Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.16 kDa 
• Atom Count: 1890 
• Modelled Residue Count: 210 
• Deposited Residue Count: 216 
• Unique protein chains: 1

1RNI

Bifunctional DNA primase/polymerase domain of ORF904 from the archaeal plasmid pRN1

• PDB DOI: 10.2210/pdb1RNI/pdb

• Classification: REPLICATION
• Organism(s): Sulfolobus islandicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-01 Released: 2004-01-27 
• Deposition Author(s): Lipps, G., Weinzierl, A.O., von Scheven, G., Buchen, C., Cramer, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.261 
• R-Value Work: 0.243 

Literature

Structure of a bifunctional DNA primase-polymerase

Lipps, G., Weinzierl, A.O., Von Scheven, G., Buchen, C., Cramer, P.

(2004) Nat Struct Mol Biol 11: 157-162

• PubMed: 14730355 
• DOI: 10.1038/nsmb723
• Primary Citation of Related Structures:  
  1RNI, 1RO0, 1RO2


• PubMed Abstract: 
  

Genome replication generally requires primases, which synthesize an initial oligonucleotide primer, and DNA polymerases, which elongate the primer. Primase and DNA polymerase activities are combined, however, in newly identified replicases from archaeal plasmids, such as pRN1 from Sulfolobus islandicus. Here we present a structure-function analysis of the pRN1 primase-polymerase (prim-pol) domain. The crystal structure shows a central depression lined by conserved residues. Mutations on one side of the depression reduce DNA affinity. On the opposite side of the depression cluster three acidic residues and a histidine, which are required for primase and DNA polymerase activity. One acidic residue binds a manganese ion, suggestive of a metal-dependent catalytic mechanism. The structure does not show any similarity to DNA polymerases, but is distantly related to archaeal and eukaryotic primases, with corresponding active-site residues. We propose that archaeal and eukaryotic primases and the prim-pol domain have a common evolutionary ancestor, a bifunctional replicase for small DNA genomes.

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Organizational Affiliation: 

Institute of Biochemistry, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF904	A	216	Sulfolobus islandicus	Mutation(s): 0
UniProt
Find proteins for Q54324 (Sulfolobus islandicus) Explore Q54324  Go to UniProtKB:  Q54324

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.261 
• R-Value Work: 0.243 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.12	α = 90
b = 123.63	β = 90
c = 41.86	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-01 
• Released Date: 2004-01-27 
Deposition Author(s): Lipps, G., Weinzierl, A.O., von Scheven, G., Buchen, C., Cramer, P.

Revision History  

• Version 1.0: 2004-01-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model