Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

tRNA-splicing ligase RtcB homolog

Gene

RTCB

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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.2 Publications

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 (PubMed:24870230).1 Publication

Catalytic activityi

ATP + (ribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(ribonucleotide)(m) = (ribonucleotide)(n+m) + AMP + diphosphate.UniRule annotation1 Publication

Cofactori

Mn2+By similarityNote: Binds 2 manganese ions per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi119Manganese 1By similarity1
Metal bindingi122Manganese 1By similarity1
Metal bindingi122Manganese 2By similarity1
Metal bindingi227Manganese 1By similarity1
Binding sitei230GMPBy similarity1
Metal bindingi259Manganese 2By similarity1
Metal bindingi353Manganese 2By similarity1
Binding sitei409GMPBy similarity1
Active sitei428GMP-histidine intermediateBy similarity1
Binding sitei504GMPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi353 – 354GMPBy similarity2
Nucleotide bindingi400 – 403GMPBy similarity4
Nucleotide bindingi428 – 431GMPBy similarity4

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • RNA binding Source: UniProtKB
  • RNA ligase (ATP) activity Source: UniProtKB
  • vinculin binding Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processtRNA processing
LigandATP-binding, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:ENSG00000100220-MONOMER
ReactomeiR-HSA-6784531 tRNA processing in the nucleus

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-splicing ligase RtcB homologUniRule annotation (EC:6.5.1.3UniRule annotation1 Publication)
Gene namesi
Name:RTCBUniRule annotation
Synonyms:C22orf28
ORF Names:HSPC117
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

EuPathDBiHostDB:ENSG00000100220.11
HGNCiHGNC:26935 RTCB
MIMi613901 gene
neXtProtiNX_Q9Y3I0

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi122C → A: Abolishes tRNA ligase activity. 1 Publication1

Organism-specific databases

DisGeNETi51493
OpenTargetsiENSG00000100220
PharmGKBiPA145149387

Chemistry databases

DrugBankiDB02772 Sucrose

Polymorphism and mutation databases

BioMutaiRTCB
DMDMi74753486

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002552411 – 505tRNA-splicing ligase RtcB homologAdd BLAST505

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei300PhosphoserineCombined sources1
Cross-linki496Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9Y3I0
MaxQBiQ9Y3I0
PaxDbiQ9Y3I0
PeptideAtlasiQ9Y3I0
PRIDEiQ9Y3I0

2D gel databases

UCD-2DPAGEiQ9Y3I0

PTM databases

iPTMnetiQ9Y3I0
PhosphoSitePlusiQ9Y3I0
SwissPalmiQ9Y3I0

Expressioni

Gene expression databases

BgeeiENSG00000100220
CleanExiHS_C22orf28
GenevisibleiQ9Y3I0 HS

Organism-specific databases

HPAiHPA000535
HPA001103

Interactioni

Subunit structurei

Catalytic component of the tRNA-splicing ligase complex.UniRule annotation3 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • vinculin binding Source: UniProtKB

Protein-protein interaction databases

BioGridi119569, 92 interactors
CORUMiQ9Y3I0
DIPiDIP-46750N
IntActiQ9Y3I0, 38 interactors
MINTiQ9Y3I0
STRINGi9606.ENSP00000216038

Structurei

3D structure databases

ProteinModelPortaliQ9Y3I0
SMRiQ9Y3I0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RtcB family.UniRule annotation

Phylogenomic databases

eggNOGiKOG3833 Eukaryota
COG1690 LUCA
GeneTreeiENSGT00830000128284
HOVERGENiHBG081383
InParanoidiQ9Y3I0
KOiK14415
OMAiYDVAHNV
OrthoDBiEOG091G053A
PhylomeDBiQ9Y3I0
TreeFamiTF314404

Family and domain databases

Gene3Di3.90.1860.10, 1 hit
HAMAPiMF_03144 RtcB_euk, 1 hit
InterProiView protein in InterPro
IPR001233 RtcB
IPR036025 RtcB-like_sf
IPR027513 RtcB_euk
PANTHERiPTHR11118 PTHR11118, 1 hit
PfamiView protein in Pfam
PF01139 RtcB, 1 hit
SUPFAMiSSF103365 SSF103365, 1 hit
PROSITEiView protein in PROSITE
PS01288 UPF0027, 1 hit

Sequencei

Sequence statusi: Complete.

Q9Y3I0-1 [UniParc]FASTAAdd to basket

« Hide

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

AVIKG
Length:505
Mass (Da):55,210
Last modified:November 1, 1999 - v1
Checksum:iC7C0CC2C95BDD27B
GO

Sequence cautioni

The sequence AAF29081 differs from that shown. Reason: Frameshift at positions 295 and 298.Curated
The sequence AAF67477 differs from that shown. Reason: Frameshift at positions 173 and 180.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti296A → P in AAF29081 (PubMed:11042152).Curated1
Sequence conflicti303G → V in AAF29081 (PubMed:11042152).Curated1
Sequence conflicti303G → V in AAF67477 (PubMed:10931946).Curated1
Sequence conflicti427C → R in CAG33456 (Ref. 4) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_052485153V → A. Corresponds to variant dbSNP:rs11545747Ensembl.1
Natural variantiVAR_028853343L → F1 PublicationCorresponds to variant dbSNP:rs17849275Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 No translation available.
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
CCDSiCCDS13905.1
PIRiT46344
RefSeqiNP_055121.1, NM_014306.4
UniGeneiHs.474643

Genome annotation databases

EnsembliENST00000216038; ENSP00000216038; ENSG00000100220
GeneIDi51493
KEGGihsa:51493
UCSCiuc003amm.3 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiRTCB_HUMAN
AccessioniPrimary (citable) accession number: Q9Y3I0
Secondary accession number(s): B2R6A8
, Q6IAI0, Q9BWL4, Q9NTH1, Q9P037, Q9P0J3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: November 1, 1999
Last modified: March 28, 2018
This is version 146 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health