4UTT

Structural characterisation of NanE, ManNac6P C2 epimerase, from Clostridium perfingens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Characterization of the Clostridium Perfringens N-Acetylmannosamine-6-Phosphate 2-Epimerase Essential for the Sialic Acid Salvage Pathway.

Pelissier, M.Sebban-Kreuzer, C.Guerlesquin, F.Brannigan, J.A.Bourne, Y.Vincent, F.

(2014) J.Biol.Chem. 289: 35215

  • DOI: 10.1074/jbc.M114.604272
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pathogenic bacteria are endowed with an arsenal of specialized enzymes to convert nutrient compounds from their cell hosts. The essential N-acetylmannosamine-6-phosphate 2-epimerase (NanE) belongs to a convergent glycolytic pathway for utilization of ...

    Pathogenic bacteria are endowed with an arsenal of specialized enzymes to convert nutrient compounds from their cell hosts. The essential N-acetylmannosamine-6-phosphate 2-epimerase (NanE) belongs to a convergent glycolytic pathway for utilization of the three amino sugars, GlcNAc, ManNAc, and sialic acid. The crystal structure of ligand-free NanE from Clostridium perfringens reveals a modified triose-phosphate isomerase (β/α)8 barrel in which a stable dimer is formed by exchanging the C-terminal helix. By retaining catalytic activity in the crystalline state, the structure of the enzyme bound to the GlcNAc-6P product identifies the topology of the active site pocket and points to invariant residues Lys(66) as a putative single catalyst, supported by the structure of the catalytically inactive K66A mutant in complex with substrate ManNAc-6P. (1)H NMR-based time course assays of native NanE and mutated variants demonstrate the essential role of Lys(66) for the epimerization reaction with participation of neighboring Arg(43), Asp(126), and Glu(180) residues. These findings unveil a one-base catalytic mechanism of C2 deprotonation/reprotonation via an enolate intermediate and provide the structural basis for the development of new antimicrobial agents against this family of bacterial 2-epimerases.


    Organizational Affiliation

    the Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom.,the Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS UMR7255, Aix-Marseille Université, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, and.,From the Aix-Marseille University, AFMB UMR7257, 163 avenue de Luminy 13288 Marseille, France, the CNRS, AFMB UMR7257, 163 avenue de Luminy, 13288 Marseille, France.,From the Aix-Marseille University, AFMB UMR7257, 163 avenue de Luminy 13288 Marseille, France, the CNRS, AFMB UMR7257, 163 avenue de Luminy, 13288 Marseille, France, florence.vincent@afmb.univ-mrs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
A, B
229Clostridium perfringens (strain 13 / Type A)Mutation(s): 0 
Gene Names: nanE (nanP)
EC: 5.1.3.9
Find proteins for Q8XNZ3 (Clostridium perfringens (strain 13 / Type A))
Go to UniProtKB:  Q8XNZ3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
C, D
229Clostridium perfringens (strain 13 / Type A)Mutation(s): 0 
Gene Names: nanE (nanP)
EC: 5.1.3.9
Find proteins for Q8XNZ3 (Clostridium perfringens (strain 13 / Type A))
Go to UniProtKB:  Q8XNZ3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 36.989α = 90.22
b = 75.501β = 90.01
c = 82.234γ = 92.83
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Database references
  • Version 1.2: 2015-01-14
    Type: Database references