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 

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This is version 1.1 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: 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 out ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase A, B, C, D, E, F363Acinetobacter baumannii D1279779Mutation(s): 0 
Gene Names: ACIN5098_0096
Find proteins for P37362 (Pyrrhocoris apterus)
Explore P37362 
Go to UniProtKB:  P37362
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,B,C,D,E,FL-PEPTIDE LINKINGC5 H11 N O2 SeMET
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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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references, Derived calculations