Biological Assembly 1  

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

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 101.16 kDa 
• Atom Count: 7720 
• Modelled Residue Count: 916 
• Deposited Residue Count: 916 
• Unique protein chains: 1

1LK5

Structure of the D-Ribose-5-Phosphate Isomerase from Pyrococcus horikoshii

• PDB DOI: 10.2210/pdb1LK5/pdb

• Classification: ISOMERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-04-24 Released: 2002-07-03 
• Deposition Author(s): Ishikawa, K., Matsui, I., Payan, F., Cambillau, C., Ishida, H., Kawarabayasi, Y., Kikuchi, H., Roussel, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.215 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Literature

A hyperthermostable D-ribose-5-phosphate isomerase from Pyrococcus horikoshii characterization and three-dimensional structure.

Ishikawa, K., Matsui, I., Payan, F., Cambillau, C., Ishida, H., Kawarabayasi, Y., Kikuchi, H., Roussel, A.

(2002) Structure 10: 877-886

• PubMed: 12057201 
• DOI: 10.1016/s0969-2126(02)00779-7
• Primary Citation of Related Structures:  
  1LK5, 1LK7


• PubMed Abstract: 
  

A gene homologous to D-ribose-5-phosphate isomerase (EC 5.3.1.6) was found in the genome of Pyrococcus horikoshii. D-ribose-5-phosphate isomerase (PRI) is of particular metabolic importance since it catalyzes the interconversion between the ribose and ribulose forms involved in the pentose phosphate cycle and in the process of photosynthesis. The gene consisting of 687 bp was overexpressed in Escherichia coli, and the resulting enzyme showed activity at high temperatures with an optimum over 90 degrees C. The crystal structures of the enzyme, free and in complex with D-4-phosphoerythronic acid inhibitor, were determined. PRI is a tetramer in the crystal and in solution, and each monomer has a new fold consisting of two alpha/beta domains. The 3D structures and the characterization of different mutants indicate a direct or indirect catalytic role for the residues E107, D85, and K98.

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Organizational Affiliation: 

AFMB UMR-6098, CNRS et Universités d'Aix-Marseille I et II, 31 Chemin Joseph Aiguier, 13402 20, Marseille Cedex, France. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-Ribose-5-Phosphate Isomerase	A, B, C, D	229	Pyrococcus horikoshii	Mutation(s): 0  EC: 5.3.1.6
UniProt
Find proteins for O50083 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O50083  Go to UniProtKB:  O50083

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth A], N [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.215 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.548	α = 90
b = 114.932	β = 90
c = 119.017	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MLPHARE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-04-24 
• Released Date: 2002-07-03 
Deposition Author(s): Ishikawa, K., Matsui, I., Payan, F., Cambillau, C., Ishida, H., Kawarabayasi, Y., Kikuchi, H., Roussel, A.

Revision History  

• Version 1.0: 2002-07-03
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance