6a3d

From Proteopedia

The crystal structure of Mandelate oxidase Y128F with 4-Br-2-hydroxy-methylphenylacetate

Structural highlights

6a3d is a 1 chain structure with sequence from Amycolatopsis orientalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.923Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HMO_AMYOR Catalyzes the oxidation of p-hydroxymandelate to p-hydroxybenzoylformate in the biosynthesis of L-(4-hydroxyphenyl)glycine and L-(3,5-dihydroxyphenyl)glycine, 2 non-proteinogenic amino acids occurring in the vancomycin group of antibiotics.^[1] ^[2]

Publication Abstract from PubMed

Though reactive flavin-N5/C4alpha-oxide intermediates can be spectroscopically profiled for some flavin-assisted enzymatic reactions, their exact chemical configurations are hardly visualized. Structural systems biology and stable isotopic labelling techniques were exploited to correct this stereotypical view. Three transition-like complexes, the alpha-ketoacid...N5-FMN(ox) complex (I), the FMN(ox) -N5-aloxyl-C'alpha(-) -C4alpha(+) zwitterion (II), and the FMN-N5-ethenol-N5-C4alpha-epoxide (III), were determined from mandelate oxidase (Hmo) or its mutant Y128F (monooxygenase) crystals soaked with monofluoropyruvate (a product mimic), establishing that N5 of FMN(ox) an alternative reaction center can polarize to an ylide-like mesomer in the active site. In contrast, four distinct flavin-C4alpha-oxide adducts (IV-VII) from Y128F crystals soaked with selected substrates materialize C4alpha of FMN an intrinsic reaction center, witnessing oxidation, Baeyer-Villiger/peroxide-assisted decarboxylation, and epoxidation reactions. In conjunction with stopped-flow kinetics, the multifaceted flavin-dependent reaction continuum is physically dissected at molecular level for the first time.

Structural and chemical trapping of flavin-oxide intermediates reveals substrate-directed reaction multiplicity.,Lin KH, Lyu SY, Yeh HW, Li YS, Hsu NS, Huang CM, Wang YL, Shih HW, Wang ZC, Wu CJ, Li TL Protein Sci. 2020 Jul;29(7):1655-1666. doi: 10.1002/pro.3879. Epub 2020 May 26. PMID:32362037^[3]

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

References

↑ Hubbard BK, Thomas MG, Walsh CT. Biosynthesis of L-p-hydroxyphenylglycine, a non-proteinogenic amino acid constituent of peptide antibiotics. Chem Biol. 2000 Dec;7(12):931-42. PMID:11137816
↑ Li TL, Choroba OW, Charles EH, Sandercock AM, Williams DH, Spencer JB. Characterisation of a hydroxymandelate oxidase involved in the biosynthesis of two unusual amino acids occurring in the vancomycin group of antibiotics. Chem Commun (Camb). 2001 Sep 21;(18):1752-3. PMID:12240298
↑ Lin KH, Lyu SY, Yeh HW, Li YS, Hsu NS, Huang CM, Wang YL, Shih HW, Wang ZC, Wu CJ, Li TL. Structural and chemical trapping of flavin-oxide intermediates reveals substrate-directed reaction multiplicity. Protein Sci. 2020 Jul;29(7):1655-1666. PMID:32362037 doi:10.1002/pro.3879