4J2O

Crystal structure of NADP-bound WbjB from A. baumannii community strain D1279779


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii.

Shah, B.S.Ashwood, H.E.Harrop, S.J.Farrugia, D.N.Paulsen, I.T.Mabbutt, B.C.

(2018) PLoS One 13: e0191610-e0191610

  • DOI: https://doi.org/10.1371/journal.pone.0191610
  • Primary Citation of Related Structures:  
    4J2O

  • PubMed Abstract: 

    With new strains of Acinetobacter baumannii undergoing genomic analysis, it has been possible to define regions of genomic plasticity (RGPs), encoding specific adaptive elements. For a selected RGP from a community-derived isolate of A. baumannii, we outline sequences compatible with biosynthetic machinery of surface polysaccharides, specifically enzymes utilized in the dehydration and conversion of UDP-N-acetyl-D-glucosamine (UDP-D-GlcNAc). We have determined the crystal structure of one of these, the epimerase Ab-WbjB. This dehydratase belongs to the 'extended' short-chain dehydrogenase/reductase (SDR) family, related in fold to previously characterised enzymes CapE and FlaA1. Our 2.65Å resolution structure of Ab-WbjB shows a hexamer, organised into a trimer of chain pairs, with coenzyme NADP+ occupying each chain. Specific active-site interactions between each coenzyme and a lysine quaternary group of a neighbouring chain interconnect adjacent dimers, so stabilising the hexameric form. We show UDP-GlcNAc to be a specific substrate for Ab-WbjB, with binding evident by ITC (Ka = 0.23 μmol-1). The sequence of Ab-WbjB shows variation from the consensus active-site motifs of many SDR enzymes, demonstrating a likely catalytic role for a specific threonine sidechain (as an alternative to tyrosine) in the canonical active site chemistry of these epimerases.


  • Organizational Affiliation

    Department of Molecular Sciences, Macquarie University, Sydney, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase
A, B, C, D, E
A, B, C, D, E, F
363Acinetobacter baumannii D1279779Mutation(s): 0 
Gene Names: ACIN5098_0096
UniProt
Find proteins for P37362 (Pyrrhocoris apterus)
Explore P37362 
Go to UniProtKB:  P37362
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37362
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.93α = 90
b = 114.54β = 90
c = 215.15γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CCP4model building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection
  • Version 1.4: 2024-11-06
    Changes: Structure summary