5JA1

EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the MbtH-Like Protein YbdZ

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d5ja1b_	Alpha and beta proteins (a+b)	MbtH/L9 domain-like	MbtH-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	AMP-binding_3rd	e5ja1A8	A: beta barrels	X: beta-barrel domain in acetyl-CoA synthetase-like proteins (From Topology)	H: beta-barrel domain in acetyl-CoA synthetase-like proteins (From Topology)	T: beta-barrel domain in acetyl-CoA synthetase-like proteins	F: AMP-binding_3rd	ECOD (1.6)
A	PP-binding	e5ja1A7	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PP-binding	ECOD (1.6)
A	AMP-binding_C	e5ja1A6	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: a+b domain in acetyl-CoA synthetase-like proteins (From Topology)	T: a+b domain in acetyl-CoA synthetase-like proteins	F: AMP-binding_C	ECOD (1.6)
A	Condensation_N	e5ja1A4	A: a+b complex topology	X: CoA-dependent acyltransferases (From Topology)	H: CoA-dependent acyltransferases (From Topology)	T: CoA-dependent acyltransferases	F: Condensation_N	ECOD (1.6)
A	Condensation_C_2	e5ja1A2	A: a+b complex topology	X: CoA-dependent acyltransferases (From Topology)	H: CoA-dependent acyltransferases (From Topology)	T: CoA-dependent acyltransferases	F: Condensation_C_2	ECOD (1.6)
A	Hydrolase_4_1	e5ja1A1	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	AMP-binding_1st	e5ja1A5	A: a/b three-layered sandwiches	X: Rossmann-like domain in Acetyl-CoA synthetase-like proteins (From Topology)	H: Rossmann-like domain in Acetyl-CoA synthetase-like proteins (From Topology)	T: Rossmann-like domain in Acetyl-CoA synthetase-like proteins	F: AMP-binding_1st	ECOD (1.6)
A	AMP-binding_2nd	e5ja1A9	A: a/b three-layered sandwiches	X: Rossmann-like domain in Acetyl-CoA synthetase-like proteins (From Topology)	H: Rossmann-like domain in Acetyl-CoA synthetase-like proteins (From Topology)	T: Rossmann-like domain in Acetyl-CoA synthetase-like proteins	F: AMP-binding_2nd	ECOD (1.6)
B	MbtH	e5ja1B1	A: a+b two layers	X: L9 N-domain-like	H: MbtH-like (From Topology)	T: MbtH-like	F: MbtH	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.820.10	Alpha Beta	Alpha-Beta Complex	Rubredoxin-like	Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00501	AMP-binding enzyme (AMP-binding)	AMP-binding enzyme	-	Family
A	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
A	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
B	PF03621	MbtH-like protein (MbtH)	MbtH-like protein	This domain is found in the MbtH protein Swiss:O05821 as well as at the N terminus of the antibiotic synthesis protein NIKP1. MbtH and its homologues were first noted in gene clusters involved in non-ribosomal peptides and other secondary metabolites ...	This domain is found in the MbtH protein Swiss:O05821 as well as at the N terminus of the antibiotic synthesis protein NIKP1. MbtH and its homologues were first noted in gene clusters involved in non-ribosomal peptides and other secondary metabolites by Quadri et al [1]. This domain is about 70 amino acids long and contains 3 fully conserved tryptophan residues [2]. The structure of the PA2412 protein shows it adopts a beta-beta-beta-alpha-alpha topology with the short C-terminal helix forming the tip of an overall arrowhead shape [3]. MbtH proteins have been shown to be required for the synthesis of antibiotics, siderophores and glycopeptidolipids [3-6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Enterobactin synthase component F	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 2,3-dihydroxybenzoate-serine ligase activity acid-amino acid ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity vitamin binding amide binding modified amino acid binding phosphopantetheine binding transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups	enterobactin biosynthetic process polyketide metabolic process organic hydroxy compound metabolic process catechol-containing compound metabolic process secondary metabolic process antibiotic biosynthetic process siderophore biosynthetic process antibiotic metabolic process secondary metabolite biosynthetic process siderophore metabolic process lactone biosynthetic process catechol-containing compound biosynthetic process catechol-containing siderophore biosynthetic process enterobactin metabolic process enterobactin biosynthetic process polyketide metabolic process organic hydroxy compound metabolic process catechol-containing compound metabolic process secondary metabolic process antibiotic biosynthetic process siderophore biosynthetic process antibiotic metabolic process secondary metabolite biosynthetic process siderophore metabolic process lactone biosynthetic process catechol-containing compound biosynthetic process catechol-containing siderophore biosynthetic process enterobactin metabolic process macrolide biosynthetic process macrolide metabolic process biosynthetic process peptide biosynthetic process polyketide biosynthetic process lactone metabolic process organic hydroxy compound biosynthetic process phenol-containing compound metabolic process phenol-containing compound biosynthetic process metabolic process nonribosomal peptide biosynthetic process peptide metabolic process amino acid activation amino acid activation for nonribosomal peptide biosynthetic process amino acid metabolic process primary metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane protein-containing complex catalytic complex enterobactin synthetase complex intracellular protein-containing complex
B	Enterobactin biosynthesis protein YbdZ	-	enterobactin biosynthetic process polyketide metabolic process organic hydroxy compound metabolic process catechol-containing compound metabolic process secondary metabolic process antibiotic biosynthetic process siderophore biosynthetic process antibiotic metabolic process secondary metabolite biosynthetic process siderophore metabolic process lactone biosynthetic process catechol-containing compound biosynthetic process catechol-containing siderophore biosynthetic process enterobactin metabolic process enterobactin biosynthetic process polyketide metabolic process organic hydroxy compound metabolic process catechol-containing compound metabolic process secondary metabolic process antibiotic biosynthetic process siderophore biosynthetic process antibiotic metabolic process secondary metabolite biosynthetic process siderophore metabolic process lactone biosynthetic process catechol-containing compound biosynthetic process catechol-containing siderophore biosynthetic process enterobactin metabolic process macrolide biosynthetic process macrolide metabolic process biosynthetic process peptide biosynthetic process polyketide biosynthetic process lactone metabolic process organic hydroxy compound biosynthetic process phenol-containing compound metabolic process phenol-containing compound biosynthetic process metabolic process nonribosomal peptide biosynthetic process peptide metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006162	Phosphopantetheine attachment site	PTM
A	IPR009081	Phosphopantetheine binding ACP domain	Domain
A	IPR010071	Amino acid adenylation domain	Domain
A	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily
A	IPR020845	AMP-binding, conserved site	Conserved Site
A	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
A	IPR020802	Polyketide synthase, thioesterase domain	Domain
A	IPR045851	AMP-binding enzyme, C-terminal domain superfamily	Homologous Superfamily
A	IPR020806	Polyketide synthase, phosphopantetheine-binding domain	Domain
A	IPR001242	Condensation domain	Domain
A	IPR036736	ACP-like superfamily	Homologous Superfamily
A	IPR000873	AMP-dependent synthetase/ligase domain	Domain
A	IPR001031	Thioesterase	Domain
B	IPR038020	MbtH-like domain superfamily	Homologous Superfamily
B	IPR037407	MbtH-like protein	Family
B	IPR005153	MbtH-like domain	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.