Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events

doi:10.1021/acs.biochem.8b00036

Title: Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events

Full Record
Other Related Research

Abstract

Bacterial primase DnaG is an essential nucleic acid polymerase that generates primers for replication of chromosomal DNA. The mechanism of DnaG remains unclear due to the paucity of structural information on DnaG in complexes with other replisome components. Furthermore we report the first crystal structures of noncovalent DnaG–DNA complexes, obtained with the RNA polymerase domain of Mycobacterium tuberculosis DnaG and various DNA ligands. One structure, obtained with ds DNA, reveals interactions with DnaG as it slides on ds DNA and suggests how DnaG binds template for primer synthesis. In another structure, DNA in the active site of DnaG mimics the primer, providing insight into mechanisms for the nucleotide transfer and DNA translocation. In conjunction with the recent cryo-EM structure of the bacteriophage T7 replisome, this study yields a model for primer elongation and hand-off to DNA polymerase.

Authors:

Hou, Caixia ^[1]; Biswas, Tapan ^[2];

^[1]

Univ. of Kentucky, Lexington, KY (United States)
Univ. of California, San Diego, La Jolla, CA (United States)

Publication Date:: 2018-03-20

Research Org.:: Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Org.:: SER-CAT

OSTI Identifier:: 1438848

Resource Type:: Accepted Manuscript

Journal Name:: Biochemistry

Additional Journal Information:: Journal Volume: 57; Journal Issue: 14; Journal ID: ISSN 0006-2960

Publisher:: American Chemical Society (ACS)

Country of Publication:: United States

Language:: ENGLISH

Subject:: 59 BASIC BIOLOGICAL SCIENCES; anions; peptides and proteins; genetics; crystal structure; ions; DNA replication; replisome; DNA binding; tuberculosis

Citation Formats


                    Hou, Caixia, Biswas, Tapan, and Tsodikov, Oleg V. Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events.  United States: N. p., 2018. 
        Web.  doi:10.1021/acs.biochem.8b00036.

Copy to clipboard


                    Hou, Caixia, Biswas, Tapan, & Tsodikov, Oleg V. Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events.  United States.  doi:10.1021/acs.biochem.8b00036.

Copy to clipboard


                    Hou, Caixia, Biswas, Tapan, and Tsodikov, Oleg V. Tue .  
        "Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events".  United States.  doi:10.1021/acs.biochem.8b00036.  https://www.osti.gov/servlets/purl/1438848.

Copy to clipboard


                    
@article{osti_1438848,

  title        = {Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events},

  author       = {Hou, Caixia and Biswas, Tapan and Tsodikov, Oleg V.},

  abstractNote = {Bacterial primase DnaG is an essential nucleic acid polymerase that generates primers for replication of chromosomal DNA. The mechanism of DnaG remains unclear due to the paucity of structural information on DnaG in complexes with other replisome components. Furthermore we report the first crystal structures of noncovalent DnaG–DNA complexes, obtained with the RNA polymerase domain of Mycobacterium tuberculosis DnaG and various DNA ligands. One structure, obtained with ds DNA, reveals interactions with DnaG as it slides on ds DNA and suggests how DnaG binds template for primer synthesis. In another structure, DNA in the active site of DnaG mimics the primer, providing insight into mechanisms for the nucleotide transfer and DNA translocation. In conjunction with the recent cryo-EM structure of the bacteriophage T7 replisome, this study yields a model for primer elongation and hand-off to DNA polymerase.},

  doi          = {10.1021/acs.biochem.8b00036},

  journal      = {Biochemistry},

  number       = 14,

  volume       = 57,

  place        = {United States},

  year         = {2018},

  month        = {3}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Accepted Manuscript (DOE)

Publisher's Version of Record

DOI: 10.1021/acs.biochem.8b00036

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 6 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Similar Records in DOE PAGES and OSTI.GOV collections:

Crosstalk between primase subunits can act to regulate primersynthesis in trans

Journal Article Corn, Jacob E ; Pease, Paul J ; Hura, Greg L ; ... - Molecular Cell

The coordination of primase function within the replisome is an essential but poorly understood feature of lagging strand synthesis. By using crystallography and small-angle X-ray scattering (SAXS), we show that functional elements of bacterial primase transition between two dominant conformations: an extended form that uncouples a regulatory domain from its associated RNA polymerase core and a compact state that sequesters the regulatory region from the site of primer synthesis. FRET studies and priming assays reveal that the regulatory domain of one primase subunit productively associates with nucleic acid that is bound to the polymerase domain of a second protomer inmore »« less
DOI: 10.1016/j.molcel.2005.09.004
DNA Recognition by the DNA Primase of Bacteriophage T7: A Structure Function Study of the Zinc-Binding Domain

Journal Article Akabayov, B ; Lee, S ; Akabayov, S ; ... - Biochemistry

Synthesis of oligoribonucleotide primers for lagging-strand DNA synthesis in the DNA replication system of bacteriophage T7 is catalyzed by the primase domain of the gene 4 helicase-primase. The primase consists of a zinc-binding domain (ZBD) and an RNA polymerase (RPD) domain. The ZBD is responsible for recognition of a specific sequence in the ssDNA template whereas catalytic activity resides in the RPD. The ZBD contains a zinc ion coordinated with four cysteine residues. We have examined the ligation state of the zinc ion by X-ray absorption spectroscopy and biochemical analysis of genetically altered primases. The ZBD of primase engaged inmore »« less
DOI: 10.1021/bi802123t
Relative roles of T7 RNA polymerase and gene 4 primase for the initiation of T7 phage DNA replication in vivo

Journal Article Sugimoto, K ; Kohara, Y ; Okazaki, T - Proc. Natl. Acad. Sci. U.S.A.; (United States)

Initiation sites of T7 phage DNA replications in the presence and absence of T7 phage gene 4 primase have been analyzed by using Escherichia coli cells infected with T7 phage amber mutants, T7/sub 3,6/ and T7/sub 3,4,6/ respectively. Restriction analysis of the (/sup 3/H)thymidine-labeled DNA, synthesized by the T7/sub 3,4,6/ phage-infected cells in the presence of 2',3'-dideoxy-3'-azidothymidine, has shown that only the light (L) strand of T7 DNA has been synthesized from the primary origin area to the right. Transition sites from RNA to DNA have been located precisely in the primary origin region of the T7 phage genome. Inmore »« less
DOI: 10.1073/pnas.84.12.3977
Characterization and modification of phage T7 DNA polymerase for use in DNA sequencing; Progress report, June 1, 1990--May 31, 1993

Technical Report Richardson, C C

This project focuses on the DNA polymerase (gene 5 protein) of phage T7 for use in DNA sequence analysis. Gene 5 protein interacts with accessory proteins to acquire properties essential for DNA replication. One goal is to understand these interactions in order to modify the proteins for use in DNA sequencing. E. coli thioredoxin, binds to gene 5 protein and clamps it to a primer-template. They have analyzed the binding of gene 5 protein-thioredoxin to primer-templates and have defined the optimal conditions to form an extremely stable complex with a dNTP in the polymerase catalytic site. The spatial proximity ofmore »« less
DOI: 10.2172/142503

Full Text Available
Atomic Structure and Nonhomologous End-Joining Function of the Polymerase Component of Bacterial DNA Ligase D

Journal Article Zhu, H ; Nandakumar, J ; Aniukwu, J ; ... - Proc Natl Acad Sci USA

DNA ligase D (LigD) is a large polyfunctional protein that participates in a recently discovered pathway of nonhomologous end-joining in bacteria. LigD consists of an ATP-dependent ligase domain fused to a polymerase domain (Pol) and a phosphoesterase module. The Pol activity is remarkable for its dependence on manganese, its ability to perform templated and nontemplated primer extension reactions, and its preference for adding ribonucleotides to blunt DNA ends. Here we report the 1.5- Angstroms crystal structure of the Pol domain of Pseudomonas LigD and its complexes with manganese and ATP-dATP substrates, which reveal a minimized polymerase with a two-metal mechanismmore »« less
DOI: 10.1073/pnas.0509083103

Similar Records