UniProt Accession

 RTCB_HUMAN; Q9Y3I0; B2R6A8; Q6IAI0; Q9BWL4; Q9NTH1; Q9P037; Q9P0J3 

Genbank Protein ID

 AL050255; AF161466; AF155658; CR457175; CR456450; AK312503; AL021937; CH471095; BC000151; BC002970; BC010308; BC016707; AL137272 

Genbank Nucleotide ID

 CAB43357.1; AAF29081.1; AAF67477.1; CAG33456.1; CAG30336.1; BAG35405.1; CAB38260.1; EAW60021.1; AAH00151.1; AAH02970.1; AAH10308.1; AAH16707.1; CAB70670.1 

Protein Name

 tRNA-splicing ligase RtcB homolog 

Protein Synonyms/Alias

  

Gene Name

 C22orf28 

Gene Synonyms/Alias

 HSPC117 

Created Date

 July 27, 2013 

Organism

 Homo sapiens (Human) 

NCBI Taxa ID

 9606 

Lysine Modification

Position	Peptide	Type	References
14	DELQFLEKINKNCWR	ubiquitination	[1, 2, 3, 4]
17	QFLEKINKNCWRIKK	ubiquitination	[3, 5]
67	GGFLPAMKQIGNVAA	ubiquitination	[1, 2, 3, 4, 5, 6, 7, 8]
140	ESDVQPVKEQLAQAM	ubiquitination	[2, 3, 8]
158	IPVGVGSKGVIPMNA	ubiquitination	[2, 9]
190	GYAWAEDKEHCEEYG	ubiquitination	[3, 9]
206	MLQADPNKVSARAKK	ubiquitination	[2, 3]
245	FNEYAAKKMGIDHKG	ubiquitination	[3]
279	DALVAMEKAMKRDKI	ubiquitination	[3, 10]
285	EKAMKRDKIIVNDRQ	acetylation	[10]
285	EKAMKRDKIIVNDRQ	ubiquitination	[3]
308	PEGQDYLKGMAAAGN	ubiquitination	[2, 3, 7, 8, 9]
366	EQHVVDGKERTLLVH	ubiquitination	[2, 3, 9, 10]
465	AIRVASPKLVMEEAP	ubiquitination	[2, 3, 5, 8, 10]
476	EEAPESYKNVTDVVN	ubiquitination	[3]
492	CHDAGISKKAIKLRP	ubiquitination	[1, 3, 4]
493	HDAGISKKAIKLRPI	ubiquitination	[3, 10]
496	GISKKAIKLRPIAVI	acetylation	[10, 11]
496	GISKKAIKLRPIAVI	ubiquitination	[1, 4, 5]

Reference

 [1] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [2] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [3] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [4] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [5] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [6] Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling.
 Xu G, Paige JS, Jaffrey SR.
 Nat Biotechnol. 2010 Aug;28(8):868-73. [PMID: 20639865]
 [7] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [8] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [9] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [10] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [11] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861] 

Functional Description

 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. 

Sequence Annotation

 METAL 122 122 Zinc (Potential).
 METAL 227 227 Zinc (Potential).
 METAL 259 259 Zinc (Potential).  

Keyword

 ATP-binding; Complete proteome; Cytoplasm; Direct protein sequencing; Ligase; Metal-binding; Nucleotide-binding; Polymorphism; Reference proteome; tRNA processing; Zinc. 

Sequence Source

 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 

Protein Length

 505 AA 

Protein Sequence

Gene Ontology

 GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
 GO:0072669; C:tRNA-splicing ligase complex; IDA:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0003972; F:RNA ligase (ATP) activity; IDA:UniProtKB.
 GO:0007160; P:cell-matrix adhesion; NAS:UniProtKB.
 GO:0001701; P:in utero embryonic development; IEA:Compara.
 GO:0001890; P:placenta development; IEA:Compara.
 GO:0034446; P:substrate adhesion-dependent cell spreading; NAS:UniProtKB.
 GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IDA:UniProtKB. 

Interpro

 IPR027513; RtcB_euk.
 IPR001233; RtcB_family. 

Pfam

 PF01139; UPF0027 

SMART

  

PROSITE

 PS01288; UPF0027 

PRINTS