2Z67
Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) selenium transferase (SepSecS)
External Resource: 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 |
---|---|---|---|---|---|
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 ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR015424 | Pyridoxal phosphate-dependent transferase | Homologous Superfamily | |
IPR015421 | Pyridoxal phosphate-dependent transferase, major domain | Homologous Superfamily | |
IPR008829 | SepSecS/SepCysS family | Family | |
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 |
---|---|---|---|
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] | EC: 2.9.1 (PDB Primary Data) |