Q9Y3I0 (RTCB_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA-splicing ligase RtcB homolog
EC=6.5.1.3

Gene names

Name:	C22orf28
ORF Names:	HSPC117

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	505 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (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 a RNA ligase with broad substrate specificity, and may function toward other RNAs. Ref.15
Catalytic activity	ATP + (ribonucleotide)(n) + (ribonucleotide)(m) = AMP + diphosphate + (ribonucleotide)(n+m). Ref.15
Subunit structure	Catalytic component of the tRNA-splicing ligase complex. Ref.12 Ref.15
Subcellular location	Cytoplasm By similarity HAMAP-Rule MF_03144.
Sequence similarities	Belongs to the RtcB family.
Sequence caution	The sequence AAF29081.1 differs from that shown. Reason: Frameshift at positions 295 and 298. The sequence AAF67477.1 differs from that shown. Reason: Frameshift at positions 173 and 180.

Ontologies

Keywords
Biological process	tRNA processing
Cellular component	Cytoplasm
Coding sequence diversity	Polymorphism
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Ligase
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	cell-matrix adhesion Non-traceable author statement PubMed 15163412. Source: UniProtKB in utero embryonic development Inferred from electronic annotation. Source: Compara placenta development Inferred from electronic annotation. Source: Compara substrate adhesion-dependent cell spreading Non-traceable author statement PubMed 15163412. Source: UniProtKB tRNA splicing, via endonucleolytic cleavage and ligation Inferred from direct assay Ref.15. Source: UniProtKB
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell tRNA-splicing ligase complex Inferred from direct assay Ref.15. Source: UniProtKB
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA ligase (ATP) activity Inferred from direct assay Ref.15. Source: UniProtKB metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 505	505	tRNA-splicing ligase RtcB homolog HAMAP-Rule MF_03144		PRO_0000255241
Sites
	Metal binding	122	1	Zinc Potential
	Metal binding	227	1	Zinc Potential
	Metal binding	259	1	Zinc Potential
Natural variations
	Natural variant	153	1	V → A. Corresponds to variant rs11545747 [ dbSNP | Ensembl ].		VAR_052485
	Natural variant	343	1	L → F. Ref.9 Corresponds to variant rs17849275 [ dbSNP | Ensembl ].		VAR_028853
Experimental info
	Mutagenesis	122	1	C → A: Abolishes tRNA ligase activity. Ref.15
	Sequence conflict	296	1	A → P in AAF29081. Ref.2
	Sequence conflict	303	1	G → V in AAF29081. Ref.2
	Sequence conflict	303	1	G → V in AAF67477. Ref.3
	Sequence conflict	427	1	C → R in CAG33456. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Q9Y3I0 [UniParc]. Last modified November 1, 1999. Version 1. Checksum: C7C0CC2C95BDD27B	FASTA	505	55,210
	10 20 30 40 50 60 MSRSYNDELQ FLEKINKNCW RIKKGFVPNM QVEGVFYVND ALEKLMFEEL RNACRGGGVG 70 80 90 100 110 120 GFLPAMKQIG NVAALPGIVH RSIGLPDVHS GYGFAIGNMA AFDMNDPEAV VSPGGVGFDI 130 140 150 160 170 180 NCGVRLLRTN LDESDVQPVK EQLAQAMFDH IPVGVGSKGV IPMNAKDLEE ALEMGVDWSL 190 200 210 220 230 240 REGYAWAEDK EHCEEYGRML QADPNKVSAR AKKRGLPQLG TLGAGNHYAE IQVVDEIFNE 250 260 270 280 290 300 YAAKKMGIDH KGQVCVMIHS GSRGLGHQVA TDALVAMEKA MKRDKIIVND RQLACARIAS 310 320 330 340 350 360 PEGQDYLKGM AAAGNYAWVN RSSMTFLTRQ AFAKVFNTTP DDLDLHVIYD VSHNIAKVEQ 370 380 390 400 410 420 HVVDGKERTL LVHRKGSTRA FPPHHPLIAV DYQLTGQPVL IGGTMGTCSY VLTGTEQGMT 430 440 450 460 470 480 ETFGTTCHGA GRALSRAKSR RNLDFQDVLD KLADMGIAIR VASPKLVMEE APESYKNVTD 490 500 VVNTCHDAGI SKKAIKLRPI AVIKG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Reevaluating human gene annotation: a second-generation analysis of chromosome 22." Collins J.E., Goward M.E., Cole C.G., Smink L.J., Huckle E.J., Knowles S., Bye J.M., Beare D.M., Dunham I. Genome Res. 13:27-36(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[2]	"Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells." Zhang Q.-H., Ye M., Wu X.-Y., Ren S.-X., Zhao M., Zhao C.-J., Fu G., Shen Y., Fan H.-Y., Lu G., Zhong M., Xu X.-R., Han Z.-G., Zhang J.-W., Tao J., Huang Q.-H., Zhou J., Hu G.-X. , Gu J., Chen S.-J., Chen Z. Genome Res. 10:1546-1560(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Umbilical cord blood.
[3]	"Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning." Hu R.-M., Han Z.-G., Song H.-D., Peng Y.-D., Huang Q.-H., Ren S.-X., Gu Y.-J., Huang C.-H., Li Y.-B., Jiang C.-L., Fu G., Zhang Q.-H., Gu B.-W., Dai M., Mao Y.-F., Gao G.-F., Rong R., Ye M. , Zhou J., Xu S.-H., Gu J., Shi J.-X., Jin W.-R., Zhang C.-K., Wu T.-M., Huang G.-Y., Chen Z., Chen M.-D., Chen J.-L. Proc. Natl. Acad. Sci. U.S.A. 97:9543-9548(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Adrenal gland.
[4]	"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)." Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B. Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[5]	"A genome annotation-driven approach to cloning the human ORFeome." Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I. Genome Biol. 5:R84.1-R84.11(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Thalamus.
[7]	"The DNA sequence of human chromosome 22." Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J., Ainscough R., Almeida J.P., Babbage A.K., Bagguley C., Bailey J., Barlow K.F., Bates K.N., Beasley O.P., Bird C.P., Blakey S.E., Bridgeman A.M. , Buck D., Burgess J., Burrill W.D., Burton J., Carder C., Carter N.P., Chen Y., Clark G., Clegg S.M., Cobley V.E., Cole C.G., Collier R.E., Connor R., Conroy D., Corby N.R., Coville G.J., Cox A.V., Davis J., Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M., Ellington A.G., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A., Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C., Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E., Jones M.C., Kershaw J., Kimberley A.M., King A., Laird G.K., Langford C.F., Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M., Matthews L.H., Mccann O.T., Mcclay J., Mclaren S., McMurray A.A., Milne S.A., Mortimore B.J., Odell C.N., Pavitt R., Pearce A.V., Pearson D., Phillimore B.J.C.T., Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y., Rogers L., Ross M.T., Scott C.E., Sehra H.K., Skuce C.D., Smalley S., Smith M.L., Soderlund C., Spragon L., Steward C.A., Sulston J.E., Swann R.M., Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.L., Williams L., Williams S.A., Williamson H., Wilmer T.E., Wilming L., Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N., Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J., Shintani A., Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S., Roe B.A., Chen F., Chu L., Crabtree J., Deschamps S., Do A., Do T., Dorman A., Fang F., Fu Y., Hu P., Hua A., Kenton S., Lai H., Lao H.I., Lewis J., Lewis S., Lin S.-P., Loh P., Malaj E., Nguyen T., Pan H., Phan S., Qi S., Qian Y., Ray L., Ren Q., Shaull S., Sloan D., Song L., Wang Q., Wang Y., Wang Z., White J., Willingham D., Wu H., Yao Z., Zhan M., Zhang G., Chissoe S., Murray J., Miller N., Minx P., Fulton R., Johnson D., Bemis G., Bentley D., Bradshaw H., Bourne S., Cordes M., Du Z., Fulton L., Goela D., Graves T., Hawkins J., Hinds K., Kemp K., Latreille P., Layman D., Ozersky P., Rohlfing T., Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K., Nelson J., Korf I., Bedell J.A., Hillier L.W., Mardis E., Waterston R., Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S., Budarf M.L., McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E., Edelmann L., Kim U.J., Shizuya H., Simon M.I., Dumanski J.P., Peyrard M., Kedra D., Seroussi E., Fransson I., Tapia I., Bruder C.E., O'Brien K.P., Wilkinson P., Bodenteich A., Hartman K., Hu X., Khan A.S., Lane L., Tilahun Y., Wright H. Nature 402:489-495(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[8]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[9]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT PHE-343. Tissue: Choriocarcinoma and Lung carcinoma.
[10]	Bienvenut W.V., Boldt K., von Kriegsheim A.F., Kolch W. Submitted (JUL-2007) to UniProtKB Cited for: PROTEIN SEQUENCE OF 4-14; 45-51; 56-81; 141-158; 199-206; 264-279; 298-308; 442-460 AND 466-476, MASS SPECTROMETRY. Tissue: Hepatoma.
[11]	"The full-ORF clone resource of the German cDNA consortium." Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I. BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 309-505. Tissue: Testis.
[12]	"Kinesin transports RNA: isolation and characterization of an RNA-transporting granule." Kanai Y., Dohmae N., Hirokawa N. Neuron 43:513-525(2004) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN A RNA TRANSPORT COMPLEX.
[13]	"Proteomic analysis of SUMO4 substrates in HEK293 cells under serum starvation-induced stress." Guo D., Han J., Adam B.-L., Colburn N.H., Wang M.-H., Dong Z., Eizirik D.L., She J.-X., Wang C.-Y. Biochem. Biophys. Res. Commun. 337:1308-1318(2005) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
[14]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]	"HSPC117 is the essential subunit of a human tRNA splicing ligase complex." Popow J., Englert M., Weitzer S., Schleiffer A., Mierzwa B., Mechtler K., Trowitzsch S., Will C.L., Luhrmann R., Soll D., Martinez J. Science 331:760-764(2011) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, CATALYTIC ACTIVITY, IDENTIFICATION IN THE TRNA SPLICING LIGASE COMPLEX, MUTAGENESIS OF CYS-122.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AL050255 mRNA. Translation: CAB43357.1. AF161466 mRNA. Translation: AAF29081.1. Frameshift. AF155658 mRNA. Translation: AAF67477.1. Frameshift. CR457175 mRNA. Translation: CAG33456.1. CR456450 mRNA. Translation: CAG30336.1. AK312503 mRNA. Translation: BAG35405.1. AL021937 Genomic DNA. Translation: CAB38260.1. CH471095 Genomic DNA. Translation: EAW60021.1. BC000151 mRNA. Translation: AAH00151.1. BC002970 mRNA. Translation: AAH02970.1. BC010308 mRNA. Translation: AAH10308.1. BC016707 mRNA. Translation: AAH16707.1. AL137272 mRNA. Translation: CAB70670.1.
IPI	IPI00550689.
PIR	T46344.
RefSeq	NP_055121.1. NM_014306.4.
UniGene	Hs.474643.
3D structure databases
ProteinModelPortal	Q9Y3I0.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9Y3I0. 10 interactions.
MINT	MINT-4654730.
STRING	9606.ENSP00000216038.
PTM databases
PhosphoSite	Q9Y3I0.
Polymorphism databases
DMDM	74753486.
2D gel databases
UCD-2DPAGE	Q9Y3I0.
Proteomic databases
PaxDb	Q9Y3I0.
PeptideAtlas	Q9Y3I0.
PRIDE	Q9Y3I0.
Protocols and materials databases
DNASU	51493.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000216038; ENSP00000216038; ENSG00000100220.
GeneID	51493.
KEGG	hsa:51493.
UCSC	uc003amm.2. human.
Organism-specific databases
CTD	51493.
GeneCards	GC22M032783.
HGNC	HGNC:26935. C22orf28.
HPA	HPA001103.
MIM	613901. gene.
neXtProt	NX_Q9Y3I0.
PharmGKB	PA145149387.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG1690.
HOVERGEN	HBG081383.
InParanoid	Q9Y3I0.
KO	K14415.
OMA	GRMLNAD.
OrthoDB	EOG4DFPN7.
PhylomeDB	Q9Y3I0.
Gene expression databases
ArrayExpress	Q9Y3I0.
Bgee	Q9Y3I0.
CleanEx	HS_C22orf28.
Genevestigator	Q9Y3I0.
GermOnline	ENSG00000100220. Homo sapiens.
Family and domain databases
HAMAP	MF_03144. RtcB_euk.
InterPro	IPR027513. RtcB_euk. IPR001233. RtcB_family. [Graphical view]
PANTHER	PTHR11118. PTHR11118. 1 hit.
Pfam	PF01139. UPF0027. 1 hit. [Graphical view]
SUPFAM	SSF103365. UPF0027. 1 hit.
PROSITE	PS01288. UPF0027. 1 hit. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	C22orf28. human.
GenomeRNAi	51493.
NextBio	55157.
SOURCE	Search...

Entry information

Entry name

RTCB_HUMAN

Accession

Primary (citable) accession number: Q9Y3I0
Secondary accession number(s): B2R6A8 , Q6IAI0, Q9BWL4, Q9NTH1, Q9P037, Q9P0J3

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 31, 2006
Last sequence update:	November 1, 1999
Last modified:	May 29, 2013
This is version 99 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.