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HAMAP rule MF_03144
General rule information
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| 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
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Identifier, protein and gene names
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| 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
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| 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 | 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 |
| 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. |
Keywords
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| case <OC:Vertebrata> | |
| Cytoplasm | |
| end case | |
| GTP-binding | |
| Ligase | |
| Manganese | |
| Metal-binding | |
| Nucleotide-binding | |
| tRNA processing | |
Gene Ontology
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| 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
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Features
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| 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
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| Size range | 457-535 amino acids |
| Related rules |
None |
| Fusion | Nter: None Cter: None |