5K8C

X-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, from Shewanella oneidensis

Summary for 5K8C

• Entry DOI: 10.2210/pdb5k8c/pdb
• Descriptor: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, PHOSPHATE ION, ... (7 entities in total)
• Functional Keywords: group iii alcohol dehydrogenase, 8-amino-3, 8-dideoxy-d-manno-octulosonic acid, deoxy sugar, transferase
• Biological source: Shewanella oneidensis (strain MR-1)
• Total number of polymer chains: 1
• Total formula weight: 40722.25

Authors

Holden, H.M.,Thoden, J.B.,Zachman-Brockmeyer, T.R. (deposition date: 2016-05-28, release date: 2016-06-15, Last modification date: 2023-09-27)

Primary citation

Zachman-Brockmeyer, T.R.,Thoden, J.B.,Holden, H.M.
Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid.
Biochemistry, 55:4485-4494, 2016

PubMed Abstract: 8-Amino-3,8-dideoxy-d-manno-octulosonic acid (Kdo8N) is a unique amino sugar that has thus far only been observed on the lipopolysaccharides of marine bacteria belonging to the genus Shewanella. Although its biological function is still unclear, it is thought that the sugar is important for the integrity of the bacterial cell outer membrane. A three-gene cluster required for the biosynthesis of Kdo8N was first identified in Shewanella oneidensis. Here we describe the three-dimensional structures of two of the enzymes required for Kdo8N biosynthesis in S. oneidensis, namely, KdnB and KdnA. The structure of KdnB was solved to 1.85-Å resolution, and its overall three-dimensional architecture places it into the Group III alcohol dehydrogenase superfamily. A previous study suggested that KdnB did not require NAD(P) for activity. Strikingly, although the protein was crystallized in the absence of any cofactors, the electron density map clearly revealed the presence of a tightly bound NAD(H). In addition, a bound metal was observed, which was shown via X-ray fluorescence to be a zinc ion. Unlike other members of the Group III alcohol dehydrogenases, the dinucleotide cofactor in KdnB is tightly bound and cannot be removed without leading to protein precipitation. With respect to KdnA, it is a pyridoxal 5'-phosphate or (PLP)-dependent aminotransferase. For this analysis, the structure of KdnA, trapped in the presence of the external aldimine with PLP and glutamate, was determined to 2.15-Å resolution. The model of KdnA represents the first structure of a sugar aminotransferase that functions on an 8-oxo sugar. Taken together the results reported herein provide new molecular insight into the biosynthesis of Kdo8N.

PubMed: 27275764
DOI: 10.1021/acs.biochem.6b00439

Experimental method

X-RAY DIFFRACTION (1.85 Å)