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Literature summary for 2.3.2.20 extracted from

  • Schmitt, E.; Bourgeois, G.; Gondry, M.; Aleksandrov, A.
    Cyclization reaction catalyzed by cyclodipeptide synthases relies on a conserved tyrosine residue (2018), Sci. Rep., 8, 7031 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 2.3.2.20

Protein Variants

Protein Variants Comment Organism
Y202F the mutation does not affect the formation of the aminoacyl enzyme intermediate5, but leads to the accumulation of the covalent dipeptidyl enzyme intermediate, which is not observed with the wild-type enzyme Streptomyces noursei

Organism

Organism UniProt Comment Textmining
Streptomyces noursei Q8GED7
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Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information mechanism of cyclization with the participation of Y202 in the catalytic function, roles of important residues E182, Y178, N40, and H203, detailed overview Streptomyces noursei ?
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Synonyms

Synonyms Comment Organism
AlbC
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 Streptomyces noursei
CDPS
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 Streptomyces noursei
cyclodipeptide synthase
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 Streptomyces noursei

General Information

General Information Comment Organism
evolution the entire family of CDPSs can be classified into two subfamilies, so called NYH and XYP, characterized by the presence of specific sequence signatures at positions N40, Y202, and H203. The residues, N40 and H203 are suggested to play a role in the stabilization of other residues in the catalytic center and are not conserved among the CDPS family, but are important for the function of AlbC Streptomyces noursei
additional information analysis of the cyclization reaction in the cyclodipeptide synthase AlbC using QM/MM methods and free energy simulations, overview. The catalytic Y202 residue is in its neutral protonated form, and thus, is not likely to serve as a general base during the reaction. The reaction relies on the conserved residue Y202 serving as a proton relay, and the direct proton transfer from the amino group to S37 of AlbC is unlikely. Calculations reveal that the hydroxyl group of tyrosine is more suitable for the proton transfer than hydroxyl groups of other amino acids, such as serine and threonine. Residues E182, N40, Y178 and H203 maintain the correct conformation of the dipeptide needed for the cyclization reaction. The mechanism discovered relies on the amino groups conserved among the entire CDPS family and, thus is expected to be universal among CDPSs. Active site pocket structure of the AlbC cyclodipeptide synthase, overview. Residues N40 and H203 are important for the function of AlbC. Residue Y202 is strictly conserved and suggested to play a key role during the cyclization step of the reaction, Y202 is involved in the cyclization process. Analysis of the cyclization reaction catalyzed by AlbC using a set of simulation techniques, including free energy calculations using molecular mechanics (MM) to establish which group of the complex might participate as proton acceptor/donor, DFT hybrid quantum chemical (QM)/MM potentials together with reaction-path-finding algorithms to test possible mechanistic pathways, and QM/MM free energy calculations to determine reaction barriers, detailed overview Streptomyces noursei