1D0Q | pdb_00001d0q

STRUCTURE OF THE ZINC-BINDING DOMAIN OF BACILLUS STEAROTHERMOPHILUS DNA PRIMASE

• PDB DOI: https://doi.org/10.2210/pdb1D0Q/pdb

• Classification: TRANSFERASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Geobacillus stearothermophilus
• Mutation(s): No 


• Deposited: 1999-09-14 Released: 2000-03-29 
• Deposition Author(s): Pan, H., Wigley, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.225 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.194 (DCC) 

Literature

Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase.

Pan, H., Wigley, D.B.

(2000) Structure 8: 231-239

• PubMed: 10745010 
• DOI: https://doi.org/10.1016/s0969-2126(00)00101-5
• Primary Citation Related Structures: 
  1D0Q


• PubMed Abstract: 
  

  DNA primases catalyse the synthesis of the short RNA primers that are required for DNA replication by DNA polymerases. Primases comprise three functional domains: a zinc-binding domain that is responsible for template recognition, a polymerase domain, and a domain that interacts with the replicative helicase, DnaB. We present the crystal structure of the zinc-binding domain of DNA primase from Bacillus stearothermophilus, determined at 1.7 A resolution. This is the first high-resolution structural information about any DNA primase. A model is discussed for the interaction of this domain with the single-stranded DNA template. The structure of the DNA primase zinc-binding domain confirms that the protein belongs to the zinc ribbon subfamily. Structural comparison with other nucleic acid binding proteins suggests that the beta sheet of primase is likely to be the DNA-binding surface, with conserved residues on this surface being involved in the binding and recognition of DNA.

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Organizational Affiliation: 
• Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.89 kDa 
• Atom Count: 1,746 
• Modeled Residue Count: 204 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA PRIMASE	A, B	103	Geobacillus stearothermophilus	Mutation(s): 0  EC: 2.7.7 (PDB Primary Data), 2.7.7.101 (UniProt)
UniProt
Find proteins for Q9X4D0 (Geobacillus stearothermophilus) Explore Q9X4D0  Go to UniProtKB:  Q9X4D0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.225 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.194 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.17	α = 90
b = 58.745	β = 91.73
c = 45.75	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-29 
Deposition Author(s): Pan, H., Wigley, D.B.

Revision History  

• Version 1.0: 2000-03-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations