Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26626.24 
• Atom Count: 1620 
• Residue Count: 245 
• Unique protein chains: 1

1OYS

Crystal Structure of the Phosphorolytic Exoribonuclease RNase PH from Bacillus subtilis

• DOI: 10.2210/pdb1OYS/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis (strain 168)
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2003-04-07 Released: 2004-03-09 
• Deposition Author(s): Harlow, L.S., Kadziola, A., Jensen, K.F., Larsen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.284 
• R-Value Work: 0.258 

Literature

Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding.

Harlow, L.S., Kadziola, A., Jensen, K.F., Larsen, S.

(2004) Protein Sci. 13: 668-677

• PubMed: 14767080 
• DOI: 10.1110/ps.03477004
• Primary Citation of Related Structures:  
  1OYR, 1OYP


• PubMed Abstract: 
  

RNase PH is a member of the family of phosphorolytic 3' --> 5' exoribonucleases that also includes polynucleotide phosphorylase (PNPase). RNase PH is involved in the maturation of tRNA precursors and especially important for removal of nucleotide residues near the CCA acceptor end of the mature tRNAs. Wild-type and triple mutant R68Q-R73Q-R76Q RNase PH from Bacillus subtilis have been crystallized and the structures determined by X-ray diffraction to medium resolution. Wild-type and triple mutant RNase PH crystallize as a hexamer and dimer, respectively. The structures contain a rare left-handed beta alpha beta-motif in the N-terminal portion of the protein. This motif has also been identified in other enzymes involved in RNA metabolism. The RNase PH structure and active site can, despite low sequence similarity, be overlayed with the N-terminal core of the structure and active site of Streptomyces antibioticus PNPase. The surface of the RNase PH dimer fit the shape of a tRNA molecule.

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Organizational Affiliation: 

Department of Biological Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ribonuclease PH	A	245	Bacillus subtilis (strain 168)	Mutation(s): 3  Gene Names: rph EC: 2.7.7.56
Find proteins for P28619 (Bacillus subtilis (strain 168)) Go to UniProtKB:  P28619

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.284 
• R-Value Work: 0.258 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 63.230	α = 90.00
b = 63.230	β = 90.00
c = 203.000	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-07 
• Released Date: 2004-03-09 
• Deposition Author(s): Harlow, L.S., Kadziola, A., Jensen, K.F., Larsen, S.

Revision History 

• Version 1.0: 2004-03-09
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance