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Annotation rule MF_01278
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General rule information [?]

Accession MF_01278
Dates 16-APR-2007 (Created)
19-NOV-2019 (Last updated, Version 16)
Name Ser_tRNA_synth_type2
Scope
Archaea
Templates Q46AN5 (SYS2_METBF); Q58477 (SYS2_METJA); O30520 (SYS2_METMP); O27194 (SYS2_METTH): [Recover all]
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

Identifier
SYS2
Protein name
RecName: Full=Type-2 serine--tRNA ligase;
EC 6.1.1.11;
AltName: Full=Seryl-tRNA synthetase;
Short=SerRS;
AltName: Full=Seryl-tRNA(Ser/Sec) synthetase;
Gene name
serS

Comments [?]

Function Catalyzes the attachment of serine to tRNA(Ser). 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).
Catalytic activity RHEA:12292: ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser)
EC 6.1.1.11
RHEA:42580: ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-seryl-tRNA(Sec)
EC 6.1.1.11
case <FTGroup:1>
Cofactor Zn(2+)
Note: Binds 1 Zn(2+) ion per subunit. This ion is coordinated with 2 cysteines, 1 glutamate and a water molecule that dissociates from the zinc ion to allow the coordination of the amino group of the serine substrate, which is essential for catalysis.
end case
Pathway Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1.
Subunit Homodimer.
Subcellular location Cytoplasm.
Domain Consists of two distinct domains, a catalytic core and a N-terminal extension that is presumably involved in tRNA binding.
Similarity Belongs to the class-II aminoacyl-tRNA synthetase family. Type-2 seryl-tRNA synthetase subfamily.

Keywords [?]

Cytoplasm
Aminoacyl-tRNA synthetase
ATP-binding
Ligase
Metal-binding
Nucleotide-binding
Protein biosynthesis
case <FTGroup:1>
Metal-binding
Zinc
end case

Gene Ontology [?]

GO:0004828; Molecular function: serine-tRNA ligase activity.
GO:0005524; Molecular function: ATP binding.
case <FTGroup:1>
GO:0008270; Molecular function: zinc ion binding.
end case
GO:0016260; Biological process: selenocysteine biosynthetic process.
GO:0006434; Biological process: seryl-tRNA aminoacylation.
GO:0005737; Cellular component: cytoplasm.

Cross-references [?]

PROSITE PS50862; AA_TRNA_LIGASE_II; 1;
Pfam PF00587; tRNA-synt_2b; 1;
TIGRFAMs TIGR00415; SerS_MJ; 1;

Features [?]

From: SYS2_METBF (Q46AN5)
Key     From     To       Description   Tag   Condition   FTGroup
NP_BIND     336     338       ATP     R-x-E  
NP_BIND     347     348       ATP     R-V  
REGION     353     355       Serine binding     R-x-E  
METAL     306     306       Zinc; catalytic     C   1
METAL     355     355       Zinc; catalytic     E   1
METAL     461     461       Zinc; catalytic     C   1
BINDING     304     304       Serine; via carbonyl oxygen     A  
BINDING     336     336       Serine     R  
BINDING (Optional)     400     400       Serine     Q  
BINDING (Optional)     432     432       ATP     E  
BINDING (Optional)     435     435       Serine     N  
BINDING     468     468       ATP     R  

Additional information [?]

Size range 500-527 amino acids
Related rules None
Fusion None
Comments  There are two distinct types of seryl-tRNA synthetase, as differentiated by primary sequence analysis, three-dimensional structure and substrate recognition mechanism: type 1 (MF_00176) is found in the majority of organisms (prokaryotes, eukaryotes and archaea) whereas type 2 (MF_01278) is confined to some methanogenic archaea. METBF (Methanosarcina barkeri) possesses two seryl-tRNA synthetases, one of each type.


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