2YVK

Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: Implications for catalytic mechanism

Tamura, H.Saito, Y.Ashida, H.Inoue, T.Kai, Y.Yokota, A.Matsumura, H.

(2008) Protein Sci. 17: 126-135

  • DOI: 10.1110/ps.073169008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The methionine salvage pathway (MSP) plays a crucial role in recycling a sulphahydryl derivative of the nucleoside. Recently, the genes and reactions in MSP from Bacillus subtilis have been identified, where 5-methylthioribose 1-phosphate isomerase ( ...

    The methionine salvage pathway (MSP) plays a crucial role in recycling a sulphahydryl derivative of the nucleoside. Recently, the genes and reactions in MSP from Bacillus subtilis have been identified, where 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes a conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). Herein, we report the crystal structures of B. subtilis M1Pi (Bs-M1Pi) in complex with its product MTRu-1-P, and a sulfate at 2.4 and 2.7 A resolution, respectively. The electron density clearly shows the presence of each compound in the active site. The structural comparison with other homologous proteins explains how the substrate uptake of Bs-M1Pi may be induced by an open/closed transition of the active site. The highly conserved residues at the active site, namely, Cys160 and Asp240 are most likely to be involved in catalysis. The structural analysis sheds light on its catalytic mechanism of M1Pi.


    Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methylthioribose-1-phosphate isomerase
A, B, C, D
374Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: mtnA (ykrS)
EC: 5.3.1.23
Find proteins for O31662 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31662
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRU
Query on MRU

Download SDF File 
Download CCD File 
A, B, C, D
5-S-METHYL-1-O-PHOSPHONO-5-THIO-D-RIBULOSE
C6 H13 O7 P S
CNSJRYUMVMWNMC-RITPCOANSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.987α = 90.00
b = 84.444β = 92.34
c = 95.299γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance