4ZDP | pdb_00004zdp

The crystal structure of Y334C mutant of human SepSecS in complex with selenocysteine tRNA (tRNASec)

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)
A	d4zdpa_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	SepSecS-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4zdpc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	SepSecS-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4zdpd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	SepSecS-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4zdpb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	SepSecS-like	automated matches	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)
A	SCOP2B Superfamily	PLP-dependent transferases	8086500	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8086500	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8086500	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8086500	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		e4zdpA1	A: HTH	X: HTH	H: winged helix domain	T: ThiF	F:	ECOD (20:10:01)
C		e4zdpC1	A: HTH	X: HTH	H: winged helix domain	T: ThiF	F:	ECOD (20:10:01)
D		e4zdpD1	A: HTH	X: HTH	H: winged helix domain	T: ThiF	F:	ECOD (20:10:01)
B		e4zdpB1	A: HTH	X: HTH	H: winged helix domain	T: ThiF	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.2160	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	1.10.10.2160	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	1.10.10.2160	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	1.10.10.2160	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	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
E	selenocysteine tRNA	-	-	-
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 tRNA binding nucleic acid binding	selenocysteine incorporation regulation of cellular process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression protein metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process translational readthrough gene expression selenocysteine incorporation regulation of cellular process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression protein metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process translational readthrough gene expression translation macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of translation translational elongation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process conversion of seryl-tRNAsec to selenocys-tRNAsec tRNA modification RNA metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification tRNA processing macromolecule modification charged-tRNA amino acid modification RNA processing	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

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	IPR019793	Peroxidases heam-ligand binding site	Binding Site
A, B, C, D	IPR008829	SepSecS/SepCysS family	Family
A, B, C, D	IPR019872	O-phosphoseryl-tRNA(Sec) selenium transferase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9HD40	pontocerebellar hypoplasia type 2D Weight Gain pontocerebellar hypoplasia pontocerebellar hypoplasia type 2 tuberculosis amelogenesis imperfecta type 1B atypical teratoid rhabdoid tumor epilepsy intellectual disability medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia amelogenesis imperfecta type 1E autoimmune hepatitis malignant ependymoma pontocerebellar hypoplasia type 2D Weight Gain pontocerebellar hypoplasia pontocerebellar hypoplasia type 2 tuberculosis amelogenesis imperfecta type 1B atypical teratoid rhabdoid tumor epilepsy intellectual disability medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia amelogenesis imperfecta type 1E autoimmune hepatitis malignant ependymoma neurodegenerative disease pancreatic ductal adenocarcinoma primitive neuroectodermal tumor glioblastoma malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.