2WFP

Crystal structure of mannose 6-phosphate isomerase (apo form) from Salmonella typhimurium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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This is version 1.1 of the entry. See complete history. 


Literature

Crystal Structures of Mannose 6-Phosphate Isomerase from Salmonella Typhimurium Bound to Metal Atoms and Substrate: Implications for Catalytic Mechanism

Sagurthi, S.R., Gowda, G., Savithri, H.S., Murthy, M.R.N.

(2009) Acta Crystallogr D Biol Crystallogr 65: 724

  • DOI: 10.1107/S0907444909013328
  • Primary Citation of Related Structures:  
    2WFP

  • PubMed Abstract: 

    • Mannose-6-phosphate isomerase (MPI) catalyzes the interconversion of mannose 6-phosphate and fructose 6-phosphate. X-ray crystal structures of MPI from Salmonella typhimurium in the apo form (with no metal bound) and in the holo form (with bound Zn2+) and two other structures with yttrium bound at an inhibitory site and complexed with Zn2+ and fructose 6-phosphate (F6P) were determined in order to gain insights into the structure and the isomerization mechanism ...

    Mannose-6-phosphate isomerase (MPI) catalyzes the interconversion of mannose 6-phosphate and fructose 6-phosphate. X-ray crystal structures of MPI from Salmonella typhimurium in the apo form (with no metal bound) and in the holo form (with bound Zn2+) and two other structures with yttrium bound at an inhibitory site and complexed with Zn2+ and fructose 6-phosphate (F6P) were determined in order to gain insights into the structure and the isomerization mechanism. Isomerization involves acid/base catalysis with proton transfer between the C1 and C2 atoms of the substrate. His99, Lys132, His131 and Asp270 are close to the substrate and are likely to be the residues involved in proton transfer. The interactions observed at the active site suggest that the ring-opening step is probably catalyzed by His99 and Asp270. An active-site loop consisting of residues 130-133 undergoes conformational changes upon substrate binding. Zn2+ binding induces structural order in the loop consisting of residues 50-54. The metal atom appears to play a role in substrate binding and is probably also important for maintaining the architecture of the active site. Isomerization probably follows the previously suggested cis-enediol mechanism.

    Organizational Affiliation: 

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MANNOSE-6-PHOSPHATE ISOMERASEA394Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: manA, pmi, STM1467
EC: 5.3.1.8
UniProt
Find proteins for P25081 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P25081 
Go to UniProtKB:  P25081
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25081
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.904α = 90
b = 92.47β = 90
c = 111.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-04-13 
  • Released Date: 2009-07-14 
    • Deposition Author(s): Sagurthi, S.R.

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance