5W36 | pdb_00005w36

Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG in complex with a double-stranded DNA oligomer with a 6-nucleotide overhang

• PDB DOI: https://doi.org/10.2210/pdb5W36/pdb
• NAKB: 5W36

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-07 Released: 2018-03-28 
• Deposition Author(s): Hou, C., Tsodikov, O.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.269 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

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

• PubMed: 29558114 
• DOI: https://doi.org/10.1021/acs.biochem.8b00036
• Primary Citation Related Structures: 
  5W33, 5W34, 5W35, 5W36


• 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 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.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , Lexington , Kentucky 40536 , United States.
Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 75.16 kDa 
• Atom Count: 5,022 
• Modeled Residue Count: 645 
• Deposited Residue Count: 664 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase	A, B	325	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: dnaG, Rv2343c, MTCY98.12c EC: 2.7.7 (PDB Primary Data), 2.7.7.101 (UniProt)
UniProt
Find proteins for P9WNW1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNW1  Go to UniProtKB:  P9WNW1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
synthetic DNA 5'-TATCGTCCCGCCTC	C [auth G]	14	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR	D [auth G]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.269 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.837	α = 90
b = 210.936	β = 106.78
c = 46.046	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-28 
Deposition Author(s): Hou, C., Tsodikov, O.V.

Revision History  

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description