2GEK

Crystal Structure of phosphatidylinositol mannosyltransferase (PimA) from Mycobacterium smegmatis in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular recognition and interfacial catalysis by the essential phosphatidylinositol mannosyltransferase PimA from mycobacteria.

Guerin, M.E.Kordulakova, J.Schaeffer, F.Svetlikova, Z.Buschiazzo, A.Giganti, D.Gicquel, B.Mikusova, K.Jackson, M.Alzari, P.M.

(2007) J.Biol.Chem. 282: 20705-20714

  • DOI: 10.1074/jbc.M702087200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mycobacterial phosphatidylinositol mannosides (PIMs) and metabolically derived cell wall lipoglycans play important roles in host-pathogen interactions, but their biosynthetic pathways are poorly understood. Here we focus on Mycobacterium smegmatis P ...

    Mycobacterial phosphatidylinositol mannosides (PIMs) and metabolically derived cell wall lipoglycans play important roles in host-pathogen interactions, but their biosynthetic pathways are poorly understood. Here we focus on Mycobacterium smegmatis PimA, an essential enzyme responsible for the initial mannosylation of phosphatidylinositol. The structure of PimA in complex with GDP-mannose shows the two-domain organization and the catalytic machinery typical of GT-B glycosyltransferases. PimA is an amphitrophic enzyme that binds mono-disperse phosphatidylinositol, but its transferase activity is stimulated by high concentrations of non-substrate anionic surfactants, indicating that the early stages of PIM biosynthesis involve lipid-water interfacial catalysis. Based on structural, calorimetric, and mutagenesis studies, we propose a model wherein PimA attaches to the membrane through its N-terminal domain, and this association leads to enzyme activation. Our results reveal a novel mode of phosphatidylinositol recognition and provide a template for the development of potential antimycobacterial compounds.


    Related Citations: 
    • Definition of the first mannosylation step in phosphatidylinositol mannoside synthesis
      Kordulakova, J.,Gilleron, M.,Mikusova, K.,Puzo, G.,Brennan, P.J.,Gicquel, B.,Jackson, M.
      (2002) J.Biol.Chem. 277: 31335
    • Lipoarabinomannans: from structure to biosynthesis
      Nigou, J.,Gilleron, M.,Puzo, G.
      (2003) Biochimie 85: 153
    • An evolving hierarchical family classification for glycosyltransferases
      Coutinho, P.M.,Deleury, E.,Davies, G.J.,Henrissat, B.
      (2003) J.Mol.Biol. 328: 307
    • Crystallization and preliminary crystallographic analysis of PimA, an essential mannosyltransferase from Mycobacterium smegmatis
      Guerin, M.E.,Buschiazzo, A.,Kordulakova, J.,Jackson, M.,Alzari, P.M.
      (2005) Acta Crystallogr.,Sect.F F61: 518
    • Mycbacterial lipoarabinomannan and related lipoglycans: from biogenesis to modulation of the immune response
      Briken, V.,Porcelli, S.A.,Besra, G.S.,Kremer, L.
      (2004) Mol.Microbiol. 53: 391


    Organizational Affiliation

    Unité de Biochimie Structurale (CNRS URA 2185), Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE (PimA)
A
406Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: pimA
EC: 2.4.1.345
Find proteins for A0QWG6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QWG6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GDPKd: 30 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.176α = 90.00
b = 72.425β = 90.00
c = 138.230γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4data scaling
AMoREphasing
SHARPphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
SOLOMONphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance