4C8R | pdb_00004c8r

Human gamma-butyrobetaine dioxygenase (BBOX1) in complex with Ni(II) and N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine (AR692B)

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d4c8rf2	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	TauD/TfdA-like	Gamma-butyrobetaine dioxygenase (BBOX1) catalytic domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d4c8rf1	Alpha and beta proteins (a+b)	GBBH N-terminal domain-like	GBBH N-terminal domain-like (DUF971)	GBBH N-terminal domain-like (DUF971)	Gamma-butyrobetaine dioxygenase (BBOX1) N-terminal domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4c8re2	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	TauD/TfdA-like	Gamma-butyrobetaine dioxygenase (BBOX1) catalytic domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4c8re1	Alpha and beta proteins (a+b)	GBBH N-terminal domain-like	GBBH N-terminal domain-like (DUF971)	GBBH N-terminal domain-like (DUF971)	Gamma-butyrobetaine dioxygenase (BBOX1) N-terminal domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4c8rd2	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	TauD/TfdA-like	Gamma-butyrobetaine dioxygenase (BBOX1) catalytic domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4c8rd1	Alpha and beta proteins (a+b)	GBBH N-terminal domain-like	GBBH N-terminal domain-like (DUF971)	GBBH N-terminal domain-like (DUF971)	Gamma-butyrobetaine dioxygenase (BBOX1) N-terminal domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4c8rc2	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	TauD/TfdA-like	Gamma-butyrobetaine dioxygenase (BBOX1) catalytic domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4c8rc1	Alpha and beta proteins (a+b)	GBBH N-terminal domain-like	GBBH N-terminal domain-like (DUF971)	GBBH N-terminal domain-like (DUF971)	Gamma-butyrobetaine dioxygenase (BBOX1) N-terminal domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4c8rb2	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	TauD/TfdA-like	Gamma-butyrobetaine dioxygenase (BBOX1) catalytic domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4c8rb1	Alpha and beta proteins (a+b)	GBBH N-terminal domain-like	GBBH N-terminal domain-like (DUF971)	GBBH N-terminal domain-like (DUF971)	Gamma-butyrobetaine dioxygenase (BBOX1) N-terminal domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4c8ra2	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	TauD/TfdA-like	Gamma-butyrobetaine dioxygenase (BBOX1) catalytic domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4c8ra1	Alpha and beta proteins (a+b)	GBBH N-terminal domain-like	GBBH N-terminal domain-like (DUF971)	GBBH N-terminal domain-like (DUF971)	Gamma-butyrobetaine dioxygenase (BBOX1) N-terminal domain	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Clavaminate synthase-like	8106688	3001848	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	NE0471 N-terminal domain-like	8106684	3000231	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Clavaminate synthase-like	8106688	3001848	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	NE0471 N-terminal domain-like	8106684	3000231	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Clavaminate synthase-like	8106688	3001848	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NE0471 N-terminal domain-like	8106684	3000231	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Clavaminate synthase-like	8106688	3001848	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NE0471 N-terminal domain-like	8106684	3000231	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NE0471 N-terminal domain-like	8106684	3000231	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Clavaminate synthase-like	8106688	3001848	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	NE0471 N-terminal domain-like	8106684	3000231	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Clavaminate synthase-like	8106688	3001848	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)
F	DUF971	e4c8rF2	A: beta barrels	X: XRCC4, N-terminal domain-like	H: NE0471 N-terminal domain-like (From Topology)	T: NE0471 N-terminal domain-like	F: DUF971	ECOD (1.6)
F	TauD	e4c8rF1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: TauD	ECOD (1.6)
E	DUF971	e4c8rE2	A: beta barrels	X: XRCC4, N-terminal domain-like	H: NE0471 N-terminal domain-like (From Topology)	T: NE0471 N-terminal domain-like	F: DUF971	ECOD (1.6)
E	TauD	e4c8rE1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: TauD	ECOD (1.6)
D	DUF971	e4c8rD2	A: beta barrels	X: XRCC4, N-terminal domain-like	H: NE0471 N-terminal domain-like (From Topology)	T: NE0471 N-terminal domain-like	F: DUF971	ECOD (1.6)
D	TauD	e4c8rD1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: TauD	ECOD (1.6)
C	DUF971	e4c8rC2	A: beta barrels	X: XRCC4, N-terminal domain-like	H: NE0471 N-terminal domain-like (From Topology)	T: NE0471 N-terminal domain-like	F: DUF971	ECOD (1.6)
C	TauD	e4c8rC1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: TauD	ECOD (1.6)
B	DUF971	e4c8rB2	A: beta barrels	X: XRCC4, N-terminal domain-like	H: NE0471 N-terminal domain-like (From Topology)	T: NE0471 N-terminal domain-like	F: DUF971	ECOD (1.6)
B	TauD	e4c8rB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: TauD	ECOD (1.6)
A	DUF971	e4c8rA2	A: beta barrels	X: XRCC4, N-terminal domain-like	H: NE0471 N-terminal domain-like (From Topology)	T: NE0471 N-terminal domain-like	F: DUF971	ECOD (1.6)
A	TauD	e4c8rA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: TauD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.2020.30	Alpha Beta	2-Layer Sandwich	NE0471 N-terminal domain-like		CATH (4.3.0)
F	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (4.3.0)
E	3.30.2020.30	Alpha Beta	2-Layer Sandwich	NE0471 N-terminal domain-like		CATH (4.3.0)
E	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (4.3.0)
D	3.30.2020.30	Alpha Beta	2-Layer Sandwich	NE0471 N-terminal domain-like		CATH (4.3.0)
D	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (4.3.0)
C	3.30.2020.30	Alpha Beta	2-Layer Sandwich	NE0471 N-terminal domain-like		CATH (4.3.0)
C	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (4.3.0)
B	3.30.2020.30	Alpha Beta	2-Layer Sandwich	NE0471 N-terminal domain-like		CATH (4.3.0)
B	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (4.3.0)
A	3.30.2020.30	Alpha Beta	2-Layer Sandwich	NE0471 N-terminal domain-like		CATH (4.3.0)
A	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02668	Taurine catabolism dioxygenase TauD, TfdA family (TauD)	Taurine catabolism dioxygenase TauD, TfdA family	This family consists of taurine catabolism dioxygenases of the TauD, TfdA family. TauD from E. coli Swiss:P37610 is a alpha-ketoglutarate-dependent taurine dioxygenase [1]. This enzyme catalyses the oxygenolytic release of sulfite from taurine [1]. ...	This family consists of taurine catabolism dioxygenases of the TauD, TfdA family. TauD from E. coli Swiss:P37610 is a alpha-ketoglutarate-dependent taurine dioxygenase [1]. This enzyme catalyses the oxygenolytic release of sulfite from taurine [1]. TfdA from Burkholderia sp. Swiss:Q45423 is a 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase [2]. TfdA from Alcaligenes eutrophus JMP134 Swiss:P10088 is a 2,4-dichlorophenoxyacetate monooxygenase [3]. Also included are gamma-Butyrobetaine hydroxylase enzymes EC:1.14.11.1 [4].	Domain
A, B, C, D, E A, B, C, D, E, F	PF06155	Gamma-butyrobetaine hydroxylase-like, N-terminal (GBBH-like_N)	Gamma-butyrobetaine hydroxylase-like, N-terminal	This domain is found in several proteins including gamma-butyrobetaine dioxygenase, Fe-S cluster assembly factor HCF101 and trimethyllysine dioxygenase proteins. Gamma-butyrobetaine hydroxylase (GBBH) is a alpha-ketoglutarate-dependent dioxygenase ...	This domain is found in several proteins including gamma-butyrobetaine dioxygenase, Fe-S cluster assembly factor HCF101 and trimethyllysine dioxygenase proteins. Gamma-butyrobetaine hydroxylase (GBBH) is a alpha-ketoglutarate-dependent dioxygenase that catalyzes the biosynthesis of L-carnitine by hydroxylation of gamma-butyrobetaine (GBB). GBBH is a dimeric enzyme. The monomer consists of a catalytic double-stranded beta-helix domain and a smaller N-terminal domain. The N-terminal domain has a bound Zn ion, which is coordinated by three cysteines and one histidine. The N-terminal domain could facilitate dimer formation, but its precise function is not known [1]. Other family members have been suggested to be involved in FeS cluster maintenance (see Supplementary note 5 in [2].)	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	GAMMA-BUTYROBETAINE DIOXYGENASE	oxidoreductase activity gamma-butyrobetaine dioxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding zinc ion binding oxidoreductase activity gamma-butyrobetaine dioxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding zinc ion binding identical protein binding protein binding	carnitine metabolic process amino-acid betaine biosynthetic process biosynthetic process carnitine biosynthetic process modified amino acid biosynthetic process modified amino acid metabolic process metabolic process cellular process amino-acid betaine metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR003819	TauD/TfdA-like domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR010376	Gamma-butyrobetaine hydroxylase-like, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR042098	Taurine dioxygenase TauD-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR038492	GBBH-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR012775	Gamma-butyrobetaine hydroxylase-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR050411	Alpha-ketoglutarate-dependent hydroxylases	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: O75936	Liver Cirrhosis, Experimental astrocytic tumor breast carcinoma glioblastoma malignant ependymoma oligodendroglioma pituitary cancer atypical teratoid rhabdoid tumor cystic fibrosis large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor breast cancer esophageal adenocarcinoma Liver Cirrhosis, Experimental astrocytic tumor breast carcinoma glioblastoma malignant ependymoma oligodendroglioma pituitary cancer atypical teratoid rhabdoid tumor cystic fibrosis large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor breast cancer esophageal adenocarcinoma nephrosclerosis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.