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HAMAP rule MF_03144

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General rule information [?]

Accession MF_03144
Dates 9-MAR-2011 (Created)
19-NOV-2022 (Last updated, Version 11)
Name RtcB_euk
Template Q9Y3I0 (RTCB_HUMAN)

Propagated annotation [?]

Identifier, protein and gene names [?]

Protein name
RecName: Full=RNA-splicing ligase RtcB homolog;
AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase;
case <OC:Vertebrata>
Gene name
end case

Comments [?]

Function Catalytic subunit of the tRNA-splicing ligase complex that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as an RNA ligase with broad substrate specificity, and may function toward other RNAs.
Catalytic activity RHEA:68076: a 3'-end 3'-phospho-ribonucleotide-RNA + a 5'-end dephospho-ribonucleoside-RNA + GTP = a ribonucleotidyl-ribonucleotide-RNA + diphosphate + GMP
RHEA:68080: a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + a 5'-end dephospho-ribonucleoside-RNA + GTP + H2O = a ribonucleotidyl-ribonucleotide-RNA + diphosphate + GMP + H(+)
Cofactor Mn(2+)
Note: Binds 2 manganese ions per subunit
Subunit Catalytic component of the tRNA-splicing ligase complex.
case <OC:Vertebrata>
Subcellular location Cytoplasm.
end case
Miscellaneous Ligation probably proceeds through 3 nucleotidyl transfer steps, with 2',3'-cyclic phosphate termini being hydrolyzed to 3'-P termini in a step that precedes 3'-P activation with GMP. In the first nucleotidyl transfer step, RTCB reacts with GTP to form a covalent RTCB-histidine-GMP intermediate with release of PPi; in the second step, the GMP moiety is transferred to the RNA 3'-P; in the third step, the 5'-OH from the opposite RNA strand attacks the activated 3'-P to form a 3',5'-phosphodiester bond and release GMP.
Similarity Belongs to the RtcB family.

Cross-references [?]

PROSITE PS01288; UPF0027; 1;
Pfam PF01139; RtcB; 1;

Keywords [?]

case <OC:Vertebrata>
end case

Gene Ontology [?]

GO:0072669; Cellular component: tRNA-splicing ligase complex.
GO:0016886; Molecular function: ligase activity, forming phosphoric ester bonds.
GO:0006388; Biological process: tRNA splicing, via endonucleolytic cleavage and ligation.

Features [?]

Key     From     To       Description   Tag   Condition   FTGroup
BINDING     226     230       /ligand="GMP" /ligand_id="ChEBI:CHEBI:58115     N-H-Y-x-E  
BINDING     353     354       /ligand="GMP" /ligand_id="ChEBI:CHEBI:58115     H-N  
BINDING     402     405       /ligand="GMP" /ligand_id="ChEBI:CHEBI:58115     G-G-[TS]-M  
BINDING     428     431       /ligand="GMP" /ligand_id="ChEBI:CHEBI:58115     H-G-[AS]-G  
ACT_SITE     428     428       GMP-histidine intermediate     H  
BINDING     119     119       /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="1     D  
BINDING     122     122       /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="1     C  
BINDING     122     122       /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="2     C  
BINDING     227     227       /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="1     H  
BINDING     259     259       /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="2     H  
BINDING     353     353       /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="2     H  
BINDING     409     409       /ligand="GMP" /ligand_id="ChEBI:CHEBI:58115     S  
BINDING     504     504       /ligand="GMP" /ligand_id="ChEBI:CHEBI:58115     K  

Additional information [?]

Size range 457-535 amino acids
Related rules None
Fusion None