4ZMH image
Deposition Date 2015-05-04
Release Date 2016-05-04
Last Version Date 2024-11-06
Entry Detail
PDB ID:
4ZMH
Keywords:
Title:
Crystal structure of a five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.93 Å
R-Value Free:
0.17
R-Value Work:
0.13
R-Value Observed:
0.13
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):Sde_1755
Chain IDs:A, B
Chain Length:939
Number of Molecules:2
Biological Source:Saccharophagus degradans
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MSE A MET modified residue
Primary Citation
Biochemical and Structural Characterization of a Five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T.
J.Biol.Chem. 291 14120 14133 (2016)
PMID: 27129264 DOI: 10.1074/jbc.M115.702944

Abstact

Glucuronic acid (GlcAp) and/or methylglucuronic acid (MeGlcAp) decorate the major forms of xylan in hardwood and coniferous softwoods as well as many cereal grains. Accordingly, the complete utilization of glucuronoxylans or conversion to sugar precursors requires the action of main chain xylanases as well as α-glucuronidases that release the α- (1→2)-linked (Me)GlcAp side groups. Herein, a family GH115 enzymefrom the marine bacterium Saccharophagus degradans 2-40(T), SdeAgu115A, demonstrated activity toward glucuronoxylan and oligomers thereof with preference toward MeGlcAp linked to internal xylopyranosyl residues. Unique biochemical characteristics of NaCl activation were also observed. The crystal structure of SdeAgu115A revealed a five-domain architecture, with an additional insertion C(+) domain that had significant impact on the domain arrangement of SdeAgu115A monomer and its dimerization. The participation of domain C(+) in substrate binding was supported by reduced substrate inhibition upon introducing W773A, W689A, and F696A substitutions within this domain. In addition to Asp-335, the catalytic essentiality of Glu-216 was revealed by site-specific mutagenesis. A primary sequence analysis suggested that the SdeAgu115A architecture is shared by more than half of GH115 members, thus defining a distinct archetype for GH115 enzymes.

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