6A9W

Structure of the bifunctional DNA primase-polymerase from phage NrS-1

Summary for 6A9W

• Entry DOI: 10.2210/pdb6a9w/pdb
• Descriptor: Primase (2 entities in total)
• Functional Keywords: prim-pol, replication
• Biological source: Nitratiruptor phage NrS-1
• Total number of polymer chains: 1
• Total formula weight: 36314.85

Authors

Guo, H.J.,Li, M.J.,Wang, T.L.,Wu, H.,Zhou, H.,Xu, C.Y.,Liu, X.P.,Yu, F.,He, J.H. (deposition date: 2018-07-16, release date: 2019-03-13, Last modification date: 2024-03-27)

Primary citation

Guo, H.J.,Li, M.J.,Wang, T.L.,Wu, H.,Zhou, H.,Xu, C.Y.,Liu, X.P.,Yu, F.,He, J.H.
Crystal structure and biochemical studies of the bifunctional DNA primase-polymerase from phage NrS-1.
Biochem. Biophys. Res. Commun., 510:573-579, 2019

PubMed Abstract: A novel DNA polymerase found in the deep-sea vent phage NrS-1, was confirmed to have both DNA polymerase and primase activities. In this polymerase, the N-terminal residues 1-300 (referred to as N300) are the core region required for polymerizing DNA and catalyzing de novo DNA synthesis. Here, the crystal structure of N300 was solved at a resolution of 1.80 Å. The overall structure consists of a prim/pol domain and a helix bundle domain, which are separated by a 14-residue-long flexible tether (residues 177-190). Both the prim/pol domain of N300 and other primase-polymerases (prim-pol) encompass an analogous fold with conserved catalytic residues. Mutagenesis and enzymatic activity assays show that the acidic active-site residue E139 is required for both polymerase and primase activities. Functional assays confirm the essentiality of the helix bundle domain for primase activity. Furthermore, we identified a mutant (N300-Y261A) of the helix bundle domain, which probably plays an indispensable role in the primer initiation and recognition of template DNA.

PubMed: 30739783
DOI: 10.1016/j.bbrc.2019.01.144

Experimental method

X-RAY DIFFRACTION (1.8 Å)