1CQJ | pdb_00001cqj

CRYSTAL STRUCTURE OF DEPHOSPHORYLATED E. COLI SUCCINYL-COA SYNTHETASE

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1cqja1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	CoA-binding domain	Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1cqja2	Alpha and beta proteins (a/b)	Flavodoxin-like	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase, alpha-chain, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth D]	d1cqjd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	CoA-binding domain	Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth D]	d1cqjd2	Alpha and beta proteins (a/b)	Flavodoxin-like	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase, alpha-chain, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1cqjb1	Alpha and beta proteins (a/b)	Flavodoxin-like	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase, beta-chain, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1cqjb2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Succinyl-CoA synthetase, beta-chain, N-terminal domain	Succinyl-CoA synthetase, beta-chain, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth E]	d1cqje1	Alpha and beta proteins (a/b)	Flavodoxin-like	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase domains	Succinyl-CoA synthetase, beta-chain, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth E]	d1cqje2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Succinyl-CoA synthetase, beta-chain, N-terminal domain	Succinyl-CoA synthetase, beta-chain, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Succinyl-CoA synthetase domain-like	8001535	3000003	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CoA-binding Rossmann-fold domain	8017583	3000049	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	CoA-binding Rossmann-fold domain	8017583	3000049	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Succinyl-CoA synthetase domain-like	8001535	3000003	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Succinyl-CoA synthetase domain-like	8017596	3000003	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8002631	3000094	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8002631	3000094	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Succinyl-CoA synthetase domain-like	8017596	3000003	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	FAD_binding_3	e1cqjA1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
A	B12-binding	e1cqjA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
C [auth D]	FAD_binding_3	e1cqjD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
C [auth D]	B12-binding	e1cqjD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
B	LRR_6,LRR_RI_capping	e1cqjB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.1)
B	B12-binding	e1cqjB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)
D [auth E]	LRR_6,LRR_RI_capping	e1cqjE1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.1)
D [auth E]	B12-binding	e1cqjE2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: B12-binding	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.40.50.261	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Succinyl-CoA synthetase domains	CATH (4.3.0)
C [auth D]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C [auth D]	3.40.50.261	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Succinyl-CoA synthetase domains	CATH (4.3.0)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.40.50.261	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Succinyl-CoA synthetase domains	CATH (4.3.0)
D [auth E]	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D [auth E]	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D [auth E]	3.40.50.261	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Succinyl-CoA synthetase domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D]	PF00549	CoA-ligase (Ligase_CoA)	CoA-ligase	This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP.	Domain
A, C [auth D]	PF02629	CoA binding domain (CoA_binding)	CoA binding domain	This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases.	Domain
B, D [auth E]	PF08442	ATP-grasp domain (ATP-grasp_2)	ATP-grasp domain		Domain
B, D [auth E]	PF00549	CoA-ligase (Ligase_CoA)	CoA-ligase	This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth D]	SUCCINYL-COA SYNTHETASE ALPHA CHAIN	succinate-CoA ligase (ADP-forming) activity succinate-CoA ligase activity ligase activity, forming carbon-sulfur bonds catalytic activity acid-thiol ligase activity ligase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding succinate-CoA ligase (GDP-forming) activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy	succinate-CoA ligase complex (ADP-forming) protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex tricarboxylic acid cycle heteromeric enzyme complex cytoplasm succinate-CoA ligase complex cytosol
B, D [auth E]	SUCCINYL-COA SYNTHETASE BETA CHAIN	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding succinate-CoA ligase (ADP-forming) activity succinate-CoA ligase activity ligase activity, forming carbon-sulfur bonds catalytic activity acid-thiol ligase activity ligase activity succinate-CoA ligase (GDP-forming) activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy nucleoside phosphate metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy nucleoside phosphate metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process small molecule metabolic process succinyl-CoA metabolic process phosphorus metabolic process	succinate-CoA ligase complex (ADP-forming) protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex tricarboxylic acid cycle heteromeric enzyme complex cytoplasm succinate-CoA ligase complex cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth D]	IPR016102	Succinyl-CoA synthetase-like	Homologous Superfamily
A, C [auth D]	IPR017440	ATP-citrate lyase/succinyl-CoA ligase, active site	Active Site
A, C [auth D]	IPR033847	ATP-citrate lyase/succinyl-CoA ligase, conserved site	Conserved Site
A, C [auth D]	IPR003781	CoA-binding	Domain
A, C [auth D]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, C [auth D]	IPR005810	Succinyl-CoA ligase, alpha subunit	Family
A, C [auth D]	IPR005811	ATP-citrate synthase/succinyl-CoA ligase, C-terminal domain	Domain
B, D [auth E]	IPR011761	ATP-grasp fold	Domain
B, D [auth E]	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
B, D [auth E]	IPR016102	Succinyl-CoA synthetase-like	Homologous Superfamily
B, D [auth E]	IPR013650	ATP-grasp fold, succinyl-CoA synthetase-type	Domain
B, D [auth E]	IPR017866	Succinyl-CoA synthetase, beta subunit, conserved site	Conserved Site
B, D [auth E]	IPR005811	ATP-citrate synthase/succinyl-CoA ligase, C-terminal domain	Domain
B, D [auth E]	IPR005809	Succinate--CoA ligase-like, beta subunit	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B	succinate---CoA ligase (ADP-forming) M-CSA #476	Succinyl-CoA synthetase (SCS) catalyses the reversible interchange of ADP, succinyl-CoA and inorganic phosphate with ATP succinate and CoA via a phosphorylated histidine intermediate. The enzyme has two subunit types with the catalysis occurring in an alpha/beta dimer. The alpha subunit is thought to bind CoA, and holds the phosphorylated His residue. It has been proposed that the beta sub unit confers nucleotide specificity.	Defined by 4 residues: GLU:A-208HIS:A-246TYR:B-109GLU:B-197 \| Explore in 3D: M-CSA Motif Definition Extent of motif is too large to support Structure Motif searching. EC: 6.2.1.5 (PDB Primary Data)

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.