5X6B | pdb_00005x6b

Crystal structure of SepCysE-SepCysS in complex with tRNACys from Methanocaldococcus jannaschii

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth E]	SCOP2B Superfamily	MJ1481 dimerisation domain-like	8091696	3002536	SCOP2B (2022-06-29)
D [auth F]	SCOP2 Family	SepCysE dimerisation domain-like	8045732	4004646	SCOP2 (2022-06-29)
D [auth F]	SCOP2 Family	SepCysE C-terminal domain-like	8091697	4007756	SCOP2 (2022-06-29)
D [auth F]	SCOP2 Superfamily	MJ1481 dimerisation domain-like	8091696	3002536	SCOP2 (2022-06-29)
D [auth F]	SCOP2 Superfamily	Toprim domain-like	8091698	3000737	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth E]	ATP-synt_A	e5x6bE1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: ATP-synt_A	ECOD (v294.1)
D [auth F]	DUF2100	e5x6bF1	A: a/b three-layered sandwiches	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: DUF2100	ECOD (v294.1)
D [auth F]	PHD	e5x6bF2	A: a/b three-layered sandwiches	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (v294.1)
A [auth I]	ATP-synt_Eps	e5x6bI1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
B [auth J]	RuBisCO_large_N	e5x6bJ1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: RuBisCO_large_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth I]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A [auth I]	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B [auth J]	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B [auth J]	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 [auth I], B [auth J]	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 [auth P]	tRNACys	-	-	-
C [auth E], D [auth F]	Uncharacterized protein MJ1481	-	-	-
A [auth I], B [auth J]	O-phospho-L-seryl-tRNA:Cys-tRNA synthase	cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity Sep-tRNA:Cys-tRNA synthase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity, transferring alkyl or aryl (other than methyl) groups	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth E], D [auth F]	IPR016736	MJ1481-like	Family
A [auth I], B [auth J]	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A [auth I], B [auth J]	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A [auth I], B [auth J]	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A [auth I], B [auth J]	IPR008829	SepSecS/SepCysS family	Family
A [auth I], B [auth J]	IPR013375	O-phosphoseryl-tRNA:Cys-tRNA synthase, archaea	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth I], B [auth J]	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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.