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8j52

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Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase mutant D304A in complex with alpha-1,4-galactobiose

Structural highlights

8j52 is a 2 chain structure with sequence from Flavihumibacter petaseus NBRC 106054. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A0E9MUN5_9BACT

Publication Abstract from PubMed

Glycoside hydrolase family 31 (GH31) contains alpha-glycoside hydrolases with different substrate specificities involved in various physiological functions. This family has recently been classified into 20 subfamilies using sequence similarity networks. An alpha-galactosidase from the gut bacterium Bacteroides salyersiae (BsGH31_19, which belongs to GH31 subfamily 19) was reported to have hydrolytic activity against the synthetic substrate p- nitrophenyl alpha-galactopyranoside, but its natural substrate remained unknown. BsGH31_19 shares low sequence identity (around 20%) with other reported GH31 alpha-galactosidases, PsGal31A from Pseudopedobacter saltans and human myogenesis-regulating glycosidase (MYORG), and was expected to have distinct specificity. Here, we characterized BsGH31_19 and its ortholog from a soil Bacteroidota bacterium, Flavihumibacter petaseus (FpGH31_19), and demonstrated that they showed high substrate specificity against alpha-(1-->4)-linkages in alpha-(1-->4)-galactobiose and globotriose [alpha-Gal-(1-->4)-beta-Gal-(1-->4)-Glc], unlike PsGal31A and MYORG. The crystallographic analyses of BsGH31_19 and FpGH31_19 showed that their overall structures resemble those of MYORG and form a dimer with an interface different from that of PsGal31A and MYORG dimers. The structures of FpGH31_19 complexed with d-galactose and alpha-(1-->4)-galactobiose revealed that amino acid residues that recognize a galactose residue at subsite +1 are not conserved between FpGH31_19 and BsGH31_19. The tryptophan (Trp153) that recognizes galactose at subsite -1 is homologous to the tryptophan residues in MYORG and alpha-galactosidases belonging to GH27, GH36, and GH97, but not in the bacterial GH31 member PsGal31A. Our results provide structural insights into molecular diversity and evolutionary relationships in the GH31 alpha-galactosidase subfamilies and the other alpha-galactosidase families.

Structure-function analysis of bacterial GH31 alpha-galactosidases specific for alpha-(1-->4)-galactobiose.,Ikegaya M, Park EY, Miyazaki T FEBS J. 2023 Jul 12. doi: 10.1111/febs.16904. PMID:37438884^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ikegaya M, Park EY, Miyazaki T. Structure-function analysis of bacterial GH31 α-galactosidases specific for α-(1→4)-galactobiose. FEBS J. 2023 Jul 12. PMID:37438884 doi:10.1111/febs.16904