5W34

Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG in complex with double-stranded DNA GACCGGAAGTGG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

Hou, C.Biswas, T.Tsodikov, O.V.

(2018) Biochemistry 57: 2084-2093

  • DOI: 10.1021/acs.biochem.8b00036
  • Primary Citation of Related Structures:  

  • PubMed 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 com ...

    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. Here 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.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , Lexington , Kentucky 40536 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA primase
A, B
325Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: dnaG
EC: 2.7.7.-
Find proteins for P9WNW1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WNW1
Entity ID: 2
MoleculeChainsLengthOrganism
DNA oligomer 5'-CCACTTCCGGTCC12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA oligomer 5'-GACCGGAAGTGGD12synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.781α = 90.00
b = 212.116β = 107.87
c = 47.418γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references