RTCB

Available protein structures:
PDB	IPR001233 PF01139 (ECOD; PDBsum)
AlphaFold	IPR001233; PF01139;

tRNA splicing ligase RtcB
tRNA splicing ligase RtcB
Identifiers
Symbol	RtcB
Pfam	PF01139
InterPro	IPR001233
PROSITE	PS01288
CATH	1uc2
SCOP2	1uc2 / SCOPe / SUPFAM
PDB
Available protein structures:
PDB	IPR001233 PF01139 (ECOD; PDBsum)
AlphaFold	IPR001233; PF01139;

RTCB
Identifiers
Aliases	RTCB, C22orf28, DJ149A16.6, FAAP, HSPC117, RNA 2',3'-cyclic phosphate and 5'-OH ligase
External IDs	OMIM: 613901; MGI: 106379; GeneCards: RTCB
Enzyme activity
Gene location (Human)
Chr.	Chromosome 22 (human)
End	32,412,248 bp
Gene location (Mouse)
Chr.	Chromosome 10 (mouse)
End	85,793,687 bp
RNA expression pattern
	Top expressed in
	jejunal mucosa; ; islet of Langerhans; ; mucosa of ileum; ; duodenum; ; rectum; ; skin of leg; ; skin of abdomen; ; beta cell; ; skin of arm; ; smooth muscle tissue;
	Top expressed in
	primitive streak; ; mandibular prominence; ; maxillary prominence; ; endocardial cushion; ; facial motor nucleus; ; vestibular sensory epithelium; ; efferent ductule; ; lobe of prostate; ; Rostral migratory stream; ; vas deferens;
	More reference expression data
	n/a
Gene ontology
Molecular function	vinculin binding; nucleotide binding; RNA ligase (ATP) activity; ligase activity; protein binding; ATP binding; RNA ligase activity; metal ion binding; RNA binding;
Cellular component	cytoplasm; tRNA-splicing ligase complex; nuclear envelope; endoplasmic reticulum membrane; nucleus; nucleoplasm; cytosol; intracellular membrane-bounded organelle;
Biological process	RNA processing; tRNA splicing, via endonucleolytic cleavage and ligation; tRNA processing; tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate; in utero embryonic development; placenta development;
	Sources:Amigo / QuickGO
Orthologs
Databases	NCBI: entry; OMA: entry
	51493
	28088
	ENSG00000100220
	ENSMUSG00000001783
	Q9Y3I0
	Q99LF4
	NM_014306
	NM_145422
	NP_055121
	NP_663397
	Wikidata
View/Edit Human	View/Edit Mouse

RNA 2',3'-cyclic phosphate and 5'-OH ligase is a protein that in humans is encoded by the RTCB gene. It is found in the stress granule of cells.

Structure

As of June 2019^[update], no crystal structure of the human RTCB is known, but homology models built from other RtcB-family ligases are available (Swiss-model: Q9Y3I0). The structure of Pyrococcus horikoshii RtcB, which uses GTP instead of ATP, shows two manganese (Mn²⁺) cofactors, and a mechanism involving a covalently linked GTP-histidine-RtcB intermediate. The residue involved, H404, is conserved in human RTCB as H428.

Crystal structures of human RTCB in complex with human archease demonstrates that archease is essential for the activation of RTCB.

Function

RTCB is an RNA ligase that catalyzes the joining of 2′,3′-cyclic phosphate and 5′-OH ends of RNA. In both humans and Escherichia coli it is involved in tRNA and mRNA splicing, specifically in excising transposable elements in animals.

Protein family

RTCB belongs to the RtcB family of ATP-dependent RNA ligases, named after the eponymous protein in E. coli.

References

1 2 3 GRCh38: Ensembl release 89: ENSG00000100220 – Ensembl, May 2017
1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000001783 – Ensembl, May 2017
↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
↑ "Entrez Gene: RNA 2',3'-cyclic phosphate and 5'-OH ligase". Retrieved 6 June 2019.
↑ Jain S, Wheeler JR, Walters RW, Agrawal A, Barsic A, Parker R (January 2016). "ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure". Cell. 164 (3): 487–498. Bibcode:2016Cell..164..487J. doi:10.1016/j.cell.2015.12.038. PMC 4733397. PMID 26777405.
↑ Desai KK, Bingman CA, Phillips GN, Raines RT (April 2013). "Structures of the noncanonical RNA ligase RtcB reveal the mechanism of histidine guanylylation". Biochemistry. 52 (15): 2518–2525. doi:10.1021/bi4002375. PMC 3670941. PMID 23560983.
↑ Gerber JL, Morales Guzmán SI, Worf L, Hubbe P, Kopp J, Peschek J (March 2024). "Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease". Nature Communications. 15 (1) 2378. Bibcode:2024NatCo..15.2378G. doi:10.1038/s41467-024-46568-2. eISSN 2041-1723. PMC 10944509. PMID 38493148.
1 2 Tanaka N, Meineke B, Shuman S (September 2011). "RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA splicing in vivo". The Journal of Biological Chemistry. 286 (35): 30253–30257. doi:10.1074/jbc.C111.274597. PMC 3162383. PMID 21757685.
↑ Zhao LW, Nardone C, Chang C, Paulo JA, Elledge SJ, Kennedy S (2026). "An RNA splicing system that excises DNA transposons from animal mRNAs". Nature. 649 (8096): 496–504. doi:10.1038/s41586-025-09853-8.
↑ Popow J, Englert M, Weitzer S, Schleiffer A, Mierzwa B, Mechtler K, et al. (February 2011). "HSPC117 is the essential subunit of a human tRNA splicing ligase complex". Science. 331 (6018). New York, N.Y.: 760–764. Bibcode:2011Sci...331..760P. doi:10.1126/science.1197847. hdl:11858/00-001M-0000-0011-5682-B. PMID 21311021. S2CID 1881494.
↑ Tanaka N, Shuman S (March 2011). "RtcB is the RNA ligase component of an Escherichia coli RNA repair operon". The Journal of Biological Chemistry. 286 (10): 7727–7731. doi:10.1074/jbc.C111.219022. PMC 3048659. PMID 21224389.

External links

MetaCyc: CPLX-9136: Homo sapiens tRNA-splicing ligase complex (GO:0072669)

This article on a gene on human chromosome 22 is a stub. You can help Wikipedia by adding missing information.

[refGRCh38Ensembl-1] 1 2 3 GRCh38: Ensembl release 89: ENSG00000100220 – Ensembl, May 2017

[refGRCm38Ensembl-2] 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000001783 – Ensembl, May 2017

[3] "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[4] "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[entrez-5] "Entrez Gene: RNA 2',3'-cyclic phosphate and 5'-OH ligase". Retrieved 6 June 2019.

[Jain_2017-6] Jain S, Wheeler JR, Walters RW, Agrawal A, Barsic A, Parker R (January 2016). "ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure". Cell. 164 (3): 487–498. Bibcode:2016Cell..164..487J. doi:10.1016/j.cell.2015.12.038. PMC 4733397. PMID 26777405.

[7] Desai KK, Bingman CA, Phillips GN, Raines RT (April 2013). "Structures of the noncanonical RNA ligase RtcB reveal the mechanism of histidine guanylylation". Biochemistry. 52 (15): 2518–2525. doi:10.1021/bi4002375. PMC 3670941. PMID 23560983.

[GerberMorales_GuzmanWorf2024-8] Gerber JL, Morales Guzmán SI, Worf L, Hubbe P, Kopp J, Peschek J (March 2024). "Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease". Nature Communications. 15 (1) 2378. Bibcode:2024NatCo..15.2378G. doi:10.1038/s41467-024-46568-2. eISSN 2041-1723. PMC 10944509. PMID 38493148.

[Journal-1-9] 1 2 Tanaka N, Meineke B, Shuman S (September 2011). "RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA splicing in vivo". The Journal of Biological Chemistry. 286 (35): 30253–30257. doi:10.1074/jbc.C111.274597. PMC 3162383. PMID 21757685.

[10] Zhao LW, Nardone C, Chang C, Paulo JA, Elledge SJ, Kennedy S (2026). "An RNA splicing system that excises DNA transposons from animal mRNAs". Nature. 649 (8096): 496–504. doi:10.1038/s41586-025-09853-8.

[11] Popow J, Englert M, Weitzer S, Schleiffer A, Mierzwa B, Mechtler K, et al. (February 2011). "HSPC117 is the essential subunit of a human tRNA splicing ligase complex". Science. 331 (6018). New York, N.Y.: 760–764. Bibcode:2011Sci...331..760P. doi:10.1126/science.1197847. hdl:11858/00-001M-0000-0011-5682-B. PMID 21311021. S2CID 1881494.

[12] Tanaka N, Shuman S (March 2011). "RtcB is the RNA ligase component of an Escherichia coli RNA repair operon". The Journal of Biological Chemistry. 286 (10): 7727–7731. doi:10.1074/jbc.C111.219022. PMC 3048659. PMID 21224389.