2YRF

Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.1110/ps.073169008
  • Primary Citation of Related Structures:  
    2YRF, 2YVK

  • 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 (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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylthioribose-1-phosphate isomerase
A, B
374Bacillus subtilisMutation(s): 0 
Gene Names: mtnA
EC: 5.3.1.23
UniProt
Find proteins for O31662 (Bacillus subtilis (strain 168))
Explore O31662 
Go to UniProtKB:  O31662
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31662
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.273α = 90
b = 69.273β = 90
c = 154.436γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description