4CE7

Crystal structure of a novel unsaturated beta-glucuronyl hydrolase enzyme, belonging to family GH105, involved in ulvan degradation

Summary for 4CE7

• Entry DOI: 10.2210/pdb4ce7/pdb
• Descriptor: UNSATURATED 3S-RHAMNOGLYCURONYL HYDROLASE, NITRATE ION (3 entities in total)
• Functional Keywords: hydrolase, exo-enzyme, ulvan degradation, family gh105, marine polysaccharide
• Biological source: NONLABENS ULVANIVORANS
• Total number of polymer chains: 3
• Total formula weight: 129671.57

Authors

Nyvall Collen, P.,Jeudy, A.,Groisillier, A.,Coutinho, P.M.,Helbert, W.,Czjzek, M. (deposition date: 2013-11-09, release date: 2014-01-22, Last modification date: 2024-05-08)

Primary citation

Nyvall-Collen, P.,Jeudy, A.,Sassi, J.,Groisillier, A.,Czjzek, M.,Coutinho, P.M.,Helbert, W.
A Novel Unsaturated Beta-Glucuronyl Hydrolase Involved in Ulvan Degradation Unveils the Versatility of Stereochemistry Requirements in Family Gh105.
J.Biol.Chem., 289:6199-, 2014

PubMed Abstract: Ulvans are cell wall matrix polysaccharides in green algae belonging to the genus Ulva. Enzymatic degradation of the polysaccharide by ulvan lyases leads to the production of oligosaccharides with an unsaturated β-glucuronyl residue located at the non-reducing end. Exploration of the genomic environment around the Nonlabens ulvanivorans (previously Percicivirga ulvanivorans) ulvan lyase revealed a gene highly similar to known unsaturated uronyl hydrolases classified in the CAZy glycoside hydrolase family 105. The gene was cloned, the protein was overexpressed in Escherichia coli, and enzymology experiments demonstrated its unsaturated β-glucuronyl activity. Kinetic analysis of purified oligo-ulvans incubated with the new enzyme showed that the full substrate specificity is attained by three subsites that preferentially bind anionic residues (sulfated rhamnose, glucuronic/iduronic acid). The three-dimensional crystal structure of the native enzyme reveals that a trimeric organization is required for substrate binding and recognition at the +2 binding subsite. This novel unsaturated β-glucuronyl hydrolase is part of a previously uncharacterized subgroup of GH105 members and exhibits only a very limited sequence similarity to known unsaturated β-glucuronyl sequences previously found only in family GH88. Clan-O formed by families GH88 and GH105 was singular in the fact that it covered families acting on both axial and equatorial glycosidic linkages, respectively. The overall comparison of active site structures between enzymes from these two families highlights how that within family GH105, and unlike for classical glycoside hydrolysis, the hydrolysis of vinyl ether groups from unsaturated saccharides occurs independently of the α or β configuration of the cleaved linkage.

PubMed: 24407291
DOI: 10.1074/JBC.M113.537480

Experimental method

X-RAY DIFFRACTION (1.9 Å)