8CSD

WbbB D232C Kdo adduct

Summary for 8CSD

• Entry DOI: 10.2210/pdb8csd/pdb
• Descriptor: N-acetyl glucosaminyl transferase, CYTIDINE-5'-MONOPHOSPHATE, 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid, ... (6 entities in total)
• Functional Keywords: glycsoyltransferase, retaining, donor adduct intermediate, transferase
• Biological source: Raoultella terrigena
• Total number of polymer chains: 2
• Total formula weight: 93464.30

Authors

Forrester, T.J.B.,Kimber, M.S. (deposition date: 2022-05-12, release date: 2022-11-09, Last modification date: 2024-10-09)

Primary citation

Forrester, T.J.B.,Ovchinnikova, O.G.,Li, Z.,Kitova, E.N.,Nothof, J.T.,Koizumi, A.,Klassen, J.S.,Lowary, T.L.,Whitfield, C.,Kimber, M.S.
The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.
Nat Commun, 13:6277-6277, 2022

PubMed Abstract: WbbB, a lipopolysaccharide O-antigen synthesis enzyme from Raoultella terrigena, contains an N-terminal glycosyltransferase domain with a highly modified architecture that adds a terminal β-Kdo (3-deoxy-D-manno-oct-2-ulosonic acid) residue to the O-antigen saccharide, with retention of stereochemistry. We show, using mass spectrometry, that WbbB forms a covalent adduct between the catalytic nucleophile, Asp232, and Kdo. We also determine X-ray structures for the CMP-β-Kdo donor complex, for Kdo-adducts with D232N and D232C WbbB variants, for a synthetic disaccharide acceptor complex, and for a ternary complex with both a Kdo-adduct and the acceptor. Together, these structures show that the enzyme-linked Asp232-Kdo adduct rotates to reposition the Kdo into a second sub-site, which then transfers Kdo to the acceptor. Retaining glycosyltransferases were thought to use only the front-side Si substitution mechanism; here we show that retaining glycosyltransferases can also potentially use double-displacement mechanisms, but incorporating an additional catalytic subsite requires rearrangement of the protein's architecture.

PubMed: 36271007
DOI: 10.1038/s41467-022-33988-1

Experimental method

X-RAY DIFFRACTION (1.95 Å)