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Structure paper

TitleThe role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis.
Journal, issue, pagesJ. Biol. Chem., Vol. 293, Page 2272-2287, Year 2018
Publish dateNov 1, 2017 (structure data deposition date)
AuthorsBailey, S.S. / Payne, K.A.P. / Fisher, K. / Marshall, S.A. / Cliff, M.J. / Spiess, R. / Parker, D.A. / Rigby, S.E.J. / Leys, D.
External linksJ. Biol. Chem. / PubMed:29259125
MethodsX-ray diffraction
Resolution1.03 - 2.06 Å
Structure data

PDB-6ev3:
Structure of wild type A. niger Fdc1 that has been illuminated with UV light, with prFMN in the iminium and ketimine form
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-6ev4:
Structure of wild type A. niger Fdc1 purified in the dark with prFMN in the iminium form
Method: X-RAY DIFFRACTION / Resolution: 1.14 Å

PDB-6ev5:
Crystal structure of E282Q A. niger Fdc1 with prFMN in the hydroxylated form
Method: X-RAY DIFFRACTION / Resolution: 1.28 Å

PDB-6ev6:
Structure of E282Q A. niger Fdc1 with prFMN in the hydroxylated and ketimine forms
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-6ev7:
Structure of E282D A. niger Fdc1 with prFMN in the iminium form
Method: X-RAY DIFFRACTION / Resolution: 1.06 Å

PDB-6ev8:
Structure of E277Q A. niger Fdc1 with prFMN in the hydroxylated form
Method: X-RAY DIFFRACTION / Resolution: 1.03 Å

PDB-6ev9:
Structure of E277D A. niger Fdc1 with prFMN in the hydroxylated form
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-6eva:
Structure of E277Q A. niger fdc1 in complex with a phenylpyruvate derived adduct to the prenylated flavin cofactor
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-6evb:
Structure of E282Q A. niger Fdc1 with prFMN in the iminium form
Method: X-RAY DIFFRACTION / Resolution: 1.13 Å

PDB-6evc:
Structure of E282Q A. niger Fdc1 in complex with pentafluoro-cinnamic acid
Method: X-RAY DIFFRACTION / Resolution: 1.18 Å

PDB-6evd:
Structure of R173A A. niger Fdc1 with prFMN in the hydroxylated form
Method: X-RAY DIFFRACTION / Resolution: 1.19 Å

PDB-6eve:
Structure of R175A S. cerevisiae Fdc1 with prFMN in the iminium form
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-6evf:
Structure of E285D S. cerevisiae Fdc1 with prFMN in the hydroxylated form
Method: X-RAY DIFFRACTION / Resolution: 2.06 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-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-HOH:
WATER

ChemComp-BYN:
hydroxylated prenyl-FMN

ChemComp-SCN:
THIOCYANATE ION

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-F5C:
penta-fluorocinnamic acid

Source
  • aspergillus niger (mold)
  • aspergillus niger (strain cbs 513.88 / fgsc a1513) (mold)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
KeywordsLYASE

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