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Protein

tRNA-splicing ligase RtcB homolog

Gene

RTCB

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

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
  • poly(A) RNA binding Source: UniProtKB
  • RNA ligase (ATP) activity Source: UniProtKB
  • vinculin binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

ATP-binding, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH: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

HGNCiHGNC:26935. RTCB.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • endoplasmic reticulum membrane Source: WormBase
  • nuclear envelope Source: WormBase
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • tRNA-splicing ligase complex Source: UniProtKB
Complete GO annotation...

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.

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

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9Y3I0.
MaxQBiQ9Y3I0.
PaxDbiQ9Y3I0.
PeptideAtlasiQ9Y3I0.
PRIDEiQ9Y3I0.

2D gel databases

UCD-2DPAGEQ9Y3I0.

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

WithEntry#Exp.IntActNotes
APPL1Q9UKG13EBI-2107208,EBI-741243

GO - Molecular functioni

  • vinculin binding Source: UniProtKB

Protein-protein interaction databases

BioGridi119569. 77 interactors.
DIPiDIP-46750N.
IntActiQ9Y3I0. 27 interactors.
MINTiMINT-4654730.
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.
GeneTreeiENSGT00390000015260.
HOVERGENiHBG081383.
InParanoidiQ9Y3I0.
KOiK14415.
OMAiNMNVEGV.
OrthoDBiEOG091G053A.
PhylomeDBiQ9Y3I0.
TreeFamiTF314404.

Family and domain databases

HAMAPiMF_03144. RtcB_euk. 1 hit.
InterProiIPR001233. RtcB.
IPR027513. RtcB_euk.
[Graphical view]
PANTHERiPTHR11118. PTHR11118. 1 hit.
PfamiPF01139. RtcB. 1 hit.
[Graphical view]
SUPFAMiSSF103365. SSF103365. 1 hit.
PROSITEiPS01288. UPF0027. 1 hit.
[Graphical view]

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 rs11545747dbSNPEnsembl.1
Natural variantiVAR_028853343L → F.1 PublicationCorresponds to variant rs17849275dbSNPEnsembl.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. 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.
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

Cross-referencesi

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. 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.
CCDSiCCDS13905.1.
PIRiT46344.
RefSeqiNP_055121.1. NM_014306.4.
UniGeneiHs.474643.

3D structure databases

ProteinModelPortaliQ9Y3I0.
SMRiQ9Y3I0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119569. 77 interactors.
DIPiDIP-46750N.
IntActiQ9Y3I0. 27 interactors.
MINTiMINT-4654730.
STRINGi9606.ENSP00000216038.

PTM databases

iPTMnetiQ9Y3I0.
PhosphoSitePlusiQ9Y3I0.
SwissPalmiQ9Y3I0.

Polymorphism and mutation databases

BioMutaiRTCB.
DMDMi74753486.

2D gel databases

UCD-2DPAGEQ9Y3I0.

Proteomic databases

EPDiQ9Y3I0.
MaxQBiQ9Y3I0.
PaxDbiQ9Y3I0.
PeptideAtlasiQ9Y3I0.
PRIDEiQ9Y3I0.

Protocols and materials databases

DNASUi51493.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi51493.
DisGeNETi51493.
GeneCardsiRTCB.
HGNCiHGNC:26935. RTCB.
HPAiHPA000535.
HPA001103.
MIMi613901. gene.
neXtProtiNX_Q9Y3I0.
OpenTargetsiENSG00000100220.
PharmGKBiPA145149387.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3833. Eukaryota.
COG1690. LUCA.
GeneTreeiENSGT00390000015260.
HOVERGENiHBG081383.
InParanoidiQ9Y3I0.
KOiK14415.
OMAiNMNVEGV.
OrthoDBiEOG091G053A.
PhylomeDBiQ9Y3I0.
TreeFamiTF314404.

Enzyme and pathway databases

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

Miscellaneous databases

ChiTaRSiRTCB. human.
GenomeRNAii51493.
PROiQ9Y3I0.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000100220.
CleanExiHS_C22orf28.
GenevisibleiQ9Y3I0. HS.

Family and domain databases

HAMAPiMF_03144. RtcB_euk. 1 hit.
InterProiIPR001233. RtcB.
IPR027513. RtcB_euk.
[Graphical view]
PANTHERiPTHR11118. PTHR11118. 1 hit.
PfamiPF01139. RtcB. 1 hit.
[Graphical view]
SUPFAMiSSF103365. SSF103365. 1 hit.
PROSITEiPS01288. UPF0027. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRTCB_HUMAN
AccessioniPrimary (citable) accession number: Q9Y3I0
Secondary accession number(s): B2R6A8
, Q6IAI0, Q9BWL4, Q9NTH1, Q9P037, Q9P0J3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: November 1, 1999
Last modified: November 30, 2016
This is version 137 of the entry and version 1 of the sequence. [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

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

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families
  6. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.