1JMK

Structural Basis for the Cyclization of the Lipopeptide Antibiotic Surfactin by the Thioesterase Domain SrfTE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth O]	d1jmko_	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	Thioesterase domain of polypeptide, polyketide and fatty acid synthases	Surfactin synthetase, SrfA	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A [auth C]	d1jmkc_	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	Thioesterase domain of polypeptide, polyketide and fatty acid synthases	Surfactin synthetase, SrfA	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth O]	SCOP2 Family	Thioesterase domain of polypeptide, polyketide and fatty acid synthases	8027567	4003342	SCOP2 (2022-06-29)
B [auth O]	SCOP2 Superfamily	alpha/beta-Hydrolases	8039946	3000102	SCOP2 (2022-06-29)
A [auth C]	SCOP2B Superfamily	alpha/beta-Hydrolases	8039946	3000102	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth O]	Hydrolase_4_1	e1jmkO1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4_1	ECOD (1.6)
A [auth C]	Hydrolase_4_1	e1jmkC1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth O]	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
B [auth O]	1.10.287.490	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
A [auth C]	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
A [auth C]	1.10.287.490	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth O]	PF00975	Thioesterase domain (Thioesterase)	Thioesterase domain	Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of v ...	Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates. There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Thioesterases (non-integrated) have molecular masses of 25-29 kDa.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth O]	Surfactin Synthetase	vitamin binding amide binding modified amino acid binding binding phosphopantetheine binding small molecule binding catalytic activity ligase activity	secondary metabolite biosynthetic process biosynthetic process metabolic process secondary metabolic process sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation antibiotic metabolic process antibiotic biosynthetic process amino acid activation peptide biosynthetic process secondary metabolite biosynthetic process biosynthetic process metabolic process secondary metabolic process sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation antibiotic metabolic process antibiotic biosynthetic process amino acid activation peptide biosynthetic process amino acid activation for nonribosomal peptide biosynthetic process amino acid metabolic process primary metabolic process nonribosomal peptide biosynthetic process peptide metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth O]	IPR006162	Phosphopantetheine attachment site	PTM
A [auth C], B [auth O]	IPR009081	Phosphopantetheine binding ACP domain	Domain
A [auth C], B [auth O]	IPR010071	Amino acid adenylation domain	Domain
A [auth C], B [auth O]	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily
A [auth C], B [auth O]	IPR020845	AMP-binding, conserved site	Conserved Site
A [auth C], B [auth O]	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
A [auth C], B [auth O]	IPR045851	AMP-binding enzyme, C-terminal domain superfamily	Homologous Superfamily
A [auth C], B [auth O]	IPR020806	Polyketide synthase, phosphopantetheine-binding domain	Domain
A [auth C], B [auth O]	IPR001242	Condensation domain	Domain
A [auth C], B [auth O]	IPR036736	ACP-like superfamily	Homologous Superfamily
A [auth C], B [auth O]	IPR025110	AMP-binding enzyme, C-terminal domain	Domain
A [auth C], B [auth O]	IPR000873	AMP-dependent synthetase/ligase domain	Domain
A [auth C], B [auth O]	IPR001031	Thioesterase	Domain

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 R01GM157729.