2Z67

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) selenium transferase (SepSecS)

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2z67a1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	SepSecS-like	Selenocysteinyl-tRNA synthase (SepSecS)	(Methanococcus maripaludis S2 ) [TaxId: 267377 ],	SCOPe (2.08)
B	d2z67b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	SepSecS-like	Selenocysteinyl-tRNA synthase (SepSecS)	(Methanococcus maripaludis S2 ) [TaxId: 267377 ],	SCOPe (2.08)
C	d2z67c_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	SepSecS-like	Selenocysteinyl-tRNA synthase (SepSecS)	(Methanococcus maripaludis S2 ) [TaxId: 267377 ],	SCOPe (2.08)
D	d2z67d_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	SepSecS-like	Selenocysteinyl-tRNA synthase (SepSecS)	(Methanococcus maripaludis S2 ) [TaxId: 267377 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SepSecS-like	8025837	4002346	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PLP-dependent transferases	8038216	3000954	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8038216	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8038216	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8038216	3000954	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	SepSecS	e2z67A1	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SepSecS	ECOD (1.6)
A	Aminotran_5_N	e2z67A2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
B	SepSecS	e2z67B2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SepSecS	ECOD (1.6)
B	Aminotran_5_N	e2z67B3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
C	SepSecS	e2z67C2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SepSecS	ECOD (1.6)
C	Aminotran_5_N	e2z67C3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
D	SepSecS	e2z67D2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SepSecS	ECOD (1.6)
D	Aminotran_5_N	e2z67D3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05889	O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS (SepSecS)	O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS	Early annotation suggested this family, SepSecS, of several eukaryotic and archaeal proteins, was involved in antigen-antibodies responses in the liver and pancreas [1,2]. Structural studies show that the family is O-phosphoseryl-tRNA(Sec) selenium t ...	Early annotation suggested this family, SepSecS, of several eukaryotic and archaeal proteins, was involved in antigen-antibodies responses in the liver and pancreas [1,2]. Structural studies show that the family is O-phosphoseryl-tRNA(Sec) selenium transferase, an enzyme involved in the synthesis of the amino acid selenocysteine (Sec). Sec is the only amino acid whose biosynthesis occurs on its cognate transfer RNA (tRNA). SepSecS catalyses the final step in the formation of the amino acid [3,4,5,6]. The early observation that autoantibodies isolated from patients with type I autoimmune hepatitis targeted a ribonucleoprotein complex containing tRNASec led to the identification and characterisation of the archaeal and the human SepSecS [2]. SepSecS forms its own branch in the family of fold-type I pyridoxal phosphate (PLP) enzymes that goes back to the last universal common ancestor which explains why the archaeal sequences Swiss:Q8TXK0 and Swiss:Q8TYR3 are annotated as being pyridoxal phosphate-dependent enzymes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	O-phosphoseryl-tRNA(Sec) selenium transferase	catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid selenotransferase activity catalytic activity, acting on a tRNA transferase activity O-phosphoseryl-tRNA(Sec) selenium transferase activity catalytic activity RNA binding binding organic cyclic compound binding tRNA binding nucleic acid binding	conversion of seryl-tRNAsec to selenocys-tRNAsec cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process charged-tRNA amino acid modification RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process conversion of seryl-tRNAsec to selenocys-tRNAsec cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process charged-tRNA amino acid modification RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process ncRNA metabolic process macromolecule modification nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process organonitrogen compound metabolic process organonitrogen compound biosynthetic process translation protein metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D	IPR008829	SepSecS/SepCysS family	Family
A, B, C, D	IPR019872	O-phosphoseryl-tRNA(Sec) selenium transferase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B	O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase M-CSA #286	A pyridoxal-phosphate dependent protein. Catalyses the conversion of O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec), part of the selenoprotein biosynthesis pathway. In archaea and eukarya, selenocysteine formation is achieved in a two-step process where O-phosphoseryl-tRNASec kinase phosphorylates the endogenous L-seryl-tRNASec to O-phospho-L-seryl-tRNASec, followed by the conversion of the mis-acylated amino acid-tRNA species to L-selenocysteinyl-tRNASec by Sep-tRNA:Sec-tRNA synthase. The active site is formed at the dimer interface of the tetrameric units, with residues necessary for catalysis originating from both chains.	Defined by 8 residues: HIS:A-186 [auth A-166]ALA:A-269 [auth A-249]LYS:A-298 [auth A-278]ARG:B-92 [auth B-72]ARG:B-114 [auth B-94]SER:B-115 [auth B-95]GLN:B-122 [auth B-102]ARG:B-327 [auth B-307] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.9.1 (PDB Primary Data) Search M-CSA Motif + EC 2.9.1

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.