1SES
CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE
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 | d1sesa1 | All alpha proteins | Long alpha-hairpin | tRNA-binding arm | Seryl-tRNA synthetase (SerRS) | Seryl-tRNA synthetase (SerRS) | (Thermus thermophilus ) [TaxId: 274 ], | SCOPe (2.08) |
A | d1sesa2 | Alpha and beta proteins (a+b) | Class II aaRS and biotin synthetases | Class II aaRS and biotin synthetases | Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | Seryl-tRNA synthetase (SerRS) | (Thermus thermophilus ) [TaxId: 274 ], | SCOPe (2.08) |
B | d1sesb1 | All alpha proteins | Long alpha-hairpin | tRNA-binding arm | Seryl-tRNA synthetase (SerRS) | Seryl-tRNA synthetase (SerRS) | (Thermus thermophilus ) [TaxId: 274 ], | SCOPe (2.08) |
B | d1sesb2 | Alpha and beta proteins (a+b) | Class II aaRS and biotin synthetases | Class II aaRS and biotin synthetases | Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | Seryl-tRNA synthetase (SerRS) | (Thermus thermophilus ) [TaxId: 274 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | tRNA-binding arm | 8036318 | 3000776 | SCOP2B (2022-06-29) |
A | SCOP2B Superfamily | Class II aaRS and biotin synthetases | 8035887 | 3000058 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Class II aaRS and biotin synthetases | 8035887 | 3000058 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | tRNA-binding arm | 8036318 | 3000776 | 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 | PF02403 | e1sesA1 | A: alpha bundles | X: Long alpha-hairpin | H: tRNA-binding arm (From Topology) | T: tRNA-binding arm | F: PF02403 | ECOD (1.6) |
A | PF00587 | e1sesA2 | A: a+b three layers | X: Class II aaRS and biotin synthetases (From Topology) | H: Class II aaRS and biotin synthetases (From Topology) | T: Class II aaRS and biotin synthetases | F: PF00587 | ECOD (1.6) |
B | PF02403 | e1sesB1 | A: alpha bundles | X: Long alpha-hairpin | H: tRNA-binding arm (From Topology) | T: tRNA-binding arm | F: PF02403 | ECOD (1.6) |
B | PF00587 | e1sesB2 | A: a+b three layers | X: Class II aaRS and biotin synthetases (From Topology) | H: Class II aaRS and biotin synthetases (From Topology) | T: Class II aaRS and biotin synthetases | F: PF00587 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 1.10.287.40 | Mainly Alpha | Orthogonal Bundle | Helix Hairpins | Serine-tRNA synthetase, tRNA binding domain | CATH (4.3.0) |
A | 3.30.930.10 | Alpha Beta | 2-Layer Sandwich | BirA Bifunctional Protein | domain 2 | CATH (4.3.0) |
B | 1.10.287.40 | Mainly Alpha | Orthogonal Bundle | Helix Hairpins | Serine-tRNA synthetase, tRNA binding domain | CATH (4.3.0) |
B | 3.30.930.10 | Alpha Beta | 2-Layer Sandwich | BirA Bifunctional Protein | domain 2 | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00587 | tRNA synthetase class II core domain (G, H, P, S and T) (tRNA-synt_2b) | tRNA synthetase class II core domain (G, H, P, S and T) | tRNA-synt_2b is a family of largely threonyl-tRNA members. | Domain | |
PF02403 | Seryl-tRNA synthetase N-terminal domain (Seryl_tRNA_N) | Seryl-tRNA synthetase N-terminal domain | This domain is found associated with the Pfam tRNA synthetase class II domain (Pfam:PF00587) and represents the N-terminal domain of seryl-tRNA synthetase. | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR045864 | Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) | Homologous Superfamily | |
IPR042103 | Serine-tRNA synthetase, type1, N-terminal domain superfamily | Homologous Superfamily | |
IPR002317 | Serine-tRNA ligase, type1 | Family | |
IPR015866 | Serine-tRNA synthetase, type1, N-terminal | Domain | |
IPR006195 | Aminoacyl-tRNA synthetase, class II | Domain | |
IPR002314 | Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) | Domain | |
IPR010978 | Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm | Homologous Superfamily | |
IPR033729 | Serine-tRNA ligase catalytic core domain | Domain |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
serine---tRNA ligase M-CSA #884 | Serine-tRNA ligase (EC:6.1.1.11) exists as monomer and belongs to the aminoacyl-tRNA synthetase class IIa. It catalyses the attachment of serine to tRNA (Ser). It is also able to aminoacylate tRNA (Sec) with serine, to form the misacylated tRNA L-seryl-tRNA (Sec), which will be further converted into selenocysteinyl-tRNA (Sec). | Defined by 5 residues: ARG:A-256ARG:A-271GLU:A-345SER:A-348ARG:A-386 | EC: 6.1.1.11 (PDB Primary Data) |