Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.22 kDa 
• Atom Count: 3310 
• Residue Count: 338 
• Unique protein chains: 1

3L9Q

Crystal structure of human polymerase alpha-primase p58 iron-sulfur cluster domain

• DOI: 10.2210/pdb3L9Q/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-05 Released: 2010-07-14 
• Deposition Author(s): Vaithiyalingam, S., Eichman, B.F., Chazin, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.169 
• R-Value Work: 0.130 
• R-Value Observed: 0.132 

Literature

Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase.

Vaithiyalingam, S., Warren, E.M., Eichman, B.F., Chazin, W.J.

(2010) Proc Natl Acad Sci U S A 107: 13684-13689

• PubMed: 20643958 
• DOI: 10.1073/pnas.1002009107
• Structures With Same Primary Citation


• PubMed Abstract: 
  

DNA replication requires priming of DNA templates by enzymes known as primases. Although DNA primase structures are available from archaea and bacteria, the mechanism of DNA priming in higher eukaryotes remains poorly understood in large part due to the absence of the structure of the unique, highly conserved C-terminal regulatory domain of the large subunit (p58C). Here, we present the structure of this domain determined to 1.7-A resolution by X-ray crystallography. The p58C structure reveals a novel arrangement of an evolutionarily conserved 4Fe-4S cluster buried deeply within the protein core and is not similar to any known protein structure. Analysis of the binding of DNA to p58C by fluorescence anisotropy measurements revealed a strong preference for ss/dsDNA junction substrates. This approach was combined with site-directed mutagenesis to confirm that the binding of DNA occurs to a distinctively basic surface on p58C. A specific interaction of p58C with the C-terminal domain of the intermediate subunit of replication protein A (RPA32C) was identified and characterized by isothermal titration calorimetry and NMR. Restraints from NMR experiments were used to drive computational docking of the two domains and generate a model of the p58C-RPA32C complex. Together, our results explain functional defects in human DNA primase mutants and provide insights into primosome loading on RPA-coated ssDNA and regulation of primase activity.

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Organizational Affiliation: 

Department of Biochemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-8725, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA primase large subunit	A, B	195	Homo sapiens	Mutation(s): 0  Gene Names: PRIM2, PRIM2A EC: 2.7.7
Find proteins for P49643 (Homo sapiens) Explore P49643  Go to UniProtKB:  P49643
NIH Common Fund Data Resources
PHAROS  P49643 GTEx  ENSG00000146143

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	A, B	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.169 
• R-Value Work: 0.130 
• R-Value Observed: 0.132 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.441	α = 90
b = 53.05	β = 115.09
c = 88.844	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
SHARP	phasing
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-05 
• Released Date: 2010-07-14 
Deposition Author(s): Vaithiyalingam, S., Eichman, B.F., Chazin, W.J.

Revision History 

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model