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Dieckmann_Cyclase

Relationship

Family: Dieckmann_Cyclase

Block: X

Parent Family: No family

Comment

Off-loading Dieckmann cyclase, NcmC, that installs the tetramate head group in nocamycin, a hybrid polyketide/nonribosomalpeptide natural product. A conserved thioesterase-like scaffold has been adapted to perform a new chemical reaction: heterocyclization. The catalytic triad for the cyclization reaction consists of Cys89, Asp116, and His254 in 9pseu-NcmC. Dieckmann cyclase (TrdC, SlgL, LipX2, KirHI,and FacH) last step which generate actinomycete-derived tetramic acid and pyridone natural products in the biosynthetic pathways for Tirandamycin, Streptolydigin, alpha-Lipomycin, Kirromycin, and Factumycin

Database

Interpro : No interpro

PIRSF : No PIRSF

Pdoc : No Pdoc

Pfam : No Pfam

Prints : No Print

EC Number : No EC Number

Sequences

Peptide in Fasta
Nucleotide in Fasta
Alignment with Multalin Text only
Seed alignment with MAFFT No colour / coloured with Mview
Alignment with MAFFT No colour / coloured with Mview
Dendrogram The dnd file

Structure Name Proteins
6E6Y Dieckmann cyclase from Saccharothrix syringae, NcmC 9pseu-NcmC
6E6T Dieckmann cyclase from Saccharothrix syringae, NcmC, bound to cerulenin 9pseu-NcmC
6E6U Variant C89S of Dieckmann cyclase, NcmC 9pseu-NcmC

Gene_locus Name Species
9actn-a0a1h9jgw2 Streptomyces radiopugnans. Uncharacterized protein Streptomyces radiopugnans
9actn-a0a0f4k5z7 Streptomyces sp. NRRL B-1568. Uncharacterized protein Streptomyces sp. NRRL B-1568
9actn-a0a5r9lrh5 Streptomyces sp. So13.3. Uncharacterized protein Streptomyces sp. So13.3
9actn-a0a514jvg4 Streptomyces asterosporus\; Streptomyces calvus. Uncharacterized protein Cal14 Streptomyces asterosporus
9actn-a0a0m8v9z7 Streptomyces sp. MMG1121. Uncharacterized protein Streptomyces sp. MMG1121
9actn-a0a2v2pzg2 Streptomyces sp. ZEA17I. Uncharacterized protein Streptomyces sp. ZEA17I
strto-a0a081xit3 Streptomyces toyocaensis. Uncharacterized protein Streptomyces toyocaensis
9actn-a0a1q4zi93 Streptomyces sp. TSRI0281. Uncharacterized protein Streptomyces sp. TSRI0281
9actn-d9xle7 Streptomyces griseoflavus Tu4000. Uncharacterized protein Streptomyces griseoflavus Tu4000
kitsk-e4nik2 Kitasatospora setae (Streptomyces setae). Uncharacterized protein Kitasatospora setae
9actn-a0a0f4k9s3 Streptomyces sp. NRRL B-1568. Uncharacterized protein Streptomyces sp. NRRL B-1568
9actn-a0a4r5c3h5 Actinomadura sp. H3C3. Uncharacterized protein Actinomadura sp. H3C3
strc3-s5vff6 Streptomyces collinus. kirHI Dieckmann_Cyclase in gene cluster of kirromycin synthesis Streptomyces collinus
9actn-a0a4r3c594 Streptomyces sp. BK308. Uncharacterized protein Streptomyces sp. BK308
9pseu-a0a542djd2 Amycolatopsis cihanbeyliensis. Uncharacterized protein Amycolatopsis cihanbeyliensis
9actn-a0a1v3zz37 Streptomyces tsukubensis. Uncharacterized protein Streptomyces tsukubensis
9actn-a0a1d2i704 Streptomyces sp. AVP053U2. Uncharacterized protein Streptomyces sp. AVP053U2
9actn-a0a438lz38 Nonomuraea polychroma. Uncharacterized protein Nonomuraea polychroma
9actn-a0a0k9xby7 Streptomyces caatingaensis. Uncharacterized protein Streptomyces caatingaensis
9actn-a0a2p4uhl0 Actinomadura sp. RB29. Uncharacterized protein Actinomadura sp. RB29
9actn-a0a0q8zxb5 Streptomyces sp. Root264. Uncharacterized protein Streptomyces sp. Root264
9actn-a0a1q5d7w2 Streptomyces sp. CB01249. Uncharacterized protein Streptomyces sp. CB01249
9actn-a0a2i0sd64 Streptomyces populi. Uncharacterized protein Streptomyces populi
9pseu-a0a495w3m4 Saccharothrix australiensis. Uncharacterized protein Saccharothrix australiensis
9actn-a0a344uav3 Streptomyces globosus. Uncharacterized protein Streptomyces globosus
9pseu-a0a4r7uw25 Actinophytocola oryzae. Uncharacterized protein Actinophytocola oryzae
9actn-a0a1q5mn15 Streptomyces sp. CB00455. Uncharacterized protein Streptomyces sp. CB00455
9pseu-a0a4r2juc1 Actinocrispum wychmicini. Uncharacterized protein Actinocrispum wychmicini
9actn-a0a4r4n079 Nonomuraea longispora. Uncharacterized protein Nonomuraea longispora
strne-a0a445ni11 Streptomyces netropsis (Streptoverticillium netropsis). Uncharacterized protein Streptomyces netropsis
9actn-a0a1h9xtl3 Streptomyces sp. yr375. Uncharacterized protein Streptomyces sp. yr375
9actn-a0a1z2kz73 Streptomyces albireticuli. Uncharacterized protein Streptomyces albireticuli
9actn-a0a1c5gdx1 Micromonospora echinofusca\; Micromonospora peucetia. Uncharacterized protein Micromonospora echinofusca
9actn-a0a0n1npe0 Actinobacteria bacterium OK074. Uncharacterized protein Actinobacteria bacterium OK074
9actn-a0a0c1x845 Streptomyces sp. AcH 505. Uncharacterized protein Streptomyces sp. AcH 505
9actn-a0a5r9mb21 Streptomyces sp. So13.3. Uncharacterized protein Streptomyces sp. So13.3
9pseu-a0a495x9w9 Saccharothrix variisporea. Uncharacterized protein Saccharothrix variisporea
9actn-a0a2g7f626 Streptomyces sp. 70. Uncharacterized protein Streptomyces sp. 70
9actn-a0a3n1d0i7 Actinocorallia herbida. Uncharacterized protein Actinocorallia herbida
9actn-a0a3a9zgz5 Micromonospora endolithica. Uncharacterized protein Micromonospora endolithica
9actn-s3bz19 Streptomyces sp. HPH0547. Uncharacterized protein Streptomyces sp. HPH0547
9actn-a0a248ypn6 Plantactinospora sp. KBS50. Uncharacterized protein Plantactinospora sp. KBS50
9actn-a0a2m9ifq0 Streptomyces sp. CB01373. Uncharacterized protein Streptomyces sp. CB01373
9pseu-a0a1b1zjb9 Pseudonocardia sp. HH130630-07. Uncharacterized protein Pseudonocardia sp. HH130630-07
9actn-a0a1h9xtc3 Streptomyces sp. yr375. Uncharacterized protein Streptomyces sp. yr375
9actn-a0a2n3uyx7 Streptomyces sp. GP55. Uncharacterized protein Streptomyces sp. GP55
9pseu-a0a4r7vjx1 Actinophytocola oryzae. Uncharacterized protein Actinophytocola oryzae
9actn-a0a101n5d4 Streptomyces cellostaticus. Uncharacterized protein Streptomyces cellostaticus
9actn-a0a0t6lq39 Streptomyces vitaminophilus. Uncharacterized protein Streptomyces vitaminophilus
9pseu-a0a1q4xtq2 Saccharothrix sp. CB00851. Uncharacterized protein Saccharothrix sp. CB00851
9pseu-a0a4v3cy71 Labedaea rhizosphaerae. Uncharacterized protein Labedaea rhizosphaerae
9pseu-a0a1v2qtm6 Saccharothrix sp. ALI-22-I. Uncharacterized protein Saccharothrix sp. ALI-22-I
9pseu-a0a5q0h698 Saccharothrix syringae. Uncharacterized protein Saccharothrix syringae
9pseu-a0a4v3ft28 Actinophytocola oryzae. Uncharacterized protein Actinophytocola oryzae
9actn-a0a1c5gc05 Micromonospora echinofusca. Uncharacterized protein Micromonospora echinofusca
9actn-a0a248yq89 Plantactinospora sp. KBS50. Uncharacterized protein Plantactinospora sp. KBS50
9actn-a0a0c5fv25 Streptomyces cyaneogriseus subsp. noncyanogenus. Uncharacterized protein Streptomyces cyaneogriseus subsp. noncyanogenus
9actn-a0a1q5le62 Streptomyces sp. CB03234. Uncharacterized protein Streptomyces sp. CB03234
9actn-a0a327vse8 Streptomyces sp. PsTaAH-137. Uncharacterized protein Streptomyces sp. PsTaAH-137
9pseu-NcmC Saccharothrix syringae. NcmC Saccharothrix syringae
9actn-a0a0n6zgx9 Streptomyces sp. CCM_MD2014. Uncharacterized protein Streptomyces sp. CCM_MD2014
9pseu-a0a1h2h606 Amycolatopsis keratiniphila. Uncharacterized protein Amycolatopsis keratiniphila
9pseu-a0a290z691 Actinosynnema pretiosum. Uncharacterized protein Actinosynnema pretiosum
strrn-a0a0a0nf48 Streptomyces rapamycinicus\; Streptomyces hygroscopicus. Uncharacterized protein D3C57_121920 Streptomyces rapamycinicus
9actn-f1di35 Streptomyces sp. TrdC\; TamC. Dieckmann_Cyclase in biosynthetic gene cluster of the bacterial RNA polymerase inhibitor tirandamycin Streptomyces sp. SCSIO 1666
9actn-a0a1h5kkh3 Streptomyces sp. 2314.4. Uncharacterized protein Streptomyces sp. 2314.4
strpt-a0a1y2njq2 Streptomyces platensis\; Streptomyces lydicamycinicus. Uncharacterized protein Streptomyces platensis
9pseu-a0a1v2q4p3 Actinosynnema sp. ALI-1.44. Uncharacterized protein Actinosynnema sp. ALI-1.44
9actn-d1glt3 Streptomyces lydicus. Uncharacterized protein slgL Streptomyces lydicus
9actn-a0a1q5fgx4 Streptomyces sp. CB00316. Uncharacterized protein Streptomyces sp. CB00316
9actn-a0a2n3zbk3 Micromonospora sp. CNZ309. Uncharacterized protein Micromonospora sp. CNZ309
9pseu-a0a1d8byt1 Actinoalloteichus hymeniacidonis. Uncharacterized protein Actinoalloteichus hymeniacidonis
9actn-a0a0p4rci1 Streptomyces lydicamycinicus. Uncharacterized protein Streptomyces lydicamycinicus
9actn-a0a243s3g0 Streptomyces swartbergensis. Uncharacterized protein Streptomyces swartbergensis
9actn-q9fb38 Streptomyces verticillus\; Streptomyces mobaraensis. Dieckmann_Cyclase in gene cluster for the antitumor drug bleomycin synthesis Streptomyces verticillus
kitau-q30cs4 Kitasatospora aureofaciens (Streptomyces aureofaciens). LipX2 Dieckmann_Cyclase in biosynthetic gene cluster for the polyenoyltetramic acid alpha-lipomycin Kitasatospora aureofaciens
9actn-a0a0n6w4z6 Streptomyces sp. CCM_MD2014. Uncharacterized protein Streptomyces sp. CCM_MD2014
9pseu-r1hz43 Amycolatopsis vancoresmycina\; Amycolatopsis sp. var15 Uncharacterized protein Amycolatopsis vancoresmycina DSM 44592
strrg-k7qrj3 Streptomyces rugosporus. PyrG2. Dieckmann_Cyclase in biosynthetic gene cluster of pyrroindomycin or Quartromicin Streptomyces rugosporus
9actn-r4lg32 Actinoplanes sp. N902-109. Uncharacterized protein Actinoplanes sp. N902-109
9pseu-a0a2n8mh05 Amycolatopsis sp. BJA-103. Uncharacterized protein Amycolatopsis sp. BJA-103
9actn-a0a2a2d3k0 Streptomyces albireticuli. Uncharacterized protein Streptomyces albireticuli
streu-a0a2n8nw41 Streptomyces eurocidicus (Streptoverticillium eurocidicus). Uncharacterized protein Streptomyces eurocidicus
9actn-a0a1c4rpf7 Streptomyces sp. Termitarium-T10T-6. Uncharacterized protein Streptomyces sp. Termitarium-T10T-6
9actn-a0a1c6uku8 Micromonospora peucetia. Uncharacterized protein Micromonospora peucetia
9pseu-a0a1h9wug6 Lentzea flaviverrucosa. Uncharacterized protein Lentzea flaviverrucosa
9actn-a0a1c6v190 Micromonospora eburnea. Uncharacterized protein Micromonospora eburnea
9actn-a0a285qt70 Streptomyces sp. 1331.2. Uncharacterized protein Streptomyces sp. 1331.2
9actn-a0a209cpb4 Streptomyces sp. CS227. Uncharacterized protein Streptomyces sp. CS227

Gene_locus_frgt Name Species
9actn-a0a365gym5 Actinomadura sp. LHW63021. Uncharacterized protein Actinomadura sp. LHW63021
9actn-a0a505dql0 Streptomyces sporangiiformans. Uncharacterized protein Streptomyces sporangiiformans
9actn-a0a0c2asz4 Streptomyces sp. AcH 505. Uncharacterized protein Streptomyces sp. AcH 505
9actn-a0a1c4tci8 Streptomyces sp. DvalAA-43. Uncharacterized protein Streptomyces sp. DvalAA-43
9actn-d9wms8 Streptomyces himastatinicus ATCC 53653. AB hydrolase-1 domain-containing protein Streptomyces himastatinicus ATCC 53653
9actn-v6lcv4 Streptomycetaceae bacterium MP113-05. Uncharacterized protein Streptomycetaceae bacterium MP113-05
9actn-a0a2w2mxp0 Streptomyces sp. NTH33. Uncharacterized protein Streptomyces sp. NTH33

Substrate Chemical Nomenclature Proteins
N-acetoacetyl-glycyl-SNAC S-(2-acetamidoethyl)2-(3-oxobutanamido)ethanethioate 9pseu-NcmC
Cerulenin-hemiaminal (1R,4R,5S)-4-hydroxy-4-[(3E,6E)-octa-3,6-dienyl]-6-oxa-3-azabicyclo[3.1.0]hexan-2-one 9pseu-NcmC
Cerulenin (2R,3S)-3-[(4E,7E)-nona-4,7-dienoyl]oxirane-2-carboxamide 9pseu-NcmC

Inhibitor Chemical Nomenclature Proteins
6E6T-HVV (4S,5R)-4,5-Dihydroxy-5-[(3E,6E)-octa-3,6-dienyl]pyrrolidin-2-one 9pseu-NcmC

References (2)

Title : Structural Basis for Enzymatic Off-Loading of Hybrid Polyketides by Dieckmann Condensation - Cogan_2020_ACS.Chem.Biol_15_2783
Author(s) : Cogan DP , Ly J , Nair SK
Ref : ACS Chemical Biology , 15 :2783 , 2020
Abstract :
PubMedSearch : Cogan_2020_ACS.Chem.Biol_15_2783
PubMedID: 33017142
Gene_locus related to this paper: 9pseu-NcmC

Title : Discovery of a new family of Dieckmann cyclases essential to tetramic acid and pyridone-based natural products biosynthesis - Gui_2015_Org.Lett_17_628
Author(s) : Gui C , Li Q , Mo X , Qin X , Ma J , Ju J
Ref : Org Lett , 17 :628 , 2015
Abstract :
PubMedSearch : Gui_2015_Org.Lett_17_628
PubMedID: 25621700