6YBQ | pdb_00006ybq

Engineered glycolyl-CoA carboxylase (quintuple mutant) with bound CoA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
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)
A	d6ybqa1	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	automated matches	automated matches	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)
B	d6ybqb1	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	automated matches	automated matches	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)
C	d6ybqc1	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	automated matches	automated matches	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)
D	d6ybqd1	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	automated matches	automated matches	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)
E	d6ybqe1	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	automated matches	automated matches	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)
F	d6ybqf1	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	automated matches	automated matches	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)

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	e6ybqA2	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	e6ybqB2	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)
C	Carboxyl_trans_C	e6ybqC1	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)
D	Carboxyl_trans_C	e6ybqD2	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)
E	Carboxyl_trans_C	e6ybqE2	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)
F	Carboxyl_trans_C	e6ybqF1	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)
H	PccA	e6ybqH2	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: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA	ECOD (1.6)
H	Biotin_lipoyl	e6ybqH1	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)
G	PccA	e6ybqG2	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: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA	ECOD (1.6)
G	Biotin_lipoyl	e6ybqG1	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)
I	PccA	e6ybqI2	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: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA	ECOD (1.6)
I	Biotin_lipoyl	e6ybqI1	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)
J	PccA	e6ybqJ2	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: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA	ECOD (1.6)
J	Biotin_lipoyl	e6ybqJ1	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)
K	PccA	e6ybqK2	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: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA	ECOD (1.6)
K	Biotin_lipoyl	e6ybqK1	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)
L	PccA	e6ybqL2	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: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA	ECOD (1.6)
L	Biotin_lipoyl	e6ybqL1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF01039	Carboxyl transferase domain (Carboxyl_trans)	Carboxyl transferase domain	-	Family
G, H, I, J, K G, H, I, J, K, L	PF18140	Propionyl-coenzyme A carboxylase BT domain (PCC_BT)	Propionyl-coenzyme A carboxylase BT domain	This domain is found in Propionyl-coenzyme A carboxylase (PCC), present in Roseobacter denitrificans. PCC is a mitochondrial biotin-dependent enzyme that is essential for the catabolism of certain amino acids, cholesterol, and fatty acids with an odd ...	This domain is found in Propionyl-coenzyme A carboxylase (PCC), present in Roseobacter denitrificans. PCC is a mitochondrial biotin-dependent enzyme that is essential for the catabolism of certain amino acids, cholesterol, and fatty acids with an odd number of carbon atoms. Since this domain mediates biotin carboxylase-carboxyltransferase interactions it is referred to as the BT domain. The BT domain is located between biotin carboxylase and the biotin carboxyl carrier protein domains. The BT domain shares some structural similarity with the pyruvate carboxylase tetramerization domain of pyruvate carboxylase [1].	Domain
G, H, I, J, K G, H, I, J, K, L	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Propionyl-CoA carboxylase beta chain	CoA carboxylase activity propionyl-CoA carboxylase activity ligase activity, forming carbon-carbon bonds catalytic activity ligase activity	-	-
G, H, I, J, K G, H, I, J, K, L	Propionyl-CoA carboxylase alpha subunit	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 CoA carboxylase activity propionyl-CoA carboxylase activity ligase activity, forming carbon-carbon bonds catalytic activity ligase activity cation binding metal ion binding	lipid catabolic process catabolic process metabolic process cellular process primary metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR011763	Acetyl-coenzyme A carboxyltransferase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR011762	Acetyl-coenzyme A carboxyltransferase, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR034733	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	Domain
A, B, C, D, E A, B, C, D, E, F	IPR051047	Acyl-CoA Carboxylase Beta Subunit	Family
G, H, I, J, K G, H, I, J, K, L	IPR005481	Biotin carboxylase-like, N-terminal domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR011761	ATP-grasp fold	Domain
G, H, I, J, K G, H, I, J, K, L	IPR011764	Biotin carboxylation domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR050856	Biotin-dependent Carboxylase Complex	Family
G, H, I, J, K G, H, I, J, K, L	IPR005482	Biotin carboxylase, C-terminal	Domain
G, H, I, J, K G, H, I, J, K, L	IPR005479	Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR011054	Rudiment single hybrid motif	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR041265	Propionyl-coenzyme A carboxylase, BT domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR011053	Single hybrid motif	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR001882	Biotin-binding site	Binding Site
G, H, I, J, K G, H, I, J, K, L	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.