1LK7

Structure of D-Ribose-5-Phosphate Isomerase from in complex with phospho-erythronic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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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

  • DOI: https://doi.org/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.

    • Organizational Affiliation: 

    AFMB UMR-6098, CNRS et Universités d'Aix-Marseille I et II, 31 Chemin Joseph Aiguier, 13402 20, Marseille Cedex, France. kazu-ishikawa@aist.go.jp


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-Ribose-5-Phosphate Isomerase
A, B, C, D
229Pyrococcus horikoshiiMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50083
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DER
Query on DER
Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
Q [auth C],
T [auth D]		D-4-PHOSPHOERYTHRONIC ACID
C4 H9 O8 P
ZCZXOHUILRHRQJ-STHAYSLISA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
R [auth D],
S [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA
Download Ideal Coordinates CCD File 
H [auth A],
P [auth C]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.689α = 90
b = 114.923β = 90
c = 119.578γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description