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Literature summary extracted from

  • Liu, L.; Chan, S.; Mo, T.; Ding, W.; Yu, S.; Zhang, Q.; Yuan, S.
    Movements of the substrate-binding clamp of cypemycin decarboxylase CypD (2019), J. Chem. Inf. Model., 59, 2924-2929 .
    View publication on PubMed

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.3.99.36 cypemycin(1-18)-L-Cys-L-Leu-L-Val-L-Cys + acceptor Streptomyces coelicolor
-
 C3.19,S21-cyclocypemycin(1-18)-L-Ala-L-Leu-N-thioethenyl-L-valinamide + CO2 + H2S + reduced acceptor
-
 ?
1.3.99.36 cypemycin(1-18)-L-Cys-L-Leu-L-Val-L-Cys + acceptor Streptomyces coelicolor M1414
-
 C3.19,S21-cyclocypemycin(1-18)-L-Ala-L-Leu-N-thioethenyl-L-valinamide + CO2 + H2S + reduced acceptor
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.3.99.36 Streptomyces coelicolor
-
-
-
1.3.99.36 Streptomyces coelicolor M1414
-
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.3.99.36 cypemycin(1-18)-L-Cys-L-Leu-L-Val-L-Cys + acceptor
-
 Streptomyces coelicolor C3.19,S21-cyclocypemycin(1-18)-L-Ala-L-Leu-N-thioethenyl-L-valinamide + CO2 + H2S + reduced acceptor
-
 ?
1.3.99.36 cypemycin(1-18)-L-Cys-L-Leu-L-Val-L-Cys + acceptor
-
 Streptomyces coelicolor M1414 C3.19,S21-cyclocypemycin(1-18)-L-Ala-L-Leu-N-thioethenyl-L-valinamide + CO2 + H2S + reduced acceptor
-
 ?

Subunits

EC Number Subunits Comment Organism
1.3.99.36 dodecamer each monomer consists of a classic Rossmann-fold domain. This domain is constructed by a central beta sheet consisting of six parallel strands, which are enclosed by eight alpha helices. A fragment spanning Asn156-Ala166 is not observed in the CypD structure, which is likely responsible in substrate binding Streptomyces coelicolor

Synonyms

EC Number Synonyms Comment Organism
1.3.99.36 CYPD
-
 Streptomyces coelicolor
1.3.99.36 cypemycin decarboxylase
-
 Streptomyces coelicolor

Cofactor

EC Number Cofactor Comment Organism Structure
1.3.99.36 FAD dependent on Streptomyces coelicolor

General Information

EC Number General Information Comment Organism
1.3.99.36 evolution CypD possesses a structural fold highly similar to two structurally characterized LanDs (EpiD in epidermin biosynthesis and MrsD in mersacidin biosynthesis). Similar to CypD, the substrate binding clamps are also not observed in the crystal structures of EpiD and MrsD when the peptide substrate is absent. But because CypD shares no detectable sequence similarity with these two LanDs, this finding reveals a convergent evolution in AviCys biosynthesis Streptomyces coelicolor
1.3.99.36 additional information movements of the substrate-binding clamp of cypemycin decarboxylase CypD, mechanism, substrate-induced secondary structure change in CypD, overview. The substrate binding clamp of CypD undergoes dramatic fluctuation. Structure and motion of the missing region by performing 3 × 300 ns unbiased molecular dynamics (MD) analysis, and principle component analysis (PCA) is utilized to analyze the protein backbone motion in MD trajectory. The substrate binding clamp of CypD undergoes dramatic fluctuation, mediating both the substrate entrance into and product release from the catalytic pocket. Extensive molecular dynamic simulations and Fourier transform IR analyses indicate that binding of the substrate induces substantial structural change of the enzyme, converting the substrate-binding clamp from a random loop to a more ordered structure comprising two beta sheets and a beta turn. The salt bridge between Arg159 guanine and the Cys carboxylate of substrate plays an important role in mediating substrate binding, while hydrophobic interactions are also important in this process. Computational construction of a CypD-substrate complex and interaction analysis. The carboxyl group of substrate forms a salt bridge with the guanine moiety of Arg159 and also hydrogen bonds with the amide NH of Ala160 and Ser161. A hydrogen bond is also found between the Val158 C=O and the penultimate amide NH in the C-terminus. The substrate also interacts with several residues (e.g. Leu23, Trp26, Trp27, Val155, Val168) via hydrophobic interactions Streptomyces coelicolor
1.3.99.36 physiological function linaridins are a small but growing class of natural products belonging to the ribosomally synthesized and posttranslationally modified peptide (RiPP) superfamily. The class A linaridins, exemplified by cypemycin, possess an unusual S-[(Z)-2-aminovinyl]-D-cysteine (AviCys) residue. Formation of the AviCys in cypemycin requires an oxidative decarboxylation of the precursor peptide C-terminal Cys, and this reaction is catalyzed by a flavin-dependent decarboxylase CypD. Analysis of the molecular recognition processes of CypD by a combination of computational and biochemical analysis, overview Streptomyces coelicolor