6NPB

X-ray crystal structure of TmpA, 2-trimethylaminoethylphosphonate hydroxylase, with Fe and 2OG

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	gamma-butyrobetaine hydroxylase (BBOX) N-terminal domain-like	8106689	4005840	SCOP2 (2022-06-29)
A	SCOP2 Family	TauD/TfdA-like	8106691	4002161	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	NE0471 N-terminal domain-like	8106690	3000231	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Clavaminate synthase-like	8106692	3001848	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	NE0471 N-terminal domain-like	8106690	3000231	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Clavaminate synthase-like	8106692	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)
A	PF06155	e6npbA1	A: beta barrels	X: XRCC4, N-terminal domain-like	H: NE0471 N-terminal domain-like (From Topology)	T: NE0471 N-terminal domain-like	F: PF06155	ECOD (1.6)
A	PF02668	e6npbA2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PF02668	ECOD (1.6)
B	PF06155	e6npbB1	A: beta barrels	X: XRCC4, N-terminal domain-like	H: NE0471 N-terminal domain-like (From Topology)	T: NE0471 N-terminal domain-like	F: PF06155	ECOD (1.6)
B	PF02668	e6npbB2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PF02668	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	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	TmpA, 2-trimethylaminoethylphosphonate hydroxylase	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	carnitine metabolic process organonitrogen compound metabolic process amino-acid betaine biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process amino-acid betaine metabolic process cellular modified amino acid metabolic process organic substance metabolic process biosynthetic process carnitine biosynthetic process cellular modified amino acid biosynthetic process organic substance biosynthetic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003819	TauD/TfdA-like domain	Domain
A, B	IPR010376	Gamma-butyrobetaine hydroxylase-like, N-terminal	Domain
A, B	IPR042098	Taurine dioxygenase TauD-like superfamily	Homologous Superfamily
A, B	IPR038492	GBBH-like, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR012775	Gamma-butyrobetaine hydroxylase-like	Family

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 R01GM133198.