5EXK

Crystal structure of M. tuberculosis lipoyl synthase with 6-thiooctanoyl peptide intermediate

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Radical SAM enzymes	8093361	3000308	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Radical SAM enzymes	8093361	3000308	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Radical SAM enzymes	8093361	3000308	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Radical SAM enzymes	8093361	3000308	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Radical SAM enzymes	8093361	3000308	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Radical SAM enzymes	8093361	3000308	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)
A	PF04055,PF16881	e5exkA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055,PF16881	ECOD (1.6)
C	PF04055,PF16881	e5exkC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055,PF16881	ECOD (1.6)
E	PF04055,PF16881	e5exkE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055,PF16881	ECOD (1.6)
G	PF04055,PF16881	e5exkG1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055,PF16881	ECOD (1.6)
I	PF04055,PF16881	e5exkI1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055,PF16881	ECOD (1.6)
K	PF04055,PF16881	e5exkK1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055,PF16881	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF04055	Radical SAM superfamily (Radical_SAM)	Radical SAM superfamily	Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.	Domain
A, C, E, G, I A, C, E, G, I, K	PF16881	N-terminal domain of lipoyl synthase of Radical_SAM family (LIAS_N)	N-terminal domain of lipoyl synthase of Radical_SAM family	-	Family
B, D, F, H, J B, D, F, H, J, L	PF01597	Glycine cleavage H-protein (GCV_H)	Glycine cleavage H-protein	This is a family of glycine cleavage H-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. A lipoyl group is attached to a comp ...	This is a family of glycine cleavage H-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. A lipoyl group is attached to a completely conserved lysine residue. The H protein shuttles the methylamine group of glycine from the P protein to the T protein.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K	Lipoyl synthase	lipoate synthase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	intracellular anatomical structure cytoplasm cellular anatomical entity
B, D, F, H, J B, D, F, H, J, L	Octanoylated peptide from M. tuberculosis H protein	-	catabolic process serine family amino acid metabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process cellular catabolic process organic substance metabolic process glycine catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process catabolic process serine family amino acid metabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process cellular catabolic process organic substance metabolic process glycine catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process glycine decarboxylation via glycine cleavage system organonitrogen compound catabolic process organonitrogen compound metabolic process cellular metabolic process L-amino acid catabolic process carboxylic acid metabolic process primary metabolic process L-amino acid metabolic process serine family amino acid catabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process organic substance catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex catalytic complex oxidoreductase complex glycine cleavage complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR003698	Lipoyl synthase	Family
A, C, E, G, I A, C, E, G, I, K	IPR007197	Radical SAM	Domain
A, C, E, G, I A, C, E, G, I, K	IPR006638	Elp3/MiaA/NifB-like, radical SAM core domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR031691	Lipoyl synthase, N-terminal	Domain
B, D, F, H, J B, D, F, H, J, L	IPR017453	Glycine cleavage system H-protein, subgroup	Family
B, D, F, H, J B, D, F, H, J, L	IPR002930	Glycine cleavage system H-protein	Family
B, D, F, H, J B, D, F, H, J, L	IPR033753	Glycine cleavage system H-protein/Simiate	Family
B, D, F, H, J B, D, F, H, J, L	IPR011053	Single hybrid motif	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
B, D, F, H, J B, D, F, H, J, L	IPR000089	Biotin/lipoyl attachment	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.