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Protein

tRNA-splicing ligase RtcB homolog

Gene

RTCB

Organism
Bos taurus (Bovine)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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.UniRule annotation

Catalytic activityi

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

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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

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

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-splicing ligase RtcB homologUniRule annotation (EC:6.5.1.3UniRule annotation)
Gene namesi
Name:RTCBUniRule annotation
OrganismiBos taurus (Bovine)
Taxonomic identifieri9913 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos
Proteomesi
  • UP000009136 Componenti: Chromosome 5

Subcellular locationi

  • Nucleus By similarity
  • Cytoplasm UniRule annotation

  • Note: Enters into the nucleus in case of active transcription while it accumulates in cytosol when transcription level is low.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002552401 – 505tRNA-splicing ligase RtcB homologAdd BLAST505

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei300PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ5E9T9.
PeptideAtlasiQ5E9T9.
PRIDEiQ5E9T9.

Expressioni

Gene expression databases

BgeeiENSBTAG00000011070.

Interactioni

Subunit structurei

Catalytic component of the tRNA-splicing ligase complex.UniRule annotation

Protein-protein interaction databases

STRINGi9913.ENSBTAP00000014699.

Structurei

3D structure databases

ProteinModelPortaliQ5E9T9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RtcB family.UniRule annotation

Phylogenomic databases

eggNOGiKOG3833. Eukaryota.
COG1690. LUCA.
GeneTreeiENSGT00390000015260.
HOVERGENiHBG081383.
InParanoidiQ5E9T9.
KOiK14415.
OMAiNMNVEGV.
OrthoDBiEOG091G053A.
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.

Q5E9T9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRSYNDELQ FLEKISKNCW RIKKGFVPNM QVEGVFYVND SLEKLMFEEL
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):55,199
Last modified:March 15, 2005 - v1
Checksum:iD7B00F8321588230
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BT020831 mRNA. Translation: AAX08848.1.
BC104498 mRNA. Translation: AAI04499.1.
RefSeqiNP_001015631.1. NM_001015631.2.
UniGeneiBt.91477.

Genome annotation databases

EnsembliENSBTAT00000014699; ENSBTAP00000014699; ENSBTAG00000011070.
GeneIDi525106.
KEGGibta:525106.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BT020831 mRNA. Translation: AAX08848.1.
BC104498 mRNA. Translation: AAI04499.1.
RefSeqiNP_001015631.1. NM_001015631.2.
UniGeneiBt.91477.

3D structure databases

ProteinModelPortaliQ5E9T9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9913.ENSBTAP00000014699.

Proteomic databases

PaxDbiQ5E9T9.
PeptideAtlasiQ5E9T9.
PRIDEiQ5E9T9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSBTAT00000014699; ENSBTAP00000014699; ENSBTAG00000011070.
GeneIDi525106.
KEGGibta:525106.

Organism-specific databases

CTDi51493.

Phylogenomic databases

eggNOGiKOG3833. Eukaryota.
COG1690. LUCA.
GeneTreeiENSGT00390000015260.
HOVERGENiHBG081383.
InParanoidiQ5E9T9.
KOiK14415.
OMAiNMNVEGV.
OrthoDBiEOG091G053A.
TreeFamiTF314404.

Gene expression databases

BgeeiENSBTAG00000011070.

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_BOVIN
AccessioniPrimary (citable) accession number: Q5E9T9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: March 15, 2005
Last modified: November 30, 2016
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

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 (By similarity).By similarity

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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.