6BYI

Crystal structure of the acid-base mutant (E477A) of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri

Summary for 6BYI

• Entry DOI: 10.2210/pdb6byi/pdb
• Descriptor: Beta-mannosidase, beta-D-mannopyranose (3 entities in total)
• Functional Keywords: carbohydrate, hydrolase-carbohydrate complex, hydrolase/carbohydrate
• Biological source: Xanthomonas axonopodis pv. citri (strain 306)
• Total number of polymer chains: 2
• Total formula weight: 194304.56

Authors

Domingues, M.N.,Vieira, P.S.,Morais, M.A.B.,Murakami, M.T. (deposition date: 2017-12-20, release date: 2018-07-18, Last modification date: 2024-03-13)

Primary citation

Domingues, M.N.,Souza, F.H.M.,Vieira, P.S.,de Morais, M.A.B.,Zanphorlin, L.M.,Dos Santos, C.R.,Pirolla, R.A.S.,Honorato, R.V.,de Oliveira, P.S.L.,Gozzo, F.C.,Murakami, M.T.
Structural basis of exo-beta-mannanase activity in the GH2 family.
J. Biol. Chem., 293:13636-13649, 2018

PubMed Abstract: The classical microbial strategy for depolymerization of β-mannan polysaccharides involves the synergistic action of at least two enzymes, endo-1,4-β-mannanases and β-mannosidases. In this work, we describe the first exo-β-mannanase from the GH2 family, isolated from pv. (XacMan2A), which can efficiently hydrolyze both manno-oligosaccharides and β-mannan into mannose. It represents a valuable process simplification in the microbial carbon uptake that could be of potential industrial interest. Biochemical assays revealed a progressive increase in the hydrolysis rates from mannobiose to mannohexaose, which distinguishes XacMan2A from the known GH2 β-mannosidases. Crystallographic analysis indicates that the active-site topology of XacMan2A underwent profound structural changes at the positive-subsite region, by the removal of the physical barrier canonically observed in GH2 β-mannosidases, generating a more open and accessible active site with additional productive positive subsites. Besides that, XacMan2A contains two residue substitutions in relation to typical GH2 β-mannosidases, Gly and Gly, which alter the active site volume and are essential to its mode of action. Interestingly, the only other mechanistically characterized mannose-releasing exo-β-mannanase so far is from the GH5 family, and its mode of action was attributed to the emergence of a blocking loop at the negative-subsite region of a cleft-like active site, whereas in XacMan2A, the same activity can be explained by the removal of steric barriers at the positive-subsite region in an originally pocket-like active site. Therefore, the GH2 exo-β-mannanase represents a distinct molecular route to this rare activity, expanding our knowledge about functional convergence mechanisms in carbohydrate-active enzymes.

PubMed: 29997257
DOI: 10.1074/jbc.RA118.002374

Experimental method

X-RAY DIFFRACTION (2.2 Å)