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Literature summary for 1.3.99.36 extracted from
- Convergent evolution of the Cys decarboxylases involved in aminovinyl-cysteine (AviCys) biosynthesis (2019), FEBS Lett., 593, 573-580 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene cypD, phylogenetic tree, recombinant expression of SeMet-substituted CypD in Escherichia coli strain BL21(DE3) | Streptomyces coelicolor |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified recombinant enzyme, X-ray diffraction structure determination and analysis at 2.6 A resolution | Streptomyces coelicolor |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 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 | - |
? |  |
| 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
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Streptomyces coelicolor | - |
- |
- |
| Streptomyces coelicolor M1414 | - |
- |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant SeMet-substituted CypD from Escherichia coli strain BL21(DE3) | Streptomyces coelicolor |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 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 | - |
? | |
| 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
| Subunits | Comment | Organism |
|---|---|---|
| dodecamer | a CypD monomer consists of a single classic Rossmann-fold domain, which is composed of a central beta-sheet formed by six parallel strands (labeled beta1-beta6) enclosed by eight alpha helices (labeled alpha1-alpha8). Residues that participate in forming the trimer (trimer contacts) are found in a region spanning alpha5 and alpha6, and a region containing alpha7 and a long loop in the terminus of alpha7, whereas interactions between trimers (dimer contacts) are found mainly within alpha1, and a region spanning alpha2 and alpha3 | Streptomyces coelicolor |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| CYPD | - |
Streptomyces coelicolor |
| cypemycin decarboxylase | - |
Streptomyces coelicolor |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| FAD | dependent on. Binding structure analysis, overview. Each monomer associates with a flavin adenine dinucleotide (FAD) cofactor. The adenine ring of FAD sits in the central cavity of a CypD trimer and forms no direct interactions with any monomers. The rest of the molecule is embedded only at the interface of two monomers, among which one predominantly interacts with FAD. This particular monomer mainly interacts with the phosphoribityl moiety of FAD via the residues in the N-termini of its three helices, namely, Ser18 in a1, Thr45 and Ala47 in a2, and Thr96 in alpha5. Specifically, Ser18, Leu97, and Thr128 form polar interactions with the isoalloxazine ring, whereas Thr45, Thr96, and Thr99 are hydrogen bonded to the oxygen atoms of phosphoribitol backbone. Meanwhile, Thr47, Arg107, and Asp109 interact with the adenosine monophosphate group: the first two residues form hydrogen bonds with the phosphate, whereas Asp109 forms similar interactions with two hydroxyl groups on the ribose ring. The second monomer forms much less interactions with FAD. Phe'51 has a weak hydrophobic contact with the isoalloxazine ring. Ala'108 and Arg'107 are hydrogen bonded to hydroxyls on the ribitol chain and ribose ring, respectively. Three water molecules are bound to the phosphoribityl backbone, of which one (Wat1) also interacts with N1 and O2 of the isoalloxazine ring. The crystal structure of the cypemycin decarboxylase CypD shows that CypD is structurally highly similar to lanthipeptide decarboxylases despite the absence of sequence similarities between them | Streptomyces coelicolor | |
| additional information | S-[(Z)-2-aminovinyl]-D-cysteine (AviCys) is a unique structural motif found in several classes of RiPPs, including lanthipeptides (e.g. epidermin), lipolanthines (e.g., microvionine), polythioamides (e.g. thioviridamide), and linaridins (e.g. cypemycin). Enzyme structure-function analysis, overview | Streptomyces coelicolor |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | flavin-dependent Cys decarboxylases are highly divergent among different RiPP classes. Cys decarboxylases from four RiPP classes have evolved independently and form two major clusters. Convergent evolution of AviCys biosynthesis, all the flavin-dependent Cys decarboxylases likely have a similar Rossmann fold despite their sequence divergences. Evolution of Cys decarboxylases involved in AviCys biosynthesis, overview | Streptomyces coelicolor |
| physiological function | S-[(Z)-2-aminovinyl]-D-cysteine (AviCys) is a unique motif found in several classes of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Biosynthesis of AviCys requires flavin-dependent Cys decarboxylases, which are highly divergent among different RiPP classes | Streptomyces coelicolor |
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