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Literature summary extracted from

  • Borgman, P.; Lopez, R.; Lane, A.
    The expanding spectrum of diketopiperazine natural product biosynthetic pathways containing cyclodipeptide synthases (2019), Org. Biomol. Chem., 17, 2305-2314 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.3.2.B16 gene dmtB1, recombinant expression of the gene cluster dmtB1-dmtC1 from Streptomyces youssoufiensis in Streptomyces coelicolor results in production of cyclic Trp-Pro, cyclic Trp-Val, and cycic Trp-Leu derivatives with a farnesyl group at indole C-3, dubbed pre-drimentines (e.g. pre-drimentine G = (3S,5aS,10bS,11aS)-3-(propan-2-yl)-10b-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]-6,10b,11,11a-tetrahydro-2H-pyrazino[1',2':1,5]pyrrolo[2,3-b]indole-1,4(3H,5aH)-dione) Streptomyces youssoufiensis
2.3.2.B16 recombinant expression in Streptomyces coelicolor, recombinant expression of the CDPS in Escherichia coli results in accumulation of cyclo(L-tryptophanyl-L-tryptophanyl) as the sole detectable 2,5-diketopiperazine (DKP) product Streptomyces sp.
2.3.2.20 gene bmcA, recombinant expression of the bcm cluster in heterologous host Streptomyces coelicolor, resulting in production of bicyclomycin Pseudomonas aeruginosa

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.3.2.B16 2 L-tryptophanyl-tRNATrp Streptomyces sp.
-
 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 2 L-tryptophanyl-tRNATrp Actinosynnema mirum
-
 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 2 L-tryptophanyl-tRNATrp Actinosynnema mirum NBRC 14064
-
 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 2 L-tryptophanyl-tRNATrp Actinosynnema mirum ATCC 29888
-
 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 2 L-tryptophanyl-tRNATrp Actinosynnema mirum IMRU 3971
-
 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 2 L-tryptophanyl-tRNATrp Actinosynnema mirum DSM 43827
-
 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 L-tryptophanyl-tRNATrp + L-prolyl-tRNAPro Streptomyces sp.
-
 tRNATrp + tRNAPro + cyclo(L-tryptophanyl-L-prolyl)
-
 ?
2.3.2.B16 L-tryptophanyl-tRNATrp + L-valyl-tRNAVal Streptomyces youssoufiensis
-
 tRNATrp + tRNAVal + cyclo(L-tryptophanyl-L-valyl)
-
 ?
2.3.2.20 L-phenylalanyl-tRNAPhe + L-leucyl-tRNALeu Streptomyces noursei
-
 tRNAPhe + tRNALeu + cyclo(L-phenylalanyl-L-leucyl)
-
 ?
2.3.2.20 additional information Streptomyces noursei assembly of the cyclo-Phe-Leu precursor of albonoursin is catalyzed by CDPS AlbC, which also yields a variety of other cyclic dipeptides as minor products ?
-
-
2.3.2.21 2 L-tyrosyl-tRNATyr Mycobacterium tuberculosis
-
 2 tRNATyr + cyclo(L-tyrosyl-L-tyrosyl)
-
 ?
2.3.2.21 additional information Mycobacterium tuberculosis Rv2275 is established as a CDPS that catalyzes formation of cyclo(L-tyrosyl-L-tyrosyl) as its major product, along with a handful of minor products containing tyrosine ?
-
-
2.3.2.22 L-leucyl-tRNALeu + L-leucyl-tRNALeu Bacillus spizizenii
-
 tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
-
 ?
2.3.2.22 L-leucyl-tRNALeu + L-leucyl-tRNALeu Bacillus spizizenii W23
-
 tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
-
 ?
2.3.2.22 L-leucyl-tRNALeu + L-leucyl-tRNALeu Bacillus spizizenii NRRL B-14472
-
 tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
-
 ?
2.3.2.22 L-leucyl-tRNALeu + L-leucyl-tRNALeu Bacillus spizizenii ATCC 23059
-
 tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
-
 ?
2.3.2.22 additional information Bacillus spizizenii the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue ?
-
-
2.3.2.22 additional information Bacillus spizizenii W23 the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue ?
-
-
2.3.2.22 additional information Bacillus spizizenii NRRL B-14472 the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue ?
-
-
2.3.2.22 additional information Bacillus spizizenii ATCC 23059 the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue ?
-
-

Organism

EC Number Organism UniProt Comment Textmining
2.3.2.B16 Actinosynnema mirum C6WMU7
-
-
2.3.2.B16 Actinosynnema mirum ATCC 29888 C6WMU7
-
-
2.3.2.B16 Actinosynnema mirum DSM 43827 C6WMU7
-
-
2.3.2.B16 Actinosynnema mirum IMRU 3971 C6WMU7
-
-
2.3.2.B16 Actinosynnema mirum NBRC 14064 C6WMU7
-
-
2.3.2.B16 Streptomyces sp.
-
-
-
2.3.2.B16 Streptomyces youssoufiensis A0A343VTS2
-
-
2.3.2.20 Nocardiopsis dassonvillei D7B1W8
-
-
2.3.2.20 Nocardiopsis dassonvillei CIP 107115 D7B1W8
-
-
2.3.2.20 Nocardiopsis dassonvillei DSM 43111 D7B1W8
-
-
2.3.2.20 Nocardiopsis dassonvillei IMRU 509 D7B1W8
-
-
2.3.2.20 Nocardiopsis dassonvillei JCM 7437 D7B1W8
-
-
2.3.2.20 Nocardiopsis dassonvillei KCTC 9190 D7B1W8
-
-
2.3.2.20 Nocardiopsis dassonvillei NBRC 14626 D7B1W8
-
-
2.3.2.20 Nocardiopsis dassonvillei NCTC 10488 D7B1W8
-
-
2.3.2.20 Nocardiopsis dassonvillei NRRL B-5397 D7B1W8
-
-
2.3.2.20 Pseudomonas aeruginosa
-
-
-
2.3.2.20 Streptomyces noursei Q8GED7
-
-
2.3.2.21 Mycobacterium tuberculosis P9WPF9
-
-
2.3.2.22 Bacillus spizizenii E0U3N2
-
-
2.3.2.22 Bacillus spizizenii ATCC 23059 E0U3N2
-
-
2.3.2.22 Bacillus spizizenii NRRL B-14472 E0U3N2
-
-
2.3.2.22 Bacillus spizizenii W23 E0U3N2
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.3.2.B16 2 L-tryptophanyl-tRNATrp
-
 Streptomyces sp. 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 2 L-tryptophanyl-tRNATrp
-
 Actinosynnema mirum 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 2 L-tryptophanyl-tRNATrp
-
 Actinosynnema mirum NBRC 14064 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 2 L-tryptophanyl-tRNATrp
-
 Actinosynnema mirum ATCC 29888 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 2 L-tryptophanyl-tRNATrp
-
 Actinosynnema mirum IMRU 3971 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 2 L-tryptophanyl-tRNATrp
-
 Actinosynnema mirum DSM 43827 2 tRNATrp + cyclo(L-tryptophanyl-L-tryptophanyl)
-
 ?
2.3.2.B16 L-tryptophanyl-tRNATrp + L-prolyl-tRNAPro
-
 Streptomyces sp. tRNATrp + tRNAPro + cyclo(L-tryptophanyl-L-prolyl)
-
 ?
2.3.2.B16 L-tryptophanyl-tRNATrp + L-valyl-tRNAVal
-
 Streptomyces youssoufiensis tRNATrp + tRNAVal + cyclo(L-tryptophanyl-L-valyl)
-
 ?
2.3.2.20 L-phenylalanyl-tRNAPhe + L-leucyl-tRNALeu
-
 Streptomyces noursei tRNAPhe + tRNALeu + cyclo(L-phenylalanyl-L-leucyl)
-
 ?
2.3.2.20 additional information assembly of the cyclo-Phe-Leu precursor of albonoursin is catalyzed by CDPS AlbC, which also yields a variety of other cyclic dipeptides as minor products Streptomyces noursei ?
-
-
2.3.2.21 2 L-tyrosyl-tRNATyr
-
 Mycobacterium tuberculosis 2 tRNATyr + cyclo(L-tyrosyl-L-tyrosyl)
-
 ?
2.3.2.21 additional information Rv2275 is established as a CDPS that catalyzes formation of cyclo(L-tyrosyl-L-tyrosyl) as its major product, along with a handful of minor products containing tyrosine Mycobacterium tuberculosis ?
-
-
2.3.2.22 L-leucyl-tRNALeu + L-leucyl-tRNALeu
-
 Bacillus spizizenii tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
-
 ?
2.3.2.22 L-leucyl-tRNALeu + L-leucyl-tRNALeu
-
 Bacillus spizizenii W23 tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
-
 ?
2.3.2.22 L-leucyl-tRNALeu + L-leucyl-tRNALeu
-
 Bacillus spizizenii NRRL B-14472 tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
-
 ?
2.3.2.22 L-leucyl-tRNALeu + L-leucyl-tRNALeu
-
 Bacillus spizizenii ATCC 23059 tRNALeu + tRNALeu + cyclo(L-leucyl-L-leucyl)
-
 ?
2.3.2.22 additional information the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue Bacillus spizizenii ?
-
-
2.3.2.22 additional information the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue Bacillus spizizenii W23 ?
-
-
2.3.2.22 additional information the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue Bacillus spizizenii NRRL B-14472 ?
-
-
2.3.2.22 additional information the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue Bacillus spizizenii ATCC 23059 ?
-
-

Synonyms

EC Number Synonyms Comment Organism
2.3.2.B16 amir_4627
-
 Actinosynnema mirum
2.3.2.B16 CDPS
-
 Streptomyces sp.
2.3.2.B16 CDPS
-
 Streptomyces youssoufiensis
2.3.2.B16 CDPS
-
 Actinosynnema mirum
2.3.2.B16 cyclodipeptide synthase
-
 Streptomyces sp.
2.3.2.B16 cyclodipeptide synthase
-
 Streptomyces youssoufiensis
2.3.2.B16 cyclodipeptide synthase
-
 Actinosynnema mirum
2.3.2.B16 DmtB
-
 Streptomyces youssoufiensis
2.3.2.B16 dmtB1
-
 Streptomyces youssoufiensis
2.3.2.B16 NascA
-
 Streptomyces sp.
2.3.2.20 AlbC
-
 Streptomyces noursei
2.3.2.20 BcmA
-
 Pseudomonas aeruginosa
2.3.2.20 CDPS
-
 Pseudomonas aeruginosa
2.3.2.20 CDPS
-
 Streptomyces noursei
2.3.2.20 CDPS
-
 Nocardiopsis dassonvillei
2.3.2.20 cyclodipeptide synthase
-
 Pseudomonas aeruginosa
2.3.2.20 cyclodipeptide synthase
-
 Streptomyces noursei
2.3.2.20 cyclodipeptide synthase
-
 Nocardiopsis dassonvillei
2.3.2.20 Ndas_1148
-
 Nocardiopsis dassonvillei
2.3.2.21 CDPS
-
 Mycobacterium tuberculosis
2.3.2.21 cyclodipeptide synthase
-
 Mycobacterium tuberculosis
2.3.2.21 Rv2275
-
 Mycobacterium tuberculosis
2.3.2.22 CDPS
-
 Bacillus spizizenii
2.3.2.22 cyclodipeptide synthase
-
 Bacillus spizizenii
2.3.2.22 YvmC
-
 Bacillus spizizenii

General Information

EC Number General Information Comment Organism
2.3.2.B16 evolution genome sequences from three Streptomyces strains share a homologous locus predicted to encode a CDPS (DmtB), membrane-associated terpene cyclase (DmtA), and phytoene synthase (DmtC) Streptomyces youssoufiensis
2.3.2.B16 evolution methyltransferase homologues are commonly encoded within putative CDPS gene clusters,47 yet methyltransferases from only two of these clusters have been characterized to date. One leads to methylated members of the nocazine/XR334 (e.g. XR334) family and the other catalyzes DKP N-methylation of cyclo(L-tryptophanyl-L-tryptophanyl) (cWW) to yield dimethyl-cyclo-Trp-Trp (Me2-cWW) Actinosynnema mirum
2.3.2.B16 metabolism comparison of different CDPS-containing biosynthetic pathways, enzyme DmtB is involved in the drimentine G (i.e. (3S,5aS,10bS,11aS)-3-(propan-2-yl)-10b-[[(8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]methyl]-6,10b,11,11a-tetrahydro-2H-pyrazino[1',2':1,5]pyrrolo[2,3-b]indole-1,4(3H,5aH)-dione) biosynthetic pathway, overview Streptomyces youssoufiensis
2.3.2.B16 metabolism comparison of different CDPS-containing biosynthetic pathways, the enzyme encoded by amir_4627 is involved in the dimethyl-cyclo-Trp-Trp (cWW) (Me2-cWW) biosynthetic pathway, it possesses an additional intrinsic methyltransferase activity, overview Actinosynnema mirum
2.3.2.B16 metabolism comparison of different CDPS-containing biosynthetic pathways, the enzyme is involved in the 1-(8-guaninyl)-cyclic-Trp-Trp (i.e. 1-(8-guaninyl)-cWW or (3S,6S)-3-[[1-(2-amino-6-oxo-6,9-dihydro-1H-purin-8-yl)-2,3-dihydro-1H-indol-3-yl]methyl]-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione) biosynthetic pathway, overview Streptomyces sp.
2.3.2.B16 metabolism comparison of nine different CDPS-containing biosynthetic pathways, enzyme NascA is involved in the naseseazine C biosynthetic pathway, overview. Unlike fungal biosynthetic pathways that utilize NRPSs to form DKP precursors of dimeric DKPs, biogenesis of naseseazine C from a marine-derived Streptomyces sp. is linked to a CDPS-containing gene cluster, nascA-nascB, via heterologous expression of this pathway in Streptomyces albus. Sequence homology to characterized CDPSs implicated NascA in assembly of the cyclo(L-tryptophanyl-L-prolyl) (cWP) precursor of naseseazine C, while functional characterization of purified recombinant NascB establishes it as the cytochrome P450 catalyst of intermolecular C-C bond formation between two cWP precursors Streptomyces sp.
2.3.2.B16 additional information the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS Streptomyces sp.
2.3.2.B16 additional information the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS Streptomyces youssoufiensis
2.3.2.B16 additional information the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS Actinosynnema mirum
2.3.2.B16 physiological function cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview Streptomyces sp.
2.3.2.B16 physiological function cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview Streptomyces youssoufiensis
2.3.2.B16 physiological function cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview Actinosynnema mirum
2.3.2.20 evolution methyltransferase homologues are commonly encoded within putative CDPS gene clusters, yet methyltransferases from only two of these clusters have been characterized to date. One leads to methylated members of the nocazine/XR334 (e.g. XR334) family and the other catalyzes DKP N-methylation of cyclo(L-tryptophanyl-L-tryptophanyl) (cWW) to yield dimethyl-cyclo-Trp-Trp (Me2-cWW) Nocardiopsis dassonvillei
2.3.2.20 metabolism comparison of different CDPS-containing biosynthetic pathways, enzyme AlbC is involved in the albonoursin biosynthetic pathway, overview. Assembly of the cyclo-Phe-Leu precursor of albonoursin is catalyzed by CDPS AlbC, which also yields a variety of other cyclic dipeptides as minor products Streptomyces noursei
2.3.2.20 metabolism comparison of different CDPS-containing biosynthetic pathways, enzyme BcmA is involved in the bicyclomycin biosynthetic pathway, overview. The proposed bicyclomycin (i.e. (1S,6R)-6-hydroxy-5-methylidene-1-[(2S)-1,2,3-trihydroxy-2-methylpropyl]-2-oxa-7,9-diazabicyclo[4.2.2]decane-8,10-dione) biosynthetic pathway features a cascade of oxidative transformations Pseudomonas aeruginosa
2.3.2.20 metabolism comparison of different CDPS-containing biosynthetic pathways, the enzyme encoded by gene ndas_1148 is involved in the XR334 (i.e. (3Z,6Z)-3-benzylidene-6-[(4-methoxyphenyl)methylidene]piperazine-2,5-dione) biosynthetic pathway, overview Nocardiopsis dassonvillei
2.3.2.20 additional information the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS Pseudomonas aeruginosa
2.3.2.20 additional information the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS Streptomyces noursei
2.3.2.20 additional information the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS Nocardiopsis dassonvillei
2.3.2.20 physiological function cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview Pseudomonas aeruginosa
2.3.2.20 physiological function cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview Streptomyces noursei
2.3.2.20 physiological function cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview Nocardiopsis dassonvillei
2.3.2.21 metabolism comparison of different CDPS-containing biosynthetic pathways, enzyme Rv2275 is involved in the mycocyclosin biosynthetic pathway, overview. Rv2275 is established as a CDPS that catalyzes formation of cyclo(L-tyrosyl-L-tyrosyl) as its major product, along with a handful of minor products containing tyrosine Mycobacterium tuberculosis
2.3.2.21 additional information the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS Mycobacterium tuberculosis
2.3.2.21 physiological function cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview Mycobacterium tuberculosis
2.3.2.22 metabolism comparison of different CDPS-containing biosynthetic pathways, enzyme YvmC is involved in the pulcherrimin biosynthetic pathway, overview. In Bacillus subtilis, the CDPS YvmC catalyzes formation of major product cyclo(L-leucyl-L-leucyl) as well as minor cyclic dipeptide products containing one leucine residue. The yvmC gene is part of a two gene operon with cypX Bacillus spizizenii
2.3.2.22 additional information the CDPS catalytic mechanism entails initial covalent tethering of the aminoacyl moiety from the first aa-tRNA substrate onto a conserved active site serine (Ser) residue. Nucleophilic attack of the amino nitrogen on the carbonyl carbon from the second aa-tRNA substrate yields the first peptide bond. The resulting enzyme-linked dipeptidyl intermediate then undergoes intramolecular peptide bond formation to yield the DKP group with concomitant release from the active site. The two aa-tRNA substrates bind at different sites of the CDPS Bacillus spizizenii
2.3.2.22 physiological function cyclodipeptide synthases (CDPSs) are recognized catalysts of 2,5-diketopiperazine (DKP) assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. Representative 2,5-diketopiperazine (DKP) natural products and bioactivities, overview Bacillus spizizenii