1PIX

Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase

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	d1pixa3	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Biotin dependent carboxylase carboxyltransferase domain	Glutaconyl-CoA decarboxylase A subunit, C-terminal domain	(Acidaminococcus fermentans ) [TaxId: 905 ],	SCOPe (2.08)
A	d1pixa2	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Biotin dependent carboxylase carboxyltransferase domain	Glutaconyl-CoA decarboxylase A subunit, N-terminal domain	(Acidaminococcus fermentans ) [TaxId: 905 ],	SCOPe (2.08)
B	d1pixb3	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Biotin dependent carboxylase carboxyltransferase domain	Glutaconyl-CoA decarboxylase A subunit, C-terminal domain	(Acidaminococcus fermentans ) [TaxId: 905 ],	SCOPe (2.08)
B	d1pixb2	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Biotin dependent carboxylase carboxyltransferase domain	Glutaconyl-CoA decarboxylase A subunit, N-terminal domain	(Acidaminococcus fermentans ) [TaxId: 905 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Biotin dependent carboxylase carboxyltransferase domain	8019865	4000456	SCOP2 (2022-06-29)
A	SCOP2 Family	Biotin dependent carboxylase carboxyltransferase domain	8019866	4000456	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ClpP/crotonase	8032245	3000033	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ClpP/crotonase	8032246	3000033	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8032245	3000033	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8032246	3000033	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	Carboxyl_trans_C	e1pixA1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_C	ECOD (1.6)
B	Carboxyl_trans_C	e1pixB1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.5.680	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single Helix bin	CATH (4.3.0)
A	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
B	1.20.5.680	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single Helix bin	CATH (4.3.0)
B	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01039	Carboxyl transferase domain (Carboxyl_trans)	Carboxyl transferase domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Glutaconyl-CoA decarboxylase A subunit	glutaconyl-CoA decarboxylase activity active transmembrane transporter activity primary active transmembrane transporter activity carboxy-lyase activity transporter activity lyase activity transmembrane transporter activity catalytic activity decarboxylation-driven active transmembrane transporter activity carbon-carbon lyase activity ligase activity	localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport catabolic process oxoacid metabolic process energy derivation by oxidation of organic compounds glutamine family amino acid catabolic process glutamate catabolic process via 2-hydroxyglutarate amino acid metabolic process organic acid metabolic process localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport catabolic process oxoacid metabolic process energy derivation by oxidation of organic compounds glutamine family amino acid catabolic process glutamate catabolic process via 2-hydroxyglutarate amino acid metabolic process organic acid metabolic process dicarboxylic acid catabolic process organic acid catabolic process alpha-amino acid metabolic process anaerobic glutamate catabolic process fermentation glutamine family amino acid metabolic process cellular catabolic process nitrogenous compound fermentation carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process glutamate catabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process generation of precursor metabolites and energy L-amino acid metabolic process anaerobic 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011763	Acetyl-coenzyme A carboxyltransferase, C-terminal	Domain
A, B	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, B	IPR011762	Acetyl-coenzyme A carboxyltransferase, N-terminal	Domain
A, B	IPR045190	Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like	Family
A, B	IPR034733	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A, B	glutaconyl-CoA decarboxylase M-CSA #675	Bacterial Glutaconyl-CoA decarboxylase is an unusual ion transport holozyme, which uses the free energy released from the decarboxylation of glutaconyl CoA to crotonyl CoA in order to power the active transport of sodium ions into the periplasm. The carboxyl transferase subunit, GCDalpha is responsible for the first step in this process whereby the transfer of carbon dioxide to the biotin cofactor on GCDalpha is carried out. This subunit displays structural homology to the family of crotonases such as methylmalonoyl CoA decarboxylase, but little sequence identity, so although it clearly shares a common ancestor, divergence is likely to have occurred a long time in the past.	Defined by 4 residues: VAL:A-152 [auth A-151]GLY:A-195 [auth A-194]ILE:B-418 [auth B-417]ALA:B-458 [auth B-457] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.1.70 (PDB Primary Data) Search M-CSA Motif + EC 4.1.1.70 EC: 7.2.4.5 (UniProt) Search M-CSA Motif + EC 7.2.4.5

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.