3Q2K

Crystal structure of the WlbA dehydrogenase from Bordetella pertussis in complex with NADH and UDP-GlcNAcA

Summary for 3Q2K

• Entry DOI: 10.2210/pdb3q2k/pdb
• Related: 3Q2I
• Descriptor: oxidoreductase, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, (2S,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4-dihydroxy-oxane-2-carboxylic acid, ... (4 entities in total)
• Functional Keywords: rossmann fold, dehydrogenase, nad, udp-sugar, oxidoreductase
• Biological source: Bordetella pertussis
• Total number of polymer chains: 16
• Total formula weight: 680579.07

Authors

Holden, H.M.,Thoden, J.B. (deposition date: 2010-12-20, release date: 2011-01-19, Last modification date: 2023-09-13)

Primary citation

Thoden, J.B.,Holden, H.M.
Biochemical and Structural Characterization of WlbA from Bordetella pertussis and Chromobacterium violaceum: Enzymes Required for the Biosynthesis of 2,3-Diacetamido-2,3-dideoxy-d-mannuronic Acid.
Biochemistry, 50:1483-1491, 2011

PubMed Abstract: The unusual sugar 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, or ManNAc3NAcA, has been observed in the lipopolysaccharides of both pathogenic and nonpathogenic Gram-negative bacteria. It is added to the lipopolysaccharides of these organisms by glycosyltransferases that use as substrates UDP-ManNAc3NAcA. Five enzymes are ultimately required for the biosynthesis of UDP-ManNAc3NAcA starting from UDP-N-acetylglucosamine. The second enzyme in the pathway, encoded by the wlba gene and referred to as WlbA, catalyzes the NAD-dependent oxidation of the C-3' hydroxyl group of the UDP-linked sugar. Here we describe a combined structural and functional investigation of the WlbA enzymes from Bordetella pertussis and Chromobacterium violaceum. For this investigation, ternary structures were determined in the presence of NAD(H) and substrate to 2.13 and 1.5 Å resolution, respectively. Both of the enzymes display octameric quaternary structures with their active sites positioned far apart. The octamers can be envisioned as tetramers of dimers. Kinetic studies demonstrate that the reaction mechanisms for these enzymes are sequential and that they do not require α-ketoglutarate for activity. These results are in sharp contrast to those recently reported for the WlbA enzymes from Pseudomonas aeruginosa and Thermus thermophilus, which function via ping-pong mechanisms that involve α-ketoglutarate. Taken together, the results reported here demonstrate that there are two distinct families of WlbA enzymes, which differ with respect to amino acid sequences, quaternary structures, active site architectures, and kinetic mechanisms.

PubMed: 21241053
DOI: 10.1021/bi101871f

Experimental method

X-RAY DIFFRACTION (2.13 Å)