7S6B | pdb_00007s6b

Crystal structure of modular polyketide synthase apo-Lsd14 from the Lasalocid biosynthesis pathway, trapped in the transacylation step


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AF_UNCLASSIFIEDe7s6bA5 A: alpha duplicates or obligate multimersX: Docking domains in modular polyketide synthasesH: Class 1 N-terminal docking domain (From Topology)T: Class 1 N-terminal docking domainF: F_UNCLASSIFIEDECOD (1.6)
AAcyl_transf_1_2nde7s6bA1 A: a+b two layersX: Alpha-beta plaitsH: Probable ACP-binding domain of malonyl-CoA ACP transacylase (From Topology)T: Probable ACP-binding domain of malonyl-CoA ACP transacylaseF: Acyl_transf_1_2ndECOD (1.6)
APksD_2e7s6bA2 A: a+b two layersX: KS-MAT linker domain in fatty acid synthase (From Topology)H: KS-MAT linker domain in fatty acid synthase (From Topology)T: KS-MAT linker domain in fatty acid synthaseF: PksD_2ECOD (1.6)
APksD,Acyl_transf_1_1ste7s6bA4 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: FabD/lysophospholipase-likeF: PksD,Acyl_transf_1_1stECOD (1.6)
Aketoacyl-synte7s6bA3 A: a/b three-layered sandwichesX: Thiolase-like (From Topology)H: Thiolase-like (From Topology)T: Thiolase-likeF: ketoacyl-syntECOD (1.6)
AKetoacyl-synt_Ce7s6bA6 A: a/b three-layered sandwichesX: Thiolase-like (From Topology)H: Thiolase-like (From Topology)T: Thiolase-likeF: Ketoacyl-synt_CECOD (1.6)
BDockinge7s6bB2 A: alpha duplicates or obligate multimersX: Docking domains in modular polyketide synthasesH: Class 1 N-terminal docking domain (From Topology)T: Class 1 N-terminal docking domainF: DockingECOD (1.6)
BAcyl_transf_1_2nde7s6bB4 A: a+b two layersX: Alpha-beta plaitsH: Probable ACP-binding domain of malonyl-CoA ACP transacylase (From Topology)T: Probable ACP-binding domain of malonyl-CoA ACP transacylaseF: Acyl_transf_1_2ndECOD (1.6)
BPksD_2e7s6bB3 A: a+b two layersX: KS-MAT linker domain in fatty acid synthase (From Topology)H: KS-MAT linker domain in fatty acid synthase (From Topology)T: KS-MAT linker domain in fatty acid synthaseF: PksD_2ECOD (1.6)
BAcyl_transf_1_1ste7s6bB1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: FabD/lysophospholipase-likeF: Acyl_transf_1_1stECOD (1.6)
Bketoacyl-synte7s6bB5 A: a/b three-layered sandwichesX: Thiolase-like (From Topology)H: Thiolase-like (From Topology)T: Thiolase-likeF: ketoacyl-syntECOD (1.6)
BKetoacyl-synt_Ce7s6bB6 A: a/b three-layered sandwichesX: Thiolase-like (From Topology)H: Thiolase-like (From Topology)T: Thiolase-likeF: Ketoacyl-synt_CECOD (1.6)
CEUF08195e7s6bC3 A: alpha duplicates or obligate multimersX: Dimerization element domain in modular polyketide synthases (From Topology)H: Dimerization element domain in modular polyketide synthases (From Topology)T: Dimerization element domain in modular polyketide synthasesF: EUF08195ECOD (1.6)
CKR_1_SDR_xe7s6bC2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: KR_1_SDR_xECOD (1.6)
Cadh_short_C2_1e7s6bC1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: adh_short_C2_1ECOD (1.6)
DEUF08195e7s6bD3 A: alpha duplicates or obligate multimersX: Dimerization element domain in modular polyketide synthases (From Topology)H: Dimerization element domain in modular polyketide synthases (From Topology)T: Dimerization element domain in modular polyketide synthasesF: EUF08195ECOD (1.6)
DKR_1_SDR_xe7s6bD2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: KR_1_SDR_xECOD (1.6)
Dadh_short_C2_1e7s6bD1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: adh_short_C2_1ECOD (1.6)
EPP-bindinge7s6bE1 A: alpha bundlesX: ACP-likeH: Acyl-carrier protein (ACP) (From Topology)T: Acyl-carrier protein (ACP)F: PP-bindingECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.40.47.10 Alpha Beta 3-Layer(aba) Sandwich Peroxisomal Thiolase Chain A, domain 1CATH (utative)
B3.40.47.10 Alpha Beta 3-Layer(aba) Sandwich Peroxisomal Thiolase Chain A, domain 1CATH (utative)
E1.10.1200.10 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF02801Beta-ketoacyl synthase, C-terminal domain (Ketoacyl-synt_C)Beta-ketoacyl synthase, C-terminal domainThe structure of beta-ketoacyl synthase is similar to that of the thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. Domain
A, B
PF00109Beta-ketoacyl synthase, N-terminal domain (ketoacyl-synt)Beta-ketoacyl synthase, N-terminal domainThe structure of beta-ketoacyl synthase is similar to that of the thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. The N-terminal domain contains m ...The structure of beta-ketoacyl synthase is similar to that of the thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. The N-terminal domain contains most of the structures involved in dimer formation and also the active site cysteine [1].
Domain
A, B
PF16197Ketoacyl-synthetase C-terminal extension (KAsynt_C_assoc)Ketoacyl-synthetase C-terminal extension- Family
A, B
PF00698Acyl transferase domain (Acyl_transf_1)Acyl transferase domainDomain
C, D
PF08659KR domain (KR)KR domain- Family
C, D
PF18369Polyketide synthase dimerisation element domain (PKS_DE)Polyketide synthase dimerisation element domainThis is the dimerisation element domain found in bacterial modular polyketide synthase ketoreductases [1]. The dimerization element (DE) domain is N-terminal to the KR domain Pfam:PF08659. DE domain is necessary for KR function, presumably because th ...This is the dimerisation element domain found in bacterial modular polyketide synthase ketoreductases [1]. The dimerization element (DE) domain is N-terminal to the KR domain Pfam:PF08659. DE domain is necessary for KR function, presumably because the dimeric DE orients the KR domains for optimal activity within a module [2].
Domain
PF00550Phosphopantetheine attachment site (PP-binding)Phosphopantetheine attachment siteA 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes memb ...A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
Polyketide synthase -
C, D
Polyketide synthase -
Polyketide synthase -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B
IPR016035Acyl transferase/acyl hydrolase/lysophospholipaseHomologous Superfamily
A, B
IPR014031Beta-ketoacyl synthase, C-terminalDomain
A, B
IPR015083Polyketide synthase NorB/C/GfsB-E-like, docking domainDomain
A, B
IPR006162Phosphopantetheine attachment sitePTM
A, B
IPR016036Malonyl-CoA ACP transacylase, ACP-bindingHomologous Superfamily
A, B
IPR050091Polyketide and Nonribosomal Peptide Biosynthesis EnzymesFamily
A, B
IPR020841Polyketide synthase, beta-ketoacyl synthase domainDomain
A, B
IPR036736ACP-like superfamilyHomologous Superfamily
A, B
IPR014043Acyl transferase domainDomain
A, B
IPR041618Polyketide synthase dimerisation element domainDomain
A, B
IPR032821Polyketide synthase, C-terminal extensionDomain
A, B
IPR009081Phosphopantetheine binding ACP domainDomain
A, B
IPR020806Polyketide synthase-like, phosphopantetheine-binding domainDomain
A, B
IPR036299Polyketide synthase, docking domain superfmailyHomologous Superfamily
A, B
IPR013968Polyketide synthase-like, ketoreductase domainDomain
A, B
IPR016039Thiolase-likeHomologous Superfamily
A, B
IPR001227Acyl transferase domain superfamilyHomologous Superfamily
A, B
IPR036291NAD(P)-binding domain superfamilyHomologous Superfamily
A, B
IPR018201Beta-ketoacyl synthase, active siteActive Site
A, B
IPR014030Beta-ketoacyl synthase-like, N-terminalDomain
C, D
IPR016035Acyl transferase/acyl hydrolase/lysophospholipaseHomologous Superfamily
C, D
IPR014031Beta-ketoacyl synthase, C-terminalDomain
C, D
IPR015083Polyketide synthase NorB/C/GfsB-E-like, docking domainDomain
C, D
IPR006162Phosphopantetheine attachment sitePTM
C, D
IPR016036Malonyl-CoA ACP transacylase, ACP-bindingHomologous Superfamily
C, D
IPR050091Polyketide and Nonribosomal Peptide Biosynthesis EnzymesFamily
C, D
IPR020841Polyketide synthase, beta-ketoacyl synthase domainDomain
C, D
IPR036736ACP-like superfamilyHomologous Superfamily
C, D
IPR014043Acyl transferase domainDomain
C, D
IPR041618Polyketide synthase dimerisation element domainDomain
C, D
IPR032821Polyketide synthase, C-terminal extensionDomain
C, D
IPR009081Phosphopantetheine binding ACP domainDomain
C, D
IPR020806Polyketide synthase-like, phosphopantetheine-binding domainDomain
C, D
IPR036299Polyketide synthase, docking domain superfmailyHomologous Superfamily
C, D
IPR013968Polyketide synthase-like, ketoreductase domainDomain
C, D
IPR016039Thiolase-likeHomologous Superfamily
C, D
IPR001227Acyl transferase domain superfamilyHomologous Superfamily
C, D
IPR036291NAD(P)-binding domain superfamilyHomologous Superfamily
C, D
IPR018201Beta-ketoacyl synthase, active siteActive Site
C, D
IPR014030Beta-ketoacyl synthase-like, N-terminalDomain
IPR016035Acyl transferase/acyl hydrolase/lysophospholipaseHomologous Superfamily
IPR014031Beta-ketoacyl synthase, C-terminalDomain
IPR015083Polyketide synthase NorB/C/GfsB-E-like, docking domainDomain
IPR006162Phosphopantetheine attachment sitePTM
IPR016036Malonyl-CoA ACP transacylase, ACP-bindingHomologous Superfamily
IPR050091Polyketide and Nonribosomal Peptide Biosynthesis EnzymesFamily
IPR020841Polyketide synthase, beta-ketoacyl synthase domainDomain
IPR036736ACP-like superfamilyHomologous Superfamily
IPR014043Acyl transferase domainDomain
IPR041618Polyketide synthase dimerisation element domainDomain
IPR032821Polyketide synthase, C-terminal extensionDomain
IPR009081Phosphopantetheine binding ACP domainDomain
IPR020806Polyketide synthase-like, phosphopantetheine-binding domainDomain
IPR036299Polyketide synthase, docking domain superfmailyHomologous Superfamily
IPR013968Polyketide synthase-like, ketoreductase domainDomain
IPR016039Thiolase-likeHomologous Superfamily
IPR001227Acyl transferase domain superfamilyHomologous Superfamily
IPR036291NAD(P)-binding domain superfamilyHomologous Superfamily
IPR018201Beta-ketoacyl synthase, active siteActive Site
IPR014030Beta-ketoacyl synthase-like, N-terminalDomain