5Z51

Helicase binding domain of primase from Mycobacterium tuberculosis

Summary for 5Z51

• Entry DOI: 10.2210/pdb5z51/pdb
• Descriptor: DNA primase, DI(HYDROXYETHYL)ETHER, ACETATE ION, ... (5 entities in total)
• Functional Keywords: helicase binding domain of primase, dna replication, primer synthesis, transferase
• Biological source: Mycobacterium tuberculosis H37Rv; More
• Total number of polymer chains: 2
• Total formula weight: 26348.83

Authors

Sharma, D.P.,Gourinath, S. (deposition date: 2018-01-16, release date: 2018-11-28, Last modification date: 2024-10-30)

Primary citation

Sharma, D.P.,Vijayan, R.,Rehman, S.A.A.,Gourinath, S.
Structural insights into the interaction of helicase and primase inMycobacterium tuberculosis.
Biochem. J., 475:3493-3509, 2018

PubMed Abstract: The helicase-primase interaction is an essential event in DNA replication and is mediated by the highly variable C-terminal domain of primase (DnaG) and N-terminal domain of helicase (DnaB). To understand the functional conservation despite the low sequence homology of the DnaB-binding domains of DnaGs of eubacteria, we determined the crystal structure of the helicase-binding domain of DnaG from (DnaG-CTD) and did so to a resolution of 1.58 Å. We observed the overall structure of DnaG-CTD to consist of two subdomains, the N-terminal globular region (GR) and the C-terminal helical hairpin region (HHR), connected by a small loop. Despite differences in some of its helices, the globular region was found to have broadly similar arrangements across the species, whereas the helical hairpins showed different orientations. To gain insights into the crucial helicase-primase interaction in , a complex was modeled using the DnaG-CTD and DnaB-NTD crystal structures. Two nonconserved hydrophobic residues (Ile605 and Phe615) of DnaG were identified as potential key residues interacting with DnaB. Biosensor-binding studies showed a significant decrease in the binding affinity of DnaB-NTD with the Ile605Ala mutant of DnaG-CTD compared with native DnaG-CTD. The loop, connecting the two helices of the HHR, was concluded to be largely responsible for the stability of the DnaB-DnaG complex. Also, DnaB-NTD showed micromolar affinity with DnaG-CTDs from and and unstable binding with DnaG-CTD from The interacting domains of both DnaG and DnaB demonstrate the species-specific evolution of the replication initiation system.

PubMed: 30315069
DOI: 10.1042/BCJ20180673

Experimental method

X-RAY DIFFRACTION (1.583 Å)