PDBsum entry 5guj

Transferase

PDB id: 5guj

Contents

Protein chain

324 a.a.

Waters ×76

PDB id:

5guj

Name:

Transferase

Title:

Crystal structure of the bacillus subtilis dnag RNA polymerase domain, natural degradation of full length dnag

Structure:

DNA primase. Chain: a. Fragment: unp residues 112-435. Engineered: yes

Source:

Bacillus subtilis (strain 168). Organism_taxid: 224308. Strain: 168. Gene: dnag, dnae, bsu25210. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.191 R-free: 0.239

Authors:

Y.Zhou,Z.Liu,G.Wang

Key ref:

Y.Zhou et al. (2017). Structural Insight into the Specific DNA Template Binding to DnaG primase in Bacteria. Sci Rep, 7, 659. PubMed id: 28386108

Date:

29-Aug-16 Release date: 19-Apr-17

Protein chain

P05096  (DNAG_BACSU) -  DNA primase from Bacillus subtilis (strain 168)

Seq: 603 a.a.

Struc: 324 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.101 - Dna primase DnaG.
• Reaction: ssDNA + n NTP = ssDNA/pppN(pN)n-1 hybrid + (n-1) diphosphate

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

Key reference

Sci Rep 7:659 (2017)

PubMed id: 28386108

Structural Insight into the Specific DNA Template Binding to DnaG primase in Bacteria.

Y.Zhou, H.Luo, Z.Liu, M.Yang, X.Pang, F.Sun, G.Wang.

ABSTRACT

Bacterial primase initiates the repeated synthesis of short RNA primers that are extended by DNA polymerase to synthesize Okazaki fragments on the lagging strand at replication forks. It remains unclear how the enzyme recognizes specific initiation sites. In this study, the DnaG primase from Bacillus subtilis (BsuDnaG) was characterized and the crystal structure of the RNA polymerase domain (RPD) was determined. Structural comparisons revealed that the tethered zinc binding domain plays an important role in the interactions between primase and specific template sequence. Structural and biochemical data defined the ssDNA template binding surface as an L shape, and a model for the template ssDNA binding to primase is proposed. The flexibility of the DnaG primases from B. subtilis and G. stearothermophilus were compared, and the results implied that the intrinsic flexibility of the primase may facilitate the interactions between primase and various partners in the replisome. These results shed light on the mechanism by which DnaG recognizes the specific initiation site.