3TW6

Structure of Rhizobium etli pyruvate carboxylase T882A with the allosteric activator, acetyl coenzyme-A

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PYC_OADA_1st	e3tw6A12	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like (From Topology)	T: post-HMGL domain-like	F: PYC_OADA_1st	ECOD (1.6)
A	PYC_OADA_2nd_1	e3tw6A17	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like (From Topology)	T: post-HMGL domain-like	F: PYC_OADA_2nd_1	ECOD (1.6)
A	PYC_OADA_3rd	e3tw6A14	A: a+b two layers	X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related (From Homology)	H: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related	T: a+b domain in pyruvate carboxylase	F: PYC_OADA_3rd	ECOD (1.6)
A	ATP-grasp	e3tw6A13	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	ECOD (1.6)
A	Biotin_carb_C	e3tw6A16	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
A	HMGL-like_2	e3tw6A11	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: HMGL-like_2	ECOD (1.6)
A	Biotin_carb_N	e3tw6A15	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
B	PYC_OADA_1st	e3tw6B2	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like (From Topology)	T: post-HMGL domain-like	F: PYC_OADA_1st	ECOD (1.6)
B	PYC_OADA_2nd_1	e3tw6B12	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like (From Topology)	T: post-HMGL domain-like	F: PYC_OADA_2nd_1	ECOD (1.6)
B	PYC_OADA_3rd	e3tw6B8	A: a+b two layers	X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related (From Homology)	H: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related	T: a+b domain in pyruvate carboxylase	F: PYC_OADA_3rd	ECOD (1.6)
B	ATP-grasp	e3tw6B11	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	ECOD (1.6)
B	Biotin_carb_C	e3tw6B10	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
B	Biotin_lipoyl	e3tw6B7	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl	ECOD (1.6)
B	HMGL-like_2	e3tw6B9	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: HMGL-like_2	ECOD (1.6)
B	Biotin_carb_N	e3tw6B6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
C	PYC_OADA_1st	e3tw6C7	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like (From Topology)	T: post-HMGL domain-like	F: PYC_OADA_1st	ECOD (1.6)
C	PYC_OADA_2nd_1	e3tw6C12	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like (From Topology)	T: post-HMGL domain-like	F: PYC_OADA_2nd_1	ECOD (1.6)
C	PYC_OADA_3rd	e3tw6C10	A: a+b two layers	X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related (From Homology)	H: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related	T: a+b domain in pyruvate carboxylase	F: PYC_OADA_3rd	ECOD (1.6)
C	ATP-grasp	e3tw6C8	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	ECOD (1.6)
C	Biotin_carb_C	e3tw6C11	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
C	HMGL-like_2	e3tw6C6	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: HMGL-like_2	ECOD (1.6)
C	Biotin_carb_N	e3tw6C9	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
D	PYC_OADA_1st	e3tw6D2	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like (From Topology)	T: post-HMGL domain-like	F: PYC_OADA_1st	ECOD (1.6)
D	PYC_OADA_2nd_1	e3tw6D12	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like (From Topology)	T: post-HMGL domain-like	F: PYC_OADA_2nd_1	ECOD (1.6)
D	PYC_OADA_3rd	e3tw6D8	A: a+b two layers	X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related (From Homology)	H: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related	T: a+b domain in pyruvate carboxylase	F: PYC_OADA_3rd	ECOD (1.6)
D	ATP-grasp	e3tw6D11	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	ECOD (1.6)
D	Biotin_carb_C	e3tw6D10	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
D	Biotin_lipoyl	e3tw6D7	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl	ECOD (1.6)
D	HMGL-like_2	e3tw6D9	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: HMGL-like_2	ECOD (1.6)
D	Biotin_carb_N	e3tw6D6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	3.10.600.10	Alpha Beta	Roll	pyruvate carboxylase f1077a mutant fold	pyruvate carboxylase f1077a mutant domain	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	1.10.472.90	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
A	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	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	3.10.600.10	Alpha Beta	Roll	pyruvate carboxylase f1077a mutant fold	pyruvate carboxylase f1077a mutant domain	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	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)
C	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
C	3.10.600.10	Alpha Beta	Roll	pyruvate carboxylase f1077a mutant fold	pyruvate carboxylase f1077a mutant domain	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	1.10.472.90	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
C	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
D	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D	3.10.600.10	Alpha Beta	Roll	pyruvate carboxylase f1077a mutant fold	pyruvate carboxylase f1077a mutant domain	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	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, B, C, D	PF00682	HMGL-like (HMGL-like)	HMGL-like	This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase.	Domain
A, B, C, D	PF00364	Biotin-requiring enzyme (Biotin_lipoyl)	Biotin-requiring enzyme	This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the HMM does not currently recognise the Glycine cleavage system H proteins.	Domain
A, B, C, D	PF02786	Carbamoyl-phosphate synthase L chain, ATP binding domain (CPSase_L_D2)	Carbamoyl-phosphate synthase L chain, ATP binding domain	Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [2]. The c ...	Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [2]. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00988. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117. The ATP binding domain (this one) has an ATP-grasp fold.	Domain
A, B, C, D	PF00289	Biotin carboxylase, N-terminal domain (Biotin_carb_N)	Biotin carboxylase, N-terminal domain	This domain is structurally related to the PreATP-grasp domain. The family contains the N-terminus of biotin carboxylase enzymes [1,3], and propionyl-CoA carboxylase A chain [2].	Domain
A, B, C, D	PF02785	Biotin carboxylase C-terminal domain (Biotin_carb_C)	Biotin carboxylase C-terminal domain	Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference [1] are i ...	Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference [1] are in this C-terminal domain.	Domain
A, B, C, D	PF02436	Conserved carboxylase domain (PYC_OADA)	Conserved carboxylase domain	This domain represents a conserved region in pyruvate carboxylase (PYC), oxaloacetate decarboxylase alpha chain (OADA), and transcarboxylase 5s subunit. The domain is found adjacent to the HMGL-like domain (Pfam:PF00682) and often close to the bio ...	This domain represents a conserved region in pyruvate carboxylase (PYC), oxaloacetate decarboxylase alpha chain (OADA), and transcarboxylase 5s subunit. The domain is found adjacent to the HMGL-like domain (Pfam:PF00682) and often close to the biotin_lipoyl domain (Pfam:PF00364) of biotin requiring enzymes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Pyruvate carboxylase protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyruvate carboxylase activity ligase activity, forming carbon-carbon bonds catalytic activity ligase activity cation binding metal ion binding	monosaccharide metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process primary metabolic process monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process biosynthetic process small molecule metabolic process metabolic process glucose metabolic process pyruvate metabolic process monosaccharide metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process primary metabolic process monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process biosynthetic process small molecule metabolic process metabolic process glucose metabolic process pyruvate metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process cellular process monocarboxylic acid metabolic process organic acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR005481	Biotin carboxylase-like, N-terminal domain	Domain
A, B, C, D	IPR011761	ATP-grasp fold	Domain
A, B, C, D	IPR011764	Biotin carboxylation domain	Domain
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR000891	Pyruvate carboxyltransferase	Domain
A, B, C, D	IPR005930	Pyruvate carboxylase	Family
A, B, C, D	IPR005482	Biotin carboxylase, C-terminal	Domain
A, B, C, D	IPR005479	Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain	Domain
A, B, C, D	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B, C, D	IPR003379	Carboxylase, conserved domain	Domain
A, B, C, D	IPR011054	Rudiment single hybrid motif	Homologous Superfamily
A, B, C, D	IPR011053	Single hybrid motif	Homologous Superfamily
A, B, C, D	IPR001882	Biotin-binding site	Binding Site
A, B, C, D	IPR000089	Biotin/lipoyl attachment	Domain