6HY3 image
Deposition Date 2018-10-19
Release Date 2019-03-13
Last Version Date 2024-11-06
Entry Detail
PDB ID:
6HY3
Keywords:
Title:
Three-dimensional structure of AgaC from Zobellia galactanivorans
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.30 Å
R-Value Free:
0.16
R-Value Work:
0.14
R-Value Observed:
0.15
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Beta-agarase C
Gene (Uniprot):agaC
Chain IDs:A
Chain Length:272
Number of Molecules:1
Biological Source:Zobellia galactanivorans
Primary Citation
The agar-specific hydrolaseZgAgaC from the marine bacteriumZobellia galactanivoransdefines a new GH16 protein subfamily.
J.Biol.Chem. 294 6923 6939 (2019)
PMID: 30846563 DOI: 10.1074/jbc.RA118.006609

Abstact

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 (e.g. 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 Zobellia galactanivorans (ZgAgaC) 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 ZgAgaC hydrolyzes not only agarose but also complex agars from Ceramiales 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 ZgAgaC on agar extracted from Osmundea pinnatifida By resolving the crystal structure of ZgAgaC at high resolution (1.3 Å) and comparison with the structures of ZgAgaB and ZgPorA in complex with their respective substrates, we determined that ZgAgaC 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 ZgAgaC homologs define a new GH16 subfamily distinct from β-porphyranases and classical β-agarases.

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