7LY7 | pdb_00007ly7

Crystal structure of the elongation module of the bacillamide NRPS, BmdB, in complex with the oxidase BmdC

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B [auth A]	AMP-binding_3rd	e7ly7A1	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)
B [auth A]	PP-binding	e7ly7A6	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PP-binding	ECOD (1.6)
B [auth A]	Condensation_N	e7ly7A3	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)
B [auth A]	Condensation_C_1	e7ly7A2	A: a+b complex topology	X: CoA-dependent acyltransferases (From Topology)	H: CoA-dependent acyltransferases (From Topology)	T: CoA-dependent acyltransferases	F: Condensation_C_1	ECOD (1.6)
B [auth A]	AMP-binding_1st	e7ly7A4	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)
B [auth A]	AMP-binding_2nd	e7ly7A5	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.30.559.10	Alpha Beta	2-Layer Sandwich	Chloramphenicol Acetyltransferase	Chloramphenicol acetyltransferase-like domain	CATH (utative)
B [auth A]	3.30.559.30	Alpha Beta	2-Layer Sandwich	Chloramphenicol Acetyltransferase	Nonribosomal peptide synthetase, condensation domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF00501	AMP-binding enzyme (AMP-binding)	AMP-binding enzyme	-	Family
B [auth A]	PF00668	Condensation domain (Condensation)	Condensation domain	-	Family
B [auth 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
A [auth B]	PF00881	Nitroreductase family (Nitroreductase)	Nitroreductase family	The nitroreductase family comprises a group of FMN- or FAD-dependent and NAD(P)H-dependent enzymes able to metabolize nitrosubstituted compounds.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A]	BmdB, Bacillamide NRPS	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 cellular process secondary metabolic process lipid biosynthetic process primary metabolic process lipid metabolic process antibiotic metabolic process antibiotic biosynthetic process amino acid activation peptide biosynthetic process amino acid activation for nonribosomal peptide biosynthetic process amino acid metabolic process secondary metabolite biosynthetic process biosynthetic process metabolic process cellular process secondary metabolic process lipid biosynthetic process primary metabolic process lipid metabolic process antibiotic metabolic process antibiotic biosynthetic process amino acid activation peptide biosynthetic process amino acid activation for nonribosomal peptide biosynthetic process amino acid metabolic process nonribosomal peptide biosynthetic process peptide metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
A [auth B]	BmdC, Oxidase	oxidoreductase activity catalytic activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR006162	Phosphopantetheine attachment site	PTM
B [auth A]	IPR009081	Phosphopantetheine binding ACP domain	Domain
B [auth A]	IPR020459	AMP-binding	Domain
B [auth A]	IPR010071	Amino acid adenylation domain	Domain
B [auth A]	IPR020845	AMP-binding, conserved site	Conserved Site
B [auth A]	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
B [auth A]	IPR045851	AMP-binding enzyme, C-terminal domain superfamily	Homologous Superfamily
B [auth A]	IPR042099	ANL, N-terminal domain	Homologous Superfamily
B [auth A]	IPR001242	Condensation domain	Domain
B [auth A]	IPR036736	ACP-like superfamily	Homologous Superfamily
B [auth A]	IPR025110	AMP-binding enzyme, C-terminal domain	Domain
B [auth A]	IPR000873	AMP-dependent synthetase/ligase domain	Domain
A [auth B]	IPR029479	Nitroreductase	Domain
A [auth B]	IPR000415	Nitroreductase-like	Homologous Superfamily
A [auth B]	IPR020051	SagB-type dehydrogenase domain	Domain
A [auth B]	IPR052544	Bacteriocin Processing Enzyme	Family

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.