HAMAP logo

HAMAP rule MF_03144

Send feedback

General rule information [?]

Accession MF_03144
Dates 9-MAR-2011 (Created)
19-NOV-2022 (Last updated, Version 11)
Name RtcB_euk
Scope(s) Eukaryota
Template(s) Q9Y3I0 (RTCB_HUMAN); [ Recover all ]
Triggered by HAMAP; MF_03144 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier RTCB
Protein name RecName: Full=RNA-splicing ligase RtcB homolog;
                 EC=6.5.1.8;
AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase;
case <OC:Vertebrata>
Gene name Name=RTCB;
end case

Comments [?]

FUNCTIONCatalytic 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 Reaction=a 3'-end 3'-phospho-ribonucleotide-RNA + a 5'-end dephospho- ribonucleoside-RNA + GTP = a ribonucleotidyl-ribonucleotide-RNA + diphosphate + GMP; Xref=Rhea:RHEA:68076, Rhea:RHEA-COMP:10463, Rhea:RHEA-COMP:13936, Rhea:RHEA-COMP:17355, ChEBI:CHEBI:33019, ChEBI:CHEBI:37565, ChEBI:CHEBI:58115, ChEBI:CHEBI:83062, ChEBI:CHEBI:138284, ChEBI:CHEBI:173118; EC=6.5.1.8;
CATALYTIC ACTIVITY Reaction=a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + a 5'-end dephospho-ribonucleoside-RNA + GTP + H2O = a ribonucleotidyl- ribonucleotide-RNA + diphosphate + GMP + H(+); Xref=Rhea:RHEA:68080, Rhea:RHEA-COMP:10464, Rhea:RHEA-COMP:13936, Rhea:RHEA-COMP:17355, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019, ChEBI:CHEBI:37565, ChEBI:CHEBI:58115, ChEBI:CHEBI:83064, ChEBI:CHEBI:138284, ChEBI:CHEBI:173118; EC=6.5.1.8;
COFACTOR Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=Binds 2 manganese ions per subunit
SUBUNITCatalytic component of the tRNA-splicing ligase complex.
case <OC:Vertebrata>
SUBCELLULAR LOCATIONCytoplasm.
end case
MISCELLANEOUSLigation 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.
SIMILARITYBelongs to the RtcB family.

Keywords [?]


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

Cross-references [?]

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

Features [?]

From: RTCB_HUMAN (Q9Y3I0)
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 /note="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 Nter: None Cter: None



View rule in raw text format (no links)