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Protein

tRNA-splicing ligase RtcB homolog

Gene

Rtcb

Organism
Rattus norvegicus (Rat)
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.

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

Catalytic activityi

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

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

Keywordsi

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

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-splicing ligase RtcB homolog (EC:6.5.1.3)
Alternative name(s):
p55
Gene namesi
Name:Rtcb
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 7

Organism-specific databases

RGDi1303261. Rtcb.

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002552451 – 505tRNA-splicing ligase RtcB homologAdd BLAST505

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei300PhosphoserineBy similarity1
Cross-linki496Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ6AYT3.
PRIDEiQ6AYT3.

PTM databases

iPTMnetiQ6AYT3.
PhosphoSitePlusiQ6AYT3.

Expressioni

Gene expression databases

BgeeiENSRNOG00000004813.
GenevisibleiQ6AYT3. RN.

Interactioni

Subunit structurei

Catalytic component of the tRNA-splicing ligase complex.

GO - Molecular functioni

Protein-protein interaction databases

BioGridi263779. 2 interactors.
IntActiQ6AYT3. 3 interactors.
MINTiMINT-4576391.
STRINGi10116.ENSRNOP00000006570.

Structurei

3D structure databases

ProteinModelPortaliQ6AYT3.
SMRiQ6AYT3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RtcB family.

Phylogenomic databases

eggNOGiKOG3833. Eukaryota.
COG1690. LUCA.
GeneTreeiENSGT00830000128284.
HOVERGENiHBG081383.
InParanoidiQ6AYT3.
KOiK14415.
OMAiYDVAHNV.
OrthoDBiEOG091G053A.
PhylomeDBiQ6AYT3.
TreeFamiTF314404.

Family and domain databases

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.

Q6AYT3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRNYNDELQ FLDKINKNCW 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
QADPNKVSPR 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):55,249
Last modified:September 13, 2004 - v1
Checksum:i3488A9BF91460480
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti316Y → C in AAS78621 (Ref. 1) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY572415 mRNA. Translation: AAS78621.1.
BC078924 mRNA. Translation: AAH78924.1.
RefSeqiNP_997497.1. NM_207614.1.
UniGeneiRn.11875.

Genome annotation databases

EnsembliENSRNOT00000006570; ENSRNOP00000006570; ENSRNOG00000004813.
GeneIDi362855.
KEGGirno:362855.
UCSCiRGD:1303261. rat.

Similar proteinsi

Entry informationi

Entry nameiRTCB_RAT
AccessioniPrimary (citable) accession number: Q6AYT3
Secondary accession number(s): Q6PX76
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: September 13, 2004
Last modified: November 22, 2017
This is version 88 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families