Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 28.61 kDa 
• Atom Count: 2079 
• Residue Count: 255 
• Unique protein chains: 1

1UDO

Crystal structure of the tRNA processing enzyme RNase PH R86A mutant from Aquifex aeolicus

• DOI: 10.2210/pdb1UDO/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-05-02 Released: 2003-09-23 
• Deposition Author(s): Ishii, R., Nureki, O., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.260 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 

Literature

Crystal Structure of the tRNA Processing Enzyme RNase PH from Aquifex aeolicus

Ishii, R., Nureki, O., Yokoyama, S.

(2003) J Biol Chem 278: 32397-32404

• PubMed: 12746447 
• DOI: 10.1074/jbc.M300639200
• Primary Citation of Related Structures:  
  1UDS, 1UDQ, 1UDO, 1UDN


• PubMed Abstract: 
  

RNase PH is one of the exoribonucleases that catalyze the 3' end processing of tRNA in bacteria. RNase PH removes nucleotides following the CCA sequence of tRNA precursors by phosphorolysis and generates mature tRNAs with amino acid acceptor activity. In this study, we determined the crystal structure of Aquifex aeolicus RNase PH bound with a phosphate, a co-substrate, in the active site at 2.3-A resolution. RNase PH has the typical alpha/beta fold, which forms a hexameric ring structure as a trimer of dimers. This ring structure resembles that of the polynucleotide phosphorylase core domain homotrimer, another phosphorolytic exoribonuclease. Four amino acid residues, Arg-86, Gly-124, Thr-125, and Arg-126, of RNase PH are involved in the phosphate-binding site. Mutational analyses of these residues showed their importance in the phosphorolysis reaction. A docking model with the tRNA acceptor stem suggests how RNase PH accommodates substrate RNAs.

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Organizational Affiliation: 

Department of Biophysics and Biochemistry, Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease PH	A	255	Aquifex aeolicus	Mutation(s): 1  EC: 2.7.7.56
Find proteins for O67069 (Aquifex aeolicus (strain VF5)) Explore O67069  Go to UniProtKB:  O67069

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.260 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.995	α = 90
b = 144.995	β = 90
c = 82.858	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-02 
• Released Date: 2003-09-23 
Deposition Author(s): Ishii, R., Nureki, O., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2003-09-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance