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Structure paper

TitleThe flavin mononucleotide cofactor in alpha-hydroxyacid oxidases exerts its electrophilic/nucleophilic duality in control of the substrate-oxidation level.
Journal, issue, pagesActa Crystallogr D Struct Biol, Vol. 75, Page 918-929, Year 2019
Publish dateJun 4, 2018 (structure data deposition date)
AuthorsLyu, S.Y. / Lin, K.H. / Yeh, H.W. / Li, Y.S. / Huang, C.M. / Wang, Y.L. / Shih, H.W. / Hsu, N.S. / Wu, C.J. / Li, T.L.
External linksActa Crystallogr D Struct Biol / PubMed:31588923
MethodsX-ray diffraction
Resolution1.31 - 2.511 Å
Structure data

PDB-5zzp:
The crystal structure of Mandelate oxidase
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-5zzr:
The crystal structure of Mandelate oxidase with (S)-mandelic acid
Method: X-RAY DIFFRACTION / Resolution: 1.31 Å

PDB-5zzz:
The crystal structure of Mandelate oxidase Y128C with benzoyl-formic acid
Method: X-RAY DIFFRACTION / Resolution: 1.446 Å

PDB-6a08:
The crystal structure of Mandelate oxidase with benzoyl-formic acid
Method: X-RAY DIFFRACTION / Resolution: 1.547 Å

PDB-6a0v:
Mandelate oxidase mutant-Y128F with (S)-mandelic acid
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-6a13:
Mandelate oxidase mutant-Y128F
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-6a19:
Mandelate oxidase mutant-Y128F with Benzoylformic acid
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-6a1h:
Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide
Method: X-RAY DIFFRACTION / Resolution: 1.36 Å

PDB-6a1l:
Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and benzoic acid
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-6a1m:
Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and benzoylformic acid
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-6a1p:
Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and phenylpyruvic acid
Method: X-RAY DIFFRACTION / Resolution: 1.51 Å

PDB-6a1r:
Mandelate oxidase mutant-Y128F with the N5-phenylacetyl-FMN adduct
Method: X-RAY DIFFRACTION / Resolution: 1.652 Å

PDB-6a21:
Mandelate oxidase mutant-Y128F with the N5-malonyl-FMN adduct
Method: X-RAY DIFFRACTION / Resolution: 1.501 Å

PDB-6a23:
Mandelate oxidase mutant-Y128F with the N5-benzyl-FMN adduct
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-6a3t:
The crystal structure of Mandelate oxidase R163L with 2-hydroxy-phenylacetamide
Method: X-RAY DIFFRACTION / Resolution: 2.511 Å

Chemicals

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

ChemComp-HOH:
WATER / Water

ChemComp-SMN:
(S)-MANDELIC ACID

ChemComp-173:
BENZOYL-FORMIC ACID / Phenylglyoxylic acid

ChemComp-MG:
Unknown entry

ChemComp-9O9:
1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol

ChemComp-BEZ:
BENZOIC ACID / Benzoic acid

ChemComp-PPY:
3-PHENYLPYRUVIC ACID / Phenylpyruvic acid

ChemComp-9OC:
1-deoxy-1-[7,8-dimethyl-2,4-dioxo-5-(phenylacetyl)-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol

ChemComp-9OR:
3-[7,8-dimethyl-2,4-bis(oxidanylidene)-10-[(2S,3S,4R)-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl]-1H-benzo[g]pteridin-5-yl]-3-oxidanylidene-propanoic acid

ChemComp-9OU:
1-[5-(benzenecarbonyl)-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-1-deoxy-5-O-phosphono-D-ribitol

ChemComp-9Q0:
1-{5-[(1S)-2-amino-1-hydroxy-2-oxo-1-phenylethyl]-7,8-dimethyl-2,4-dioxo-1,2,3,4-tetrahydrobenzo[g]pteridine-5,10-diium-10-yl}-1-deoxy-5-O-phosphono-D-ribitol

Source
  • amycolatopsis orientalis (bacteria)
KeywordsFLAVOPROTEIN / FMN-dependent oxidase

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