1O8B | pdb_00001o8b

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

• PDB DOI: https://doi.org/10.2210/pdb1O8B/pdb

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


• 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 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1016/s0969-2126(02)00933-4
• Primary Citation 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.88 kDa 
• Atom Count: 2,958 
• Modeled Residue Count: 380 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ABF	C [auth A], D [auth B]	5-O-phosphono-beta-D-arabinofuranose 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.240 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.049	α = 90.23
b = 42.4	β = 100.98
c = 60.195	γ = 98.98

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-08-21
  Changes: Data collection, Database references, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary