1LK7 | pdb_00001lk7

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

PDB DOI: https://doi.org/10.2210/pdb1LK7/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.247 (Depositor), 0.252 (DCC)
R-Value Work:
0.202 (Depositor), 0.213 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00779-7
Primary Citation 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

Macromolecule Content

Total Structure Weight: 102.02 kDa
Atom Count: 7,493
Modeled Residue Count: 916
Deposited Residue Count: 916
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O50083
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DER Query on DER Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain I [auth A] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A]	I [auth A], M [auth B], Q [auth C], T [auth D]	D-4-PHOSPHOERYTHRONIC ACID C₄ H₉ O₈ P ZCZXOHUILRHRQJ-STHAYSLISA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain H [auth A] MOL2 format, chain P [auth C] MOL2 format, chain H [auth A] mmCIF format, chain P [auth C] mmCIF format, chain H [auth A]	H [auth A], P [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth C] Interactions & Density Focus chain H [auth A] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.247 (Depositor), 0.252 (DCC)
R-Value Work: 0.202 (Depositor), 0.213 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.689	α = 90
b = 114.923	β = 90
c = 119.578	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-07-03

Deposition Author(s):

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

1LK7 | pdb_00001lk7

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

Literature

A Hyperthermostable D-Ribose-5-Phosphate Isomerase from Pyrococcus horikoshii Characterization and Three-Dimensional Structure

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand