4MIM | pdb_00004mim

Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with 3-bromopyruvate

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)
D	PYC_OADA_1st	e4mimD1	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	e4mimD3	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	e4mimD4	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	HMGL-like_2	e4mimD2	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	PYC_OADA_1st	e4mimC1	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	e4mimC3	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	e4mimC4	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	HMGL-like_2	e4mimC2	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	PYC_OADA_1st	e4mimB1	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	e4mimB3	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	e4mimB4	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	HMGL-like_2	e4mimB2	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	PYC_OADA_1st	e4mimA1	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	e4mimA3	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	e4mimA4	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	HMGL-like_2	e4mimA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: HMGL-like_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	1.10.472.90	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
D	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	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)
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	1.10.472.90	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
B	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	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)

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	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	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 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 cellular process glucose metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

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	IPR005479	Carbamoyl phosphate synthase, ATP-binding domain	Domain
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	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	IPR055268	Pyruvate carboxylase-like	Family
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

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.