1KS2

Crystal Structure Analysis of the rpiA, Structural Genomics, protein EC1268.

• PDB DOI: https://doi.org/10.2210/pdb1KS2/pdb

• Classification: Structural Genomics, ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-01-10 Released: 2002-08-14 
• Deposition Author(s): Zhang, R., Joachimiak, A., Edwards, A.M., Skarina, T., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.237 
• R-Value Work: 0.224 
• R-Value Observed: 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., 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: 31-42

• PubMed: 12517338 
• DOI: https://doi.org/10.1016/s0969-2126(02)00933-4
• Primary Citation of Related Structures:  
  1KS2, 1O8B


• 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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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.33 kDa 
• Atom Count: 3,850 
• Modelled Residue Count: 436 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein EC1268, RPIA	A, B	219	Escherichia coli	Mutation(s): 6  EC: 5.3.1.6
UniProt
Find proteins for P0A7Z0 (Escherichia coli (strain K12)) Explore P0A7Z0  Go to UniProtKB:  P0A7Z0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.237 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.119	α = 89.94
b = 42.12	β = 100.95
c = 59.429	γ = 98.73

Software Package:

Software Name	Purpose
d*TREK	data scaling
HKL-2000	data reduction
CNS	refinement
d*TREK	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-14 
Deposition Author(s): Zhang, R., Joachimiak, A., Edwards, A.M., Skarina, T., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2002-08-14
  Type: Initial release
  
• Version 1.1: 2007-11-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary