7S6B

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

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF08990	e7s6bA5	A: alpha duplicates or obligate multimers	X: Docking domains in modular polyketide synthases	H: Class 1 N-terminal docking domain (From Topology)	T: Class 1 N-terminal docking domain	F: PF08990	ECOD (1.6)
A	PF00698	e7s6bA1	A: a+b two layers	X: Alpha-beta plaits	H: Probable ACP-binding domain of malonyl-CoA ACP transacylase (From Topology)	T: Probable ACP-binding domain of malonyl-CoA ACP transacylase	F: PF00698	ECOD (1.6)
A	PF22621	e7s6bA2	A: a+b two layers	X: 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 synthase	F: PF22621	ECOD (1.6)
A	PF00698	e7s6bA4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: FabD/lysophospholipase-like	F: PF00698	ECOD (1.6)
A	PF00109	e7s6bA3	A: a/b three-layered sandwiches	X: Thiolase-like (From Topology)	H: Thiolase-like (From Topology)	T: Thiolase-like	F: PF00109	ECOD (1.6)
A	PF02801,PF16197	e7s6bA6	A: a/b three-layered sandwiches	X: Thiolase-like (From Topology)	H: Thiolase-like (From Topology)	T: Thiolase-like	F: PF02801,PF16197	ECOD (1.6)
B	PF08990	e7s6bB2	A: alpha duplicates or obligate multimers	X: Docking domains in modular polyketide synthases	H: Class 1 N-terminal docking domain (From Topology)	T: Class 1 N-terminal docking domain	F: PF08990	ECOD (1.6)
B	PF00698	e7s6bB4	A: a+b two layers	X: Alpha-beta plaits	H: Probable ACP-binding domain of malonyl-CoA ACP transacylase (From Topology)	T: Probable ACP-binding domain of malonyl-CoA ACP transacylase	F: PF00698	ECOD (1.6)
B	PF22621	e7s6bB3	A: a+b two layers	X: 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 synthase	F: PF22621	ECOD (1.6)
B	PF00698	e7s6bB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: FabD/lysophospholipase-like	F: PF00698	ECOD (1.6)
B	PF00109	e7s6bB5	A: a/b three-layered sandwiches	X: Thiolase-like (From Topology)	H: Thiolase-like (From Topology)	T: Thiolase-like	F: PF00109	ECOD (1.6)
B	PF02801,PF16197	e7s6bB6	A: a/b three-layered sandwiches	X: Thiolase-like (From Topology)	H: Thiolase-like (From Topology)	T: Thiolase-like	F: PF02801,PF16197	ECOD (1.6)
C	PF18369	e7s6bC3	A: alpha duplicates or obligate multimers	X: 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 synthases	F: PF18369	ECOD (1.6)
C	F_UNCLASSIFIED	e7s6bC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF08659	e7s6bC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF08659	ECOD (1.6)
D	PF18369	e7s6bD3	A: alpha duplicates or obligate multimers	X: 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 synthases	F: PF18369	ECOD (1.6)
D	F_UNCLASSIFIED	e7s6bD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF08659	e7s6bD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF08659	ECOD (1.6)
E	PF00550	e7s6bE1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PF00550	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02801	Beta-ketoacyl synthase, C-terminal domain (Ketoacyl-synt_C)	Beta-ketoacyl synthase, C-terminal domain	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.	Domain
A, B	PF00109	Beta-ketoacyl synthase, N-terminal domain (ketoacyl-synt)	Beta-ketoacyl synthase, N-terminal domain	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 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	PF16197	Ketoacyl-synthetase C-terminal extension (KAsynt_C_assoc)	Ketoacyl-synthetase C-terminal extension	-	Family
A, B	PF00698	Acyl transferase domain (Acyl_transf_1)	Acyl transferase domain	-	Domain
C, D	PF08659	KR domain (KR)	KR domain	-	Family
C, D	PF18369	Polyketide synthase dimerisation element domain (PKS_DE)	Polyketide synthase dimerisation element domain	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 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
E	PF00550	Phosphopantetheine attachment site (PP-binding)	Phosphopantetheine attachment site	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 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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Polyketide synthase	vitamin binding amide binding modified amino acid binding binding phosphopantetheine binding small molecule binding acyltransferase activity 3-oxoacyl-[acyl-carrier-protein] synthase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity fatty acid synthase activity	cellular component biogenesis cellular component organization peptidoglycan-based cell wall biogenesis cellular component assembly cell wall biogenesis DIM/DIP cell wall layer assembly cell wall organization or biogenesis cellular process Actinobacterium-type cell wall biogenesis cellular component organization or biogenesis fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular component biogenesis cellular component organization peptidoglycan-based cell wall biogenesis cellular component assembly cell wall biogenesis DIM/DIP cell wall layer assembly cell wall organization or biogenesis cellular process Actinobacterium-type cell wall biogenesis cellular component organization or biogenesis fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process cellular lipid metabolic process small molecule metabolic process metabolic process monocarboxylic acid metabolic process lipid metabolic process macrolide biosynthetic process polyketide metabolic process macrolide metabolic process secondary metabolic process antibiotic biosynthetic process antibiotic metabolic process polyketide biosynthetic process secondary metabolite biosynthetic process lactone metabolic process lactone biosynthetic process	cell periphery plasma membrane membrane cellular anatomical entity intracellular anatomical structure cytoplasm
C, D	Polyketide synthase	vitamin binding amide binding modified amino acid binding binding phosphopantetheine binding small molecule binding acyltransferase activity 3-oxoacyl-[acyl-carrier-protein] synthase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity fatty acid synthase activity	cellular component biogenesis cellular component organization peptidoglycan-based cell wall biogenesis cellular component assembly cell wall biogenesis DIM/DIP cell wall layer assembly cell wall organization or biogenesis cellular process Actinobacterium-type cell wall biogenesis cellular component organization or biogenesis fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular component biogenesis cellular component organization peptidoglycan-based cell wall biogenesis cellular component assembly cell wall biogenesis DIM/DIP cell wall layer assembly cell wall organization or biogenesis cellular process Actinobacterium-type cell wall biogenesis cellular component organization or biogenesis fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process cellular lipid metabolic process small molecule metabolic process metabolic process monocarboxylic acid metabolic process lipid metabolic process macrolide biosynthetic process polyketide metabolic process macrolide metabolic process secondary metabolic process antibiotic biosynthetic process antibiotic metabolic process polyketide biosynthetic process secondary metabolite biosynthetic process lactone metabolic process lactone biosynthetic process	cell periphery plasma membrane membrane cellular anatomical entity intracellular anatomical structure cytoplasm
E	Polyketide synthase	vitamin binding amide binding modified amino acid binding binding phosphopantetheine binding small molecule binding acyltransferase activity 3-oxoacyl-[acyl-carrier-protein] synthase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity fatty acid synthase activity	cellular component biogenesis cellular component organization peptidoglycan-based cell wall biogenesis cellular component assembly cell wall biogenesis DIM/DIP cell wall layer assembly cell wall organization or biogenesis cellular process Actinobacterium-type cell wall biogenesis cellular component organization or biogenesis fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular component biogenesis cellular component organization peptidoglycan-based cell wall biogenesis cellular component assembly cell wall biogenesis DIM/DIP cell wall layer assembly cell wall organization or biogenesis cellular process Actinobacterium-type cell wall biogenesis cellular component organization or biogenesis fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process cellular lipid metabolic process small molecule metabolic process metabolic process monocarboxylic acid metabolic process lipid metabolic process macrolide biosynthetic process polyketide metabolic process macrolide metabolic process secondary metabolic process antibiotic biosynthetic process antibiotic metabolic process polyketide biosynthetic process secondary metabolite biosynthetic process lactone metabolic process lactone biosynthetic process	cell periphery plasma membrane membrane cellular anatomical entity intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016035	Acyl transferase/acyl hydrolase/lysophospholipase	Homologous Superfamily
A, B	IPR014031	Beta-ketoacyl synthase, C-terminal	Domain
A, B	IPR006162	Phosphopantetheine attachment site	PTM
A, B	IPR014030	Beta-ketoacyl synthase, N-terminal	Domain
A, B	IPR013968	Polyketide synthase, ketoreductase domain	Domain
A, B	IPR016036	Malonyl-CoA ACP transacylase, ACP-binding	Homologous Superfamily
A, B	IPR020806	Polyketide synthase, phosphopantetheine-binding domain	Domain
A, B	IPR014043	Acyl transferase	Domain
A, B	IPR020841	Polyketide synthase, beta-ketoacyl synthase domain	Domain
A, B	IPR036736	ACP-like superfamily	Homologous Superfamily
A, B	IPR041618	Polyketide synthase dimerisation element domain	Domain
A, B	IPR015083	Polyketide synthase, docking domain	Domain
A, B	IPR032821	Polyketide synthase, C-terminal extension	Domain
A, B	IPR009081	Phosphopantetheine binding ACP domain	Domain
A, B	IPR036299	Polyketide synthase, docking domain superfmaily	Homologous Superfamily
A, B	IPR016039	Thiolase-like	Homologous Superfamily
A, B	IPR001227	Acyl transferase domain superfamily	Homologous Superfamily
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR018201	Beta-ketoacyl synthase, active site	Active Site
C, D	IPR016035	Acyl transferase/acyl hydrolase/lysophospholipase	Homologous Superfamily
C, D	IPR014031	Beta-ketoacyl synthase, C-terminal	Domain
C, D	IPR006162	Phosphopantetheine attachment site	PTM
C, D	IPR014030	Beta-ketoacyl synthase, N-terminal	Domain
C, D	IPR013968	Polyketide synthase, ketoreductase domain	Domain
C, D	IPR016036	Malonyl-CoA ACP transacylase, ACP-binding	Homologous Superfamily
C, D	IPR020806	Polyketide synthase, phosphopantetheine-binding domain	Domain
C, D	IPR014043	Acyl transferase	Domain
C, D	IPR020841	Polyketide synthase, beta-ketoacyl synthase domain	Domain
C, D	IPR036736	ACP-like superfamily	Homologous Superfamily
C, D	IPR041618	Polyketide synthase dimerisation element domain	Domain
C, D	IPR015083	Polyketide synthase, docking domain	Domain
C, D	IPR032821	Polyketide synthase, C-terminal extension	Domain
C, D	IPR009081	Phosphopantetheine binding ACP domain	Domain
C, D	IPR036299	Polyketide synthase, docking domain superfmaily	Homologous Superfamily
C, D	IPR016039	Thiolase-like	Homologous Superfamily
C, D	IPR001227	Acyl transferase domain superfamily	Homologous Superfamily
C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
C, D	IPR018201	Beta-ketoacyl synthase, active site	Active Site
E	IPR016035	Acyl transferase/acyl hydrolase/lysophospholipase	Homologous Superfamily
E	IPR014031	Beta-ketoacyl synthase, C-terminal	Domain
E	IPR006162	Phosphopantetheine attachment site	PTM
E	IPR014030	Beta-ketoacyl synthase, N-terminal	Domain
E	IPR013968	Polyketide synthase, ketoreductase domain	Domain
E	IPR016036	Malonyl-CoA ACP transacylase, ACP-binding	Homologous Superfamily
E	IPR020806	Polyketide synthase, phosphopantetheine-binding domain	Domain
E	IPR014043	Acyl transferase	Domain
E	IPR020841	Polyketide synthase, beta-ketoacyl synthase domain	Domain
E	IPR036736	ACP-like superfamily	Homologous Superfamily
E	IPR041618	Polyketide synthase dimerisation element domain	Domain
E	IPR015083	Polyketide synthase, docking domain	Domain
E	IPR032821	Polyketide synthase, C-terminal extension	Domain
E	IPR009081	Phosphopantetheine binding ACP domain	Domain
E	IPR036299	Polyketide synthase, docking domain superfmaily	Homologous Superfamily
E	IPR016039	Thiolase-like	Homologous Superfamily
E	IPR001227	Acyl transferase domain superfamily	Homologous Superfamily
E	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
E	IPR018201	Beta-ketoacyl synthase, active site	Active Site

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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7S6B

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

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage