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 
  • R-Value Observed: 0.152 

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:  
    4UTT, 4UTU, 4UTW

  • 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 the three amino sugars, GlcNAc, ManNAc, and sialic acid ...

    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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASEA, B229Clostridium perfringens str. 13Mutation(s): 0 
Gene Names: nanEnanPCPE0184
EC: 5.1.3.9
UniProt
Find proteins for Q8XNZ3 (Clostridium perfringens (strain 13 / Type A))
Explore Q8XNZ3 
Go to UniProtKB:  Q8XNZ3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASEC, D229Clostridium perfringens str. 13Mutation(s): 0 
Gene Names: nanEnanPCPE0184
EC: 5.1.3.9
UniProt
Find proteins for Q8XNZ3 (Clostridium perfringens (strain 13 / Type A))
Explore Q8XNZ3 
Go to UniProtKB:  Q8XNZ3
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • 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
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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