6Z3B

Low resolution structure of RgNanOx

Summary for 6Z3B

• Entry DOI: 10.2210/pdb6z3b/pdb
• Descriptor: Gfo/Idh/MocA family oxidoreductase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, CITRIC ACID, ... (5 entities in total)
• Functional Keywords: enzyme, sialic acid, epimerase, oxidase, reductase, carbohydrate
• Biological source: Ruminococcus gnavus; More
• Total number of polymer chains: 2
• Total formula weight: 85202.59

Authors

Naismith, J.H.,Lee, M. (deposition date: 2020-05-19, release date: 2020-07-22, Last modification date: 2024-01-24)

Primary citation

Bell, A.,Severi, E.,Lee, M.,Monaco, S.,Latousakis, D.,Angulo, J.,Thomas, G.H.,Naismith, J.H.,Juge, N.
Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria.
J.Biol.Chem., 295:13724-13736, 2020

PubMed Abstract: The human gut symbiont scavenges host-derived -acetylneuraminic acid (Neu5Ac) from mucins by converting it to 2,7-anhydro-Neu5Ac. We previously showed that 2,7-anhydro-Neu5Ac is transported into ATCC 29149 before being converted back to Neu5Ac for further metabolic processing. However, the molecular mechanism leading to the conversion of 2,7-anhydro-Neu5Ac to Neu5Ac remained elusive. Using 1D and 2D NMR, we elucidated the multistep enzymatic mechanism of the oxidoreductase (NanOx) that leads to the reversible conversion of 2,7-anhydro-Neu5Ac to Neu5Ac through formation of a 4-keto-2-deoxy-2,3-dehydro--acetylneuraminic acid intermediate and NAD regeneration. The crystal structure of NanOx in complex with the NAD cofactor showed a protein dimer with a Rossman fold. Guided by the NanOx structure, we identified catalytic residues by site-directed mutagenesis. Bioinformatics analyses revealed the presence of NanOx homologues across Gram-negative and Gram-positive bacterial species and co-occurrence with sialic acid transporters. We showed by electrospray ionization spray MS that the homologue YjhC displayed activity against 2,7-anhydro-Neu5Ac and that could catabolize 2,7-anhydro-Neu5Ac. Differential scanning fluorimetry analyses confirmed the binding of YjhC to the substrates 2,7-anhydro-Neu5Ac and Neu5Ac, as well as to co-factors NAD and NADH. Finally, using mutants and complementation growth assays, we demonstrated that 2,7-anhydro-Neu5Ac catabolism in depended on YjhC and on the predicted sialic acid transporter YjhB. These results revealed the molecular mechanisms of 2,7-anhydro-Neu5Ac catabolism across bacterial species and a novel sialic acid transport and catabolism pathway in .

PubMed: 32669363
DOI: 10.1074/jbc.RA120.014454

Experimental method

X-RAY DIFFRACTION (2.58 Å)