6PFN | pdb_00006pfn

Succinyl-CoA synthase from Francisella tularensis

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
D	d6pfnd1	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	automated matches	automated matches	(Francisella tularensis subsp. tularensis SCHU S4 ) [TaxId: 177416 ],	SCOPe (2.08)
B	d6pfnb1	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	automated matches	automated matches	(Francisella tularensis subsp. tularensis SCHU S4 ) [TaxId: 177416 ],	SCOPe (2.08)
C	d6pfnc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Francisella tularensis subsp. tularensis SCHU S4 ) [TaxId: 177416 ],	SCOPe (2.08)
C	d6pfnc2	Alpha and beta proteins (a/b)	Flavodoxin-like	Succinyl-CoA synthetase domains	automated matches	automated matches	(Francisella tularensis subsp. tularensis SCHU S4 ) [TaxId: 177416 ],	SCOPe (2.08)
C	d6pfnc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Francisella tularensis subsp. tularensis SCHU S4 ) [TaxId: 177416 ],	SCOPe (2.08)
A	d6pfna1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Francisella tularensis subsp. tularensis SCHU S4 ) [TaxId: 177416 ],	SCOPe (2.08)
A	d6pfna2	Alpha and beta proteins (a/b)	Flavodoxin-like	Succinyl-CoA synthetase domains	automated matches	automated matches	(Francisella tularensis subsp. tularensis SCHU S4 ) [TaxId: 177416 ],	SCOPe (2.08)
A	d6pfna3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Francisella tularensis subsp. tularensis SCHU S4 ) [TaxId: 177416 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	ATP-grasp_2	e6pfnD1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp_2	ECOD (1.6)
D	Citrate_bind	e6pfnD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Succinyl-CoA synthetase domains (From Topology)	T: Succinyl-CoA synthetase domains	F: Citrate_bind	ECOD (1.6)
B	ATP-grasp_2	e6pfnB2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp_2	ECOD (1.6)
B	Citrate_bind	e6pfnB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Succinyl-CoA synthetase domains (From Topology)	T: Succinyl-CoA synthetase domains	F: Citrate_bind	ECOD (1.6)
C	CoA_binding	e6pfnC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding	ECOD (1.6)
C	Succ_CoA_lig	e6pfnC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Succinyl-CoA synthetase domains (From Topology)	T: Succinyl-CoA synthetase domains	F: Succ_CoA_lig	ECOD (1.6)
A	CoA_binding	e6pfnA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding	ECOD (1.6)
A	Succ_CoA_lig	e6pfnA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Succinyl-CoA synthetase domains (From Topology)	T: Succinyl-CoA synthetase domains	F: Succ_CoA_lig	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF08442	ATP-grasp domain (ATP-grasp_2)	ATP-grasp domain		Domain
B, 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	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
A, C	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
B, D	Succinate--CoA ligase [ADP-forming] subunit beta	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 amide metabolic process phosphorus metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex tricarboxylic acid cycle heteromeric enzyme complex succinate-CoA ligase complex
A, C	Succinate--CoA ligase [ADP-forming] subunit alpha	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 cation binding ion binding metal ion 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 binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion 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

InterPro: Protein Family Classification InterPro Database Homepage

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