7BOB

Exo-beta-1,4-mannosidase Op5Man5 from Opitutaceae bacterium strain TAV5

Summary for 7BOB

• Entry DOI: 10.2210/pdb7bob/pdb
• Descriptor: Endo-beta-mannanase (2 entities in total)
• Functional Keywords: exo-beta-1, 4-mannosidase, termite hindgut, reticulitermes flavipes, glycosyl hydrolase family 5, verrucomicrobia, opitutaceae, hydrolase
• Biological source: Opitutaceae bacterium TAV5
• Total number of polymer chains: 3
• Total formula weight: 201098.25

Authors

Kalyani, D.C.,Reichenbach, T.,Keskitalo, M.M.,Conrad, J.,Aspeborg, H.,Divne, C. (deposition date: 2021-01-24, release date: 2021-07-14, Last modification date: 2024-05-01)

Primary citation

Kalyani, D.C.,Reichenbach, T.,Keskitalo, M.M.,Conrad, J.,Aspeborg, H.,Divne, C.
Crystal structure of a homotrimeric verrucomicrobial exo - beta -1,4-mannosidase active in the hindgut of the wood-feeding termite Reticulitermes flavipes .
J Struct Biol X, 5:100048-100048, 2021

PubMed Abstract: The termite causes extensive damage due to the high efficiency and broad specificity of the ligno- and hemicellulolytic enzyme systems produced by its symbionts. Thus, the gut microbiome is expected to constitute an excellent source of enzymes that can be used for the degradation and valorization of plant biomass. The symbiont bacterium strain TAV5 belongs to the phylum Verrucomicrobia and thrives in the hindgut of . The sequence of the gene with the locus tag opit5_10225 in the bacterium strain TAV5 genome has been classified as a member of glycoside hydrolase family 5 (GH5), and provisionally annotated as an --mannanase. We characterized biochemically and structurally the opit5_10225 gene product, and show that the enzyme, Man5, is an --1,4-mannosidase [EC 3.2.1.25] that is highly specific for -1,4-mannosidic bonds in mannooligosaccharides and ivory nut mannan. The structure of Man5 was phased using electron cryo-microscopy and further determined and refined at 2.2 Å resolution using X-ray crystallography. Man5 features a 200-kDa large homotrimer composed of three modular monomers. Despite insignificant sequence similarity, the structure of the monomer, and homotrimeric assembly are similar to that of the GH42-family -galactosidases and the GH164-family --1,4-mannosidase 164 from . To the best of our knowledge Man5 is the first structure of a glycoside hydrolase from a bacterial symbiont isolated from the digestive tract, as well as the first example of a GH5 glycoside hydrolase with a GH42 -galactosidase-type homotrimeric structure.

PubMed: 34195602
DOI: 10.1016/j.yjsbx.2021.100048

Experimental method

X-RAY DIFFRACTION (2.2 Å)