Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 46883.43 
• Atom Count: 2799 
• Residue Count: 438 
• Unique protein chains: 1

1O8B

Structure of Escherichia coli ribose-5-phosphate isomerase, RpiA, complexed with arabinose-5-phosphate.

• DOI: 10.2210/pdb1O8B/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2002-11-26 Released: 2003-01-24 
• Deposition Author(s): Zhang, R.-g., Andersson, C.E., Savchenko, A., Skarina, T., Evdokimova, E., Beasley, S., Arrowsmith, C.H., Edwards, A.M., Joachimiak, A., Mowbray, S.L., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.240 
• R-Value Work: 0.224 

Literature

Structure of Escherichia Coli Ribose-5-Phosphate Isomerase: A Ubiquitous Enzyme of the Pentose Phosphate Pathway and the Calvin Cycle

Zhang, R.-G., Andersson, C.E., Savchenko, A., Skarina, T., Evdokimova, E., Beasley, S., Arrowsmith, C.H., Edwards, A.M., Joachimiak, A., Mowbray, S.L.

(2003) Structure 11: 31

• PubMed: 12517338 
• Primary Citation of Related Structures:  
  1KS2


• PubMed Abstract: 
  

Ribose-5-phosphate isomerase A (RpiA; EC 5.3.1.6) interconverts ribose-5-phosphate and ribulose-5-phosphate. This enzyme plays essential roles in carbohydrate anabolism and catabolism; it is ubiquitous and highly conserved. The structure of RpiA from Escherichia coli was solved by multiwavelength anomalous diffraction (MAD) phasing, and refined to 1.5 A resolution (R factor 22.4%, R(free) 23.7%). RpiA exhibits an alpha/beta/(alpha/beta)/beta/alpha fold, some portions of which are similar to proteins of the alcohol dehydrogenase family. The two subunits of the dimer in the asymmetric unit have different conformations, representing the opening/closing of a cleft. Active site residues were identified in the cleft using sequence conservation, as well as the structure of a complex with the inhibitor arabinose-5-phosphate at 1.25 A resolution. A mechanism for acid-base catalysis is proposed.

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Related Citations: 

• Escherichia Coli Rpia Gene Encoding Ribose Phosphate Isomerase A
  Hove-Jensen, B.,Maigaard, M.
  (1993) J.Bacteriol. 175: 5628




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Organizational Affiliation: 

Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, Argonne, IL 60439, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RIBOSE 5-PHOSPHATE ISOMERASE	A, B	219	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpiA (ygfC) EC: 5.3.1.6
Find proteins for P0A7Z0 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7Z0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ABF	A, B	BETA-D-ARABINOFURANOSE-5'-PHOSPHATE C5 H11 O8 P KTVPXOYAKDPRHY-SQOUGZDYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ABF	Ki: 2100000 nM BINDINGMOAD
ABF	Ki: 2100000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.240 
• R-Value Work: 0.224 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.049	α = 90.23
b = 42.400	β = 100.98
c = 60.195	γ = 98.98

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
MOLREP	phasing
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-26 
• Released Date: 2003-01-24 
• Deposition Author(s): Zhang, R.-g., Andersson, C.E., Savchenko, A., Skarina, T., Evdokimova, E., Beasley, S., Arrowsmith, C.H., Edwards, A.M., Joachimiak, A., Mowbray, S.L., Midwest Center for Structural Genomics (MCSG)

Revision History 

• Version 1.0: 2003-01-24
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.2: 2019-08-21
  Type: Data collection, Database references, Derived calculations