2WVK

Mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 apoprotein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


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


Literature

Structural Analysis of Thermus Thermophilus Hb27 Mannosyl-3-Phosphoglycerate Synthase Provides Evidence for a Second Catalytic Metal Ion and New Insight Into the Retaining Mechanism of Glycosyltransferases.

Goncalves, S., Borges, N., Esteves, A.M., Victor, B., Soares, C.M., Santos, H., Matias, P.M.

(2010) J Biol Chem 285: 17857

  • DOI: 10.1074/jbc.M109.095976
  • Primary Citation of Related Structures:  
    2WVK, 2WVL, 2WVM

  • PubMed Abstract: 

    • Mannosyl-3-phosphoglycerate synthase is a glycosyltransferase involved in the two-step synthetic pathway of mannosylglycerate, a compatible solute that accumulates in response to salt and/or heat stresses in many microorganisms thriving in hot environments ...

    Mannosyl-3-phosphoglycerate synthase is a glycosyltransferase involved in the two-step synthetic pathway of mannosylglycerate, a compatible solute that accumulates in response to salt and/or heat stresses in many microorganisms thriving in hot environments. The three-dimensional structure of mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 in its binary complex form, with GDP-alpha-D-mannose and Mg(2+), shows a second metal binding site, about 6 A away from the mannose moiety. Kinetic and mutagenesis studies have shown that this metal site plays a role in catalysis. Additionally, Asp(167) in the DXD motif is found within van der Waals contact distance of the C1' atom in the mannopyranose ring, suggesting its action as a catalytic nucleophile, either in the formation of a glycosyl-enzyme intermediate according to the double-displacement S(N)2 reaction mechanism or in the stabilization of the oxocarbenium ion-like intermediate according to the D(N)*A(Nss) (S(N)i-like) reaction mechanism. We propose that either mechanism may occur in retaining glycosyltransferases with a GT-A fold, and, based on the gathered structural information, we identified an extended structural signature toward a common scaffold between the inverting and retaining glycosyltransferases.

    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of Mannosyl-3-Phosphoglycerate Synthase from Thermus Thermophilus Hb27
      Goncalves, S., Borges, N., Santos, H., Matias, P.M.
      (2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1014
    Organizational Affiliation: 

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASEA, B391Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C0588
EC: 2.4.1.217 (PDB Primary Data), 2.4.1 (UniProt)
UniProt
Find proteins for Q72K30 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72K30 
Go to UniProtKB:  Q72K30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72K30
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.456α = 90
b = 113.456β = 90
c = 195.982γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2014-02-19
    Changes: Database references, Source and taxonomy