PubMed id: 33976175 DOI: 10.1038/s41467-021-22937-z

Date:

17-Sep-20 Release date: 03-Mar-21

Protein chain

E1C9K5  (E1C9K5_GEOSE) -  DNA polymerase I from Geobacillus stearothermophilus

Seq: 580 a.a.

Struc: 577 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-G-A-T-C-A-C-G-T-A-C 11 bases

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

DOI no: 10.1038/s41467-021-22937-z

Nat Commun 12:2641 (2021)

PubMed id: 33976175

Following replicative DNA synthesis by time-resolved X-ray crystallography.

N.Chim, R.A.Meza, A.M.Trinh, K.Yang, J.C.Chaput.

ABSTRACT

The mechanism of DNA synthesis has been inferred from static structures, but the absence of temporal information raises longstanding questions about the order of events in one of life's most central processes. Here we follow the reaction pathway of a replicative DNA polymerase using time-resolved X-ray crystallography to elucidate the order and transition between intermediates. In contrast to the canonical model, the structural changes observed in the time-lapsed images reveal a catalytic cycle in which translocation precedes catalysis. The translocation step appears to follow a push-pull mechanism where the O-O1 loop of the finger subdomain acts as a pawl to facilitate unidirectional movement along the template with conserved tyrosine residues 714 and 719 functioning as tandem gatekeepers of DNA synthesis. The structures capture the precise order of critical events that may be a general feature of enzymatic catalysis among replicative DNA polymerases.