Structural highlights
7yqs is a 1 chain structure with sequence from Fusarium oxysporum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
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| Method: | Hybrid , Neutron Diffraction , X-ray diffraction, Resolution 1.25Å |
| Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
A0A8D5PZ14_FUSOX
Publication Abstract from PubMed
Gum arabic (GA) is widely used as an emulsion stabilizer and edible coating and consists of a complex carbohydrate moiety with a rhamnosyl-glucuronate group capping the non-reducing ends. Enzymes that can specifically cleave the glycosidic chains of GA and modify their properties are valuable for structural analysis and industrial application. Cryogenic X-ray crystal structure of GA-specific L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum (FoRham1), belonging to the polysaccharide lyase (PL) family 42, has been previously reported. To determine the specific reaction mechanism based on its hydrogen-containing enzyme structure, we performed joint X-ray/neutron crystallography of FoRham1. Large crystals were grown in the presence of L-rhamnose (a reaction product), and neutron and X-ray diffraction datasets were collected at room temperature at 1.80 and 1.25 A resolutions, respectively. The active site contained L-rhamnose and acetate, the latter being a partial analog of glucuronate. Incomplete H/D exchange between Arg166 and acetate suggested that a strong salt-bridge interaction was maintained. Doubly deuterated His105 and deuterated Tyr150 supported the interaction between Arg166 and the acetate. The unique hydrogen-rich environment functions as a charge neutralizer for glucuronate and stabilizes the oxyanion intermediate. The NE2 atom of His85 was deprotonated and formed a hydrogen bond with the deuterated O1 hydroxy of L-rhamnose, indicating the function of His85 as the base/acid catalyst for bond cleavage via beta-elimination. Asp83 functions as a pivot between the two catalytic histidine residues by bridging them. This His-His-Asp structural motif is conserved in the PL 24, 25, and 42 families.
Charge neutralization and beta-elimination cleavage mechanism of family 42 L-rhamnose-alpha-1,4-D-glucuronate lyase revealed using neutron crystallography.,Yano N, Kondo T, Kusaka K, Arakawa T, Sakamoto T, Fushinobu S J Biol Chem. 2024 Mar;300(3):105774. doi: 10.1016/j.jbc.2024.105774. Epub 2024 , Feb 19. PMID:38382672[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yano N, Kondo T, Kusaka K, Arakawa T, Sakamoto T, Fushinobu S. Charge neutralization and β-elimination cleavage mechanism of family 42 L-rhamnose-α-1,4-D-glucuronate lyase revealed using neutron crystallography. J Biol Chem. 2024 Mar;300(3):105774. PMID:38382672 doi:10.1016/j.jbc.2024.105774
