3O9Z

Crystal structure of the WlbA (WbpB) dehydrogenase from Thermus thermophilus in complex with NAD and alpha-ketoglutarate at 1.45 angstrom resolution

Summary for 3O9Z

• Entry DOI: 10.2210/pdb3o9z/pdb
• Related: 3OA0 3OA2
• Descriptor: Lipopolysaccharide biosynthesis protein wbpB, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 2-OXOGLUTARIC ACID, ... (6 entities in total)
• Functional Keywords: oxidoreductase, sugar biosynthesis, dehydrogenase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 4
• Total formula weight: 142892.87

Authors

Holden, H.M.,Thoden, J.B. (deposition date: 2010-08-04, release date: 2010-08-18, Last modification date: 2024-02-21)

Primary citation

Thoden, J.B.,Holden, H.M.
Structural and Functional Studies of WlbA: A Dehydrogenase Involved in the Biosynthesis of 2,3-Diacetamido-2,3-dideoxy-d-mannuronic Acid .
Biochemistry, 49:7939-7948, 2010

PubMed Abstract: 2,3-Diacetamido-2,3-dideoxy-d-mannuronic acid (ManNAc3NAcA) is an unusual dideoxy sugar first identified nearly 30 years ago in the lipopolysaccharide of Pseudomonas aeruginosa O:3a,d. It has since been observed in other organisms, including Bordetella pertussis, the causative agent of whooping cough. Five enzymes are required for the biosynthesis of UDP-ManNAc3NAcA starting from UDP-N-acetyl-d-glucosamine. Here we describe a structural study of WlbA, the NAD-dependent dehydrogenase that catalyzes the second step in the pathway, namely, the oxidation of the C-3' hydroxyl group on the UDP-linked sugar to a keto moiety and the reduction of NAD(+) to NADH. This enzyme has been shown to use alpha-ketoglutarate as an oxidant to regenerate the oxidized dinucleotide. For this investigation, three different crystal structures were determined: the enzyme with bound NAD(H), the enzyme in a complex with NAD(H) and alpha-ketoglutarate, and the enzyme in a complex with NAD(H) and its substrate (UDP-N-acetyl-d-glucosaminuronic acid). The tetrameric enzyme assumes an unusual quaternary structure with the dinucleotides positioned quite closely to one another. Both alpha-ketoglutarate and the UDP-linked sugar bind in the WlbA active site with their carbon atoms (C-2 and C-3', respectively) abutting the re face of the cofactor. They are positioned approximately 3 A from the nicotinamide C-4. The UDP-linked sugar substrate adopts a highly unusual curved conformation when bound in the WlbA active site cleft. Lys 101 and His 185 most likely play key roles in catalysis.

PubMed: 20690587
DOI: 10.1021/bi101103s

Experimental method

X-RAY DIFFRACTION (1.449 Å)