4ZMH: Crystal structure of a five-domain GH115 alpha-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T

Citation:
Abstract
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 alpha-glucuronidases that release the alpha- (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.
PDB ID: 4ZMHDownload
MMDB ID: 138769
PDB Deposition Date: 2015/5/4
Updated in MMDB: 2016/08
Experimental Method:
x-ray diffraction
Resolution: 1.93  Å
Source Organism:
Similar Structures:
Biological Unit for 4ZMH: dimeric; determined by author and by software (PISA)
Molecular Components in 4ZMH
Label Count Molecule
Proteins (2 molecules)
2
Uncharacterized Protein
Molecule annotation
Chemicals (9 molecules)
1
4
2
2
3
2
4
1
* Click molecule labels to explore molecular sequence information.

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