3A7A | pdb_00003a7a

Crystal structure of E. coli lipoate-protein ligase A in complex with octyl-amp and apoH-protein

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)
A	d3a7aa1	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	LplA-like	Two-domain LplA, N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3a7aa2	Alpha and beta proteins (a+b)	SufE/NifU	SufE/NifU	SP1160 C-terminal domain-like	Two-domain LplA, C-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3a7ac1	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	LplA-like	Two-domain LplA, N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3a7ac2	Alpha and beta proteins (a+b)	SufE/NifU	SufE/NifU	SP1160 C-terminal domain-like	Two-domain LplA, C-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3a7ab_	All beta proteins	Barrel-sandwich hybrid	Single hybrid motif	Biotinyl/lipoyl-carrier proteins and domains	Protein H of glycine cleavage system	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3a7ad_	All beta proteins	Barrel-sandwich hybrid	Single hybrid motif	Biotinyl/lipoyl-carrier proteins and domains	Protein H of glycine cleavage system	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SufE/NifU	8033382	3000436	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8033385	3000058	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8033385	3000058	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SufE/NifU	8033382	3000436	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Single hybrid motif	8077749	3001880	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Single hybrid motif	8077749	3001880	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	Lip_prot_lig_C	e3a7aA4	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: SufE/NifU (From Topology)	T: SufE/NifU	F: Lip_prot_lig_C	ECOD (1.6)
A	BPL_LplA_LipB_1	e3a7aA3	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: BPL_LplA_LipB_1	ECOD (1.6)
C	Lip_prot_lig_C	e3a7aC4	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: SufE/NifU (From Topology)	T: SufE/NifU	F: Lip_prot_lig_C	ECOD (1.6)
C	BPL_LplA_LipB_1	e3a7aC3	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: BPL_LplA_LipB_1	ECOD (1.6)
B	GCV_H	e3a7aB1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: GCV_H	ECOD (1.6)
D	GCV_H	e3a7aD1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: GCV_H	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	3.30.390.50	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
C	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
C	3.30.390.50	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
B	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
D	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF21948	Lipoyl protein ligase A/B catalytic domain (LplA-B_cat)	Lipoyl protein ligase A/B catalytic domain	This entry represents the catalytic domain of a group of lipoyl ligases/lipoyltransferases, such as Lipoate-protein ligase A/B (LipA/B) from E.coli and mammalian lipoyltransferases [1-5]. These proteins catalyse the transfer of the lipoyl group from ...	This entry represents the catalytic domain of a group of lipoyl ligases/lipoyltransferases, such as Lipoate-protein ligase A/B (LipA/B) from E.coli and mammalian lipoyltransferases [1-5]. These proteins catalyse the transfer of the lipoyl group from lipoyl-AMP to the specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Lipoic acid is an essential cofactor of the alpha-ketoacid dehydrogenase complexes and the glycine cleavage system.	Domain
A, C	PF10437	Bacterial lipoate protein ligase C-terminus (Lip_prot_lig_C)	Bacterial lipoate protein ligase C-terminus	This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C-terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with the domain BPL_LipA_LipB Pfam:PF03099, furthe ...	This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C-terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with the domain BPL_LipA_LipB Pfam:PF03099, further upstream. This domain is required for adenylation of lipoic acid by lipoate protein ligases. The domain is not required for transfer of lipoic acid from the adenylate to the lipoyl domain. Upon adenylation, this domain rotates 180 degrees away from the active site cleft. Therefore, the domain does not interact with the lipoyl domain during transfer.	Domain
B, D	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	Lipoate-protein ligase A	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding lipoyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity catalytic activity, acting on a protein lipoate-protein ligase activity nucleotidyltransferase activity ligase activity, forming carbon-nitrogen bonds transferase activity, transferring phosphorus-containing groups ligase activity	peptidyl-lysine modification primary metabolic process gene expression protein lipoylation macromolecule biosynthetic process protein maturation biosynthetic process macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
B, D	Glycine cleavage system H protein	-	small molecule metabolic process metabolic process cellular process one-carbon metabolic process glycine decarboxylation via glycine cleavage system catabolic process serine family amino acid metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process small molecule metabolic process metabolic process cellular process one-carbon metabolic process glycine decarboxylation via glycine cleavage system catabolic process serine family amino acid metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process serine family amino acid catabolic process proteinogenic amino acid catabolic process alpha-amino acid catabolic process glycine catabolic process carboxylic acid catabolic process small molecule catabolic process amino acid catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex oxidoreductase complex glycine cleavage complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR004143	Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain	Domain
A, C	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, C	IPR019491	Lipoate protein ligase, C-terminal	Domain
A, C	IPR023741	Lipoate-protein ligase A	Family
A, C	IPR004562	Lipoyltransferase/lipoate-protein ligase	Family
B, D	IPR017453	Glycine cleavage system H-protein, subgroup	Family
B, D	IPR002930	Glycine cleavage system H-protein	Family
B, D	IPR033753	Glycine cleavage system H-protein/Simiate	Family
B, D	IPR011053	Single hybrid motif	Homologous Superfamily
B, D	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site	Binding Site
B, D	IPR000089	Biotin/lipoyl attachment	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.