4R1M | pdb_00004r1m

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.48 A resolution

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)
D		e4r1mD1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: GntR	F:	ECOD (20:10:01)
D		e4r1mD4	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T:	F:	ECOD (20:10:01)
C		e4r1mC2	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: GntR	F:	ECOD (20:10:01)
C		e4r1mC4	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T:	F:	ECOD (20:10:01)
B		e4r1mB1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: GntR	F:	ECOD (20:10:01)
B		e4r1mB4	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T:	F:	ECOD (20:10:01)
A		e4r1mA1	A: Middle and GTPase effector domains in dynamin-related proteins	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: GntR	F:	ECOD (20:10:01)
A		e4r1mA3	A: Alpha-beta plaits	X: Protease propeptides/inhibitors	H: Protease propeptides/inhibitors	T: SBP_bac_5	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.12780	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	ANL, N-terminal domain	CATH (4.3.0)
D	3.30.300.30	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
C	3.40.50.12780	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	ANL, N-terminal domain	CATH (4.3.0)
C	3.30.300.30	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
B	3.40.50.12780	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	ANL, N-terminal domain	CATH (4.3.0)
B	3.30.300.30	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
A	3.40.50.12780	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	ANL, N-terminal domain	CATH (4.3.0)
A	3.30.300.30	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00501	AMP-binding enzyme (AMP-binding)	AMP-binding enzyme	-	Family
A, B, C, D	PF14535	AMP-binding enzyme C-terminal domain (AMP-binding_C_2)	AMP-binding enzyme C-terminal domain	This is a small domain that is found C terminal to Pfam:PF00501. It has a central beta sheet core that is flanked by alpha helices.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Phenylacetate-coenzyme A ligase	CoA-ligase activity ligase activity, forming carbon-sulfur bonds catalytic activity ligase activity phenylacetate-CoA ligase activity acid-thiol ligase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	cellular response to stimulus catabolic process benzene-containing compound metabolic process response to stimulus oxoacid metabolic process cellular response to xenobiotic stimulus carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus monocarboxylic acid catabolic process response to chemical cellular response to stimulus catabolic process benzene-containing compound metabolic process response to stimulus oxoacid metabolic process cellular response to xenobiotic stimulus carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus monocarboxylic acid catabolic process response to chemical carboxylic acid catabolic process phenylacetate catabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process small molecule catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR051414	Adenylate-forming_Reductase	Unknown
A, B, C, D	IPR042099	ANL, N-terminal domain	Homologous Superfamily
A, B, C, D	IPR028154	AMP-dependent ligase, C-terminal	Domain
A, B, C, D	IPR045851	AMP-binding enzyme domain superfamily	Homologous Superfamily
A, B, C, D	IPR011880	Phenylacetate-CoA ligase	Family
A, B, C, D	IPR000873	AMP-dependent synthetase/ligase 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.