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Structure paper

TitleNew cofactor supports alpha , beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition.
Journal, issue, pagesNature, Vol. 522, Page 502-506, Year 2015
Publish dateApr 13, 2015 (structure data deposition date)
AuthorsPayne, K.A. / White, M.D. / Fisher, K. / Khara, B. / Bailey, S.S. / Parker, D. / Rattray, N.J. / Trivedi, D.K. / Goodacre, R. / Beveridge, R. ...Payne, K.A. / White, M.D. / Fisher, K. / Khara, B. / Bailey, S.S. / Parker, D. / Rattray, N.J. / Trivedi, D.K. / Goodacre, R. / Beveridge, R. / Barran, P. / Rigby, S.E. / Scrutton, N.S. / Hay, S. / Leys, D.
External linksNature / PubMed:26083754
MethodsX-ray diffraction
Resolution1.01 - 2.46 Å
Structure data

PDB-4za4:
Structure of A. niger Fdc1 with the prenylated-flavin cofactor in the iminium form.
Method: X-RAY DIFFRACTION / Resolution: 1.22 Å

PDB-4za5:
Structure of A. niger Fdc1 with the prenylated-flavin cofactor in the iminium and ketimine forms.
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-4za7:
Structure of A. niger Fdc1 in complex with alpha-methyl cinnamic acid
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-4za8:
Crystal structure of A niger Fdc1 in complex with penta-fluorocinnamic acid
Method: X-RAY DIFFRACTION / Resolution: 1.06 Å

PDB-4za9:
Structure of A. niger fdc1 in complex with a phenylpyruvate derived adduct to the prenylated flavin cofactor
Method: X-RAY DIFFRACTION / Resolution: 1.01 Å

PDB-4zaa:
Structure of A. niger Fdc1 in complex with 4-vinyl guaiacol
Method: X-RAY DIFFRACTION / Resolution: 1.242 Å

PDB-4zab:
Structure of A. niger Fdc1 in complex with alpha-fluoro cinnamic acid
Method: X-RAY DIFFRACTION / Resolution: 1.16 Å

PDB-4zac:
Structure of S. cerevisiae Fdc1 with the prenylated-flavin cofactor in the iminium form.
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-4zad:
Structure of C. dubliensis Fdc1 with the prenylated-flavin cofactor in the iminium form.
Method: X-RAY DIFFRACTION / Resolution: 2.46 Å

Chemicals

ChemComp-4LU:
1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y

ChemComp-MN:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-FZZ:
1-deoxy-5-O-phosphono-1-[(10aR)-2,2,3,4-tetramethyl-8,10-dioxo-1,2,8,9,10,10a-hexahydro-6H-indeno[1,7-ef]pyrimido[4,5-b][1,4]diazepin-6-yl]-D-ribitol

ChemComp-4LV:
(2E)-2-methyl-3-phenylprop-2-enoic acid

ChemComp-F5C:
penta-fluorocinnamic acid

ChemComp-4MJ:
1-deoxy-5-O-phosphono-1-[(1S)-3,3,4,5-tetramethyl-9,11-dioxo-1-(phenylacetyl)-2,3,8,9,10,11-hexahydro-1H,7H-quinolino[1

ChemComp-4M4:
2-Methoxy-4-vinylphenol

ChemComp-CO2:
CARBON DIOXIDE

ChemComp-4LW:
(2Z)-2-fluoro-3-phenylprop-2-enoic acid

ChemComp-NA:
Unknown entry

Source
  • aspergillus niger (mold)
  • aspergillus niger (strain cbs 513.88 / fgsc a1513) (mold)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • candida dubliniensis (yeast)
KeywordsLYASE / (de)carboxylase / prenylated flavin binding / UbiD-type enzyme / prenylated flavin / UbiD-like enzyme / UbiD-enzyme

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