2VVP

Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with its substrates ribose 5-phosphate and ribulose 5-phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

D-Ribose-5-Phosphate Isomerase B from Escherichia Coli is Also a Functional D-Allose-6-Phosphate Isomerase, While the Mycobacterium Tuberculosis Enzyme is not.

Roos, A.K., Mariano, S., Kowalinski, E., Salmon, L., Mowbray, S.L.

(2008) J.Mol.Biol. 382: 667

  • DOI: 10.1016/j.jmb.2008.06.090
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Interconversion of D-ribose-5-phosphate (R5P) and D-ribulose-5-phosphate is an important step in the pentose phosphate pathway. Two unrelated enzymes with R5P isomerase activity were first identified in Escherichia coli, RpiA and RpiB. In this organi ...

    Interconversion of D-ribose-5-phosphate (R5P) and D-ribulose-5-phosphate is an important step in the pentose phosphate pathway. Two unrelated enzymes with R5P isomerase activity were first identified in Escherichia coli, RpiA and RpiB. In this organism, the essential 5-carbon sugars were thought to be processed by RpiA, while the primary role of RpiB was suggested to instead be interconversion of the rare 6-carbon sugars D-allose-6-phosphate (All6P) and D-allulose-6-phosphate. In Mycobacterium tuberculosis, where only an RpiB is found, the 5-carbon sugars are believed to be the enzyme's primary substrates. Here, we present kinetic studies examining the All6P isomerase activity of the RpiBs from these two organisms and show that only the E. coli enzyme can catalyze the reaction efficiently. All6P instead acts as an inhibitor of the M. tuberculosis enzyme in its action on R5P. X-ray studies of the M. tuberculosis enzyme co-crystallized with All6P and 5-deoxy-5-phospho-D-ribonohydroxamate (an inhibitor designed to mimic the 6-carbon sugar) and comparison with the E. coli enzyme's structure allowed us to identify differences in the active sites that explain the kinetic results. Two other structures, that of a mutant E. coli RpiB in which histidine 99 was changed to asparagine and that of wild-type M. tuberculosis enzyme, both co-crystallized with the substrate ribose-5-phosphate, shed additional light on the reaction mechanism of RpiBs generally.

    Organizational Affiliation: 

    Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBOSE-5-PHOSPHATE ISOMERASE B
A, B, C, D, E
162Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: rpiB
EC: 5.3.1.6
Find proteins for P9WKD7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WKD7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5RP
Query on 5RP
Download SDF File 
Download CCD File 
A, B, C, D, E
RIBULOSE-5-PHOSPHATE
C5 H11 O8 P
FNZLKVNUWIIPSJ-UHNVWZDZSA-N
 Ligand Interaction
R52
Query on R52
Download SDF File 
Download CCD File 
A, B, C, D, E
5-O-phosphono-D-ribose
C5 H11 O8 P
PPQRONHOSHZGFQ-LMVFSUKVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5RPKi: 400000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.832α = 90.00
b = 103.058β = 95.51
c = 69.728γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
REFMACphasing
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance