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Structure paper

TitleAtomic description of an enzyme reaction dependent on reversible 1,3-dipolar cycloaddition
Journal, issue, pagesTo Be Published
Publish dateMar 18, 2019 (structure data deposition date)
AuthorsBailey, S.S. / Payne, K.A.P. / Saaret, A. / Marshall, S.A. / Gostimskaya, I. / Kosov, I. / Fisher, K. / Hay, S. / Leys, D.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution1.01 - 1.39 Å
Structure data

PDB-6r2p:
Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with FMN and cinnamic acid
Method: X-RAY DIFFRACTION / Resolution: 1.26 Å

PDB-6r2r:
Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with prFMN (purified in dark) and alphafluorocinnamic acid
Method: X-RAY DIFFRACTION / Resolution: 1.13 Å

PDB-6r2t:
Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with prFMN (purified in the radical form) and phenylpropiolic acid
Method: X-RAY DIFFRACTION / Resolution: 1.29 Å

PDB-6r2z:
Aspergillus niger ferulic acid decarboxylase (Fdc) F437L variant in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid (Int1')
Method: X-RAY DIFFRACTION / Resolution: 1.08 Å

PDB-6r30:
Aspergillus niger ferulic acid decarboxylase (Fdc) L439G variant in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid (Int1')
Method: X-RAY DIFFRACTION / Resolution: 1.12 Å

PDB-6r32:
Aspergillus niger ferrulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid (Int1')
Method: X-RAY DIFFRACTION / Resolution: 1.21 Å

PDB-6r33:
Aspergillus niger ferulic acid decarboxylase (Fdc)in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid, following decarboxylation (Int3')
Method: X-RAY DIFFRACTION / Resolution: 1.01 Å

PDB-6r34:
Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and phenyl acetylene (Int3')
Method: X-RAY DIFFRACTION / Resolution: 1.1 Å

PDB-6r3f:
Aspergillus niger ferulic acid decarboxylase (Fdc) E282Q variant in complex with the covalent adduct formed between prFMN cofactor and cinnamic acid (Int2)
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-6r3g:
Aspergillus niger ferulic acid decarboxylase (Fdc) E282Q variant in complex with the covalent adduct formed between prFMN cofactor and alphafluoro-cinnamic acid (Int2)
Method: X-RAY DIFFRACTION / Resolution: 1.13 Å

PDB-6r3i:
Aspergillus niger ferulic acid decarboxylase (Fdc) E282Q variant in complex with the covalent adduct formed between prFMN cofactor and pentafluorocinnamic acid (Int2)
Method: X-RAY DIFFRACTION / Resolution: 1.14 Å

PDB-6r3j:
Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and crotonic acid following decarboxylation (Int3)
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-6r3l:
Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and cinnamic acid following decarboxylation (Int3)
Method: X-RAY DIFFRACTION / Resolution: 1.24 Å

PDB-6r3n:
Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and butynoic acid (Int1')
Method: X-RAY DIFFRACTION / Resolution: 1.02 Å

PDB-6r3o:
Aspergillus niger ferric acid decarboxylase (Fdc) L439G variant in complex with prFMN (purified in the radical form) and phenylpropiolic acid
Method: X-RAY DIFFRACTION / Resolution: 1.13 Å

Chemicals

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

ChemComp-MN:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-TCA:
PHENYLETHYLENECARBOXYLIC ACID

ChemComp-HOH:
WATER

ChemComp-BYN:
hydroxylated prenyl-FMN

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

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-JQ8:
phenylpropiolic acid

ChemComp-JQZ:
prFMN cofactor and phenylpropiolic acid

ChemComp-JQH:
prFMN cofactor and phenylpropiolic acid adduct

ChemComp-JQK:
[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[(16~{R})-11,12,14,14-tetramethyl-5-oxidanyl-3-oxidanylidene-16-(2-phenylethyl)-1,4,6,8-tetrazatetracyclo[7.7.1.0^{2,7}.0^{13,17}]heptadeca-2(7),5,9(17),10,12-pentaen-8-yl]pentyl] dihydrogen phosphate

ChemComp-JQQ:
[(2~{R},3~{S},4~{S})-5-[(16~{S})-16-[(1~{S})-1-fluoranyl-2-phenyl-ethyl]-11,12,14,14-tetramethyl-5-oxidanyl-3-oxidanylidene-1,4,6,8-tetrazatetracyclo[7.7.1.0^{2,7}.0^{13,17}]heptadeca-2(7),5,9(17),10,12-pentaen-8-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate

ChemComp-JRN:
prFMN cofactor and pentafluorocinnamic acid adduct

ChemComp-JRH:
prFMN cofactor and crotonic acid adduct

ChemComp-JSH:
prFMN cofactor and cinnamic acid adduct

ChemComp-SYN:
ethenylbenzene

ChemComp-JRK:
prFMN cofactor and butynoic acid adduct

Source
  • aspergillus niger (mold)
KeywordsLYASE / (de)carboxylase / UbiD / prFMN binding

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