4J2O

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

Summary for 4J2O

• Entry DOI: 10.2210/pdb4j2o/pdb
• Descriptor: UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (3 entities in total)
• Functional Keywords: rossmann fold, dehydratase, nadp, nucleoside-diphosphate sugar epimerase, isomerase
• Biological source: Acinetobacter baumannii
• Total number of polymer chains: 6
• Total formula weight: 254259.77

Authors

Shah, B.S.,Harrop, S.J.,Paulsen, I.T.,Mabbutt, B.C. (deposition date: 2013-02-05, release date: 2013-04-17, Last modification date: 2024-11-06)

Primary citation

Shah, B.S.,Ashwood, H.E.,Harrop, S.J.,Farrugia, D.N.,Paulsen, I.T.,Mabbutt, B.C.
Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii.
Plos One, 13:e0191610-e0191610, 2018

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.

PubMed: 29352301
DOI: 10.1371/journal.pone.0191610

Experimental method

X-RAY DIFFRACTION (2.653 Å)