HAMAP rule MF_03144

General rule information [?]

Accession	MF_03144
Dates	9-MAR-2011 (Created) 19-NOV-2022 (Last updated, Version 11)

Name

RtcB_euk

Scope

Eukaryota

Template

Q9Y3I0 (RTCB_HUMAN)

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

RTCB

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 EC 6.5.1.8
	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(+) EC 6.5.1.8
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>

Cytoplasm

end case

GTP-binding
Ligase
Manganese
Metal-binding
Nucleotide-binding
tRNA processing

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 [?]

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 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

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