6HY3

Three-dimensional structure of AgaC from Zobellia galactanivorans

Summary for 6HY3

• Entry DOI: 10.2210/pdb6hy3/pdb
• Descriptor: Beta-agarase C, MAGNESIUM ION, GLYCEROL, ... (5 entities in total)
• Functional Keywords: glycoside hydrolase, zobellia galactanivorans, agar, marine bacteria, red algae, hydrolase
• Biological source: Zobellia galactanivorans
• Total number of polymer chains: 1
• Total formula weight: 31724.22

Authors

Naretto, A.,Fanuel, M.,Ropartz, D.,Rogniaux, H.,Larocque, R.,Czjzek, M.,Tellier, C.,Michel, G. (deposition date: 2018-10-19, release date: 2019-03-13, Last modification date: 2024-11-06)

Primary citation

Naretto, A.,Fanuel, M.,Ropartz, D.,Rogniaux, H.,Larocque, R.,Czjzek, M.,Tellier, C.,Michel, G.
The agar-specific hydrolaseZgAgaC from the marine bacteriumZobellia galactanivoransdefines a new GH16 protein subfamily.
J.Biol.Chem., 294:6923-6939, 2019

PubMed Abstract: Agars are sulfated galactans from red macroalgae and are composed of a d-galactose (G unit) and l-galactose (L unit) alternatively linked by α-1,3 and β-1,4 glycosidic bonds. These polysaccharides display high complexity, with numerous modifications of their backbone ( presence of a 3,6-anhydro-bridge (LA unit) and sulfations and methylation). Currently, bacterial polysaccharidases that hydrolyze agars (β-agarases and β-porphyranases) have been characterized on simple agarose and more rarely on porphyran, a polymer containing both agarobiose (G-LA) and porphyranobiose (GL6S) motifs. How bacteria can degrade complex agars remains therefore an open question. Here, we studied an enzyme from the marine bacterium (AgaC) that is distantly related to the glycoside hydrolase 16 (GH16) family β-agarases and β-porphyranases. Using a large red algae collection, we demonstrate that AgaC hydrolyzes not only agarose but also complex agars from s species. Using tandem MS analysis, we elucidated the structure of a purified hexasaccharide product, L6S-G-LA2Me-G(2Pentose)-LA2S-G, released by the activity of AgaC on agar extracted from By resolving the crystal structure of AgaC at high resolution (1.3 Å) and comparison with the structures of AgaB and PorA in complex with their respective substrates, we determined that AgaC recognizes agarose via a mechanism different from that of classical β-agarases. Moreover, we identified conserved residues involved in the binding of complex oligoagars and demonstrate a probable influence of the acidic polysaccharide's pH microenvironment on hydrolase activity. Finally, a phylogenetic analysis supported the notion that AgaC homologs define a new GH16 subfamily distinct from β-porphyranases and classical β-agarases.

PubMed: 30846563
DOI: 10.1074/jbc.RA118.006609

Experimental method

X-RAY DIFFRACTION (1.3 Å)