3F1Y

Mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus reveals its dual substrate specificity

Empadinhas, N.Pereira, P.J.B.Albuquerque, L.Costa, J.Sa-Moura, B.Marques, A.T.Macedo-Ribeiro, S.da Costa, M.S.

(2011) Mol.Microbiol. 79: 76-93

  • DOI: 10.1111/j.1365-2958.2010.07432.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rubrobacter xylanophilus is the only actinobacterium known to accumulate the organic solute mannosylglycerate (MG); moreover, the accumulation of MG is constitutive. The key enzyme for MG synthesis, catalysing the conversion of GDP-mannose (GDP-Man) ...

    Rubrobacter xylanophilus is the only actinobacterium known to accumulate the organic solute mannosylglycerate (MG); moreover, the accumulation of MG is constitutive. The key enzyme for MG synthesis, catalysing the conversion of GDP-mannose (GDP-Man) and D-3-phosphoglycerate (3-PGA) into the phosphorylated intermediate mannosyl-3-phosphoglycerate and GDP, was purified from R. xylanophilus cell extracts and the corresponding gene was expressed in E. coli. Despite the related solute glucosylglycerate (GG) having never been detected in R. xylanophilus, the cell extracts and the pure recombinant mannosyl-3-phosphoglycerate synthase (MpgS) could also synthesize glucosyl-3-phosphoglycerate (GPG), the precursor of GG, in agreement with the higher homology of the novel MpgS towards GPG-synthesizing mycobacterial glucosyl-3-phosphoglycerate synthases (GpgS) than towards MpgSs from hyper/thermophiles, known to accumulate MG under salt or thermal stress. To understand the specificity and substrate ambiguity of this novel enzyme, we determined the crystal structure of the unliganded MpgS and of its complexes with the nucleotide and sugar donors, at 2.2, 2.8 and 2.5 Å resolution respectively. The first three-dimensional structures of a protein from this extremely gamma-radiation-resistant thermophile here reported show that MpgS (GT81 family) contains a GT-A like fold and clearly explain its nucleotide and sugar-donor specificity. In the GDP-Man complex, a flexible loop ((254) RQNRHQ(259) ), located close to the active site moves towards the incoming sugar moiety, providing the ligands for both magnesium ion co-ordination and sugar binding. A triple mutant of R. xylanophilus MpgS, mimicking the (206) PLAGE(210) loop stabilizing hydrogen bond network observed for mycobacterial GpgSs, reduces significantly the affinity to GDP-Man, implicating this loop in the sugar-donor discrimination.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus
      Sa-Moura, B.,Albuquerque, L.,Empadinhas, N.,da Costa, M.S.,Pereira, P.J.,Macedo-Ribeiro, S.
      (2008) Acta Crystallogr.,Sect.F 64: 760


    Organizational Affiliation

    Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mannosyl-3-phosphoglycerate synthase
A, C
387Rubrobacter xylanophilusMutation(s): 0 
EC: 2.4.1.217
Find proteins for B7SY86 (Rubrobacter xylanophilus)
Go to UniProtKB:  B7SY86
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.881α = 90.00
b = 108.881β = 90.00
c = 311.651γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
SHARPphasing
MOSFLMdata reduction
PHENIXrefinement
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-06-28
    Type: Source and taxonomy