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Protein

tRNA-splicing ligase RtcB homolog

Gene

Rtcb

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 3 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 (By similarity).By similarity

Catalytic activityi

ATP + (ribonucleotide)(n) + (ribonucleotide)(m) = AMP + diphosphate + (ribonucleotide)(n+m).UniRule annotation

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi119 – 1191Manganese 1By similarity
Metal bindingi122 – 1221Manganese 1By similarity
Metal bindingi122 – 1221Manganese 2By similarity
Metal bindingi227 – 2271Manganese 1By similarity
Binding sitei230 – 2301GMPBy similarity
Metal bindingi259 – 2591Manganese 2By similarity
Metal bindingi353 – 3531Manganese 2By similarity
Binding sitei409 – 4091GMPBy similarity
Active sitei428 – 4281GMP-histidine intermediateBy similarity
Binding sitei504 – 5041GMPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi353 – 3542GMPBy similarity
Nucleotide bindingi400 – 4034GMPBy similarity
Nucleotide bindingi428 – 4314GMPBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. metal ion binding Source: UniProtKB-KW
  3. RNA ligase (ATP) activity Source: UniProtKB

GO - Biological processi

  1. tRNA splicing, via endonucleolytic cleavage and ligation Source: UniProtKB
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)
Alternative name(s):
p55
Gene namesi
Name:Rtcb
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494 Componenti: Chromosome 7

Organism-specific databases

RGDi1303261. Rtcb.

Subcellular locationi

  1. Nucleus By similarity
  2. Cytoplasm UniRule annotation

  3. 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

  1. cytoplasm Source: UniProtKB
  2. nucleus Source: UniProtKB
  3. tRNA-splicing ligase complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 505505tRNA-splicing ligase RtcB homologPRO_0000255245Add
BLAST

Proteomic databases

PaxDbiQ6AYT3.
PRIDEiQ6AYT3.

PTM databases

PhosphoSiteiQ6AYT3.

Expressioni

Gene expression databases

GenevestigatoriQ6AYT3.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi263779. 2 interactions.
IntActiQ6AYT3. 1 interaction.
MINTiMINT-4576391.
STRINGi10116.ENSRNOP00000006570.

Structurei

3D structure databases

ProteinModelPortaliQ6AYT3.
SMRiQ6AYT3. Positions 12-505.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RtcB family.UniRule annotation

Phylogenomic databases

eggNOGiCOG1690.
GeneTreeiENSGT00390000015260.
HOVERGENiHBG081383.
InParanoidiQ6AYT3.
KOiK14415.
OMAiGRMLNAD.
OrthoDBiEOG7DRJ2Q.
PhylomeDBiQ6AYT3.
TreeFamiTF314404.

Family and domain databases

HAMAPiMF_03144. RtcB_euk.
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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti316 – 3161Y → C in AAS78621 (Ref. 1) Curated

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.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliQ6AYT3.
SMRiQ6AYT3. Positions 12-505.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi263779. 2 interactions.
IntActiQ6AYT3. 1 interaction.
MINTiMINT-4576391.
STRINGi10116.ENSRNOP00000006570.

PTM databases

PhosphoSiteiQ6AYT3.

Proteomic databases

PaxDbiQ6AYT3.
PRIDEiQ6AYT3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi51493.
RGDi1303261. Rtcb.

Phylogenomic databases

eggNOGiCOG1690.
GeneTreeiENSGT00390000015260.
HOVERGENiHBG081383.
InParanoidiQ6AYT3.
KOiK14415.
OMAiGRMLNAD.
OrthoDBiEOG7DRJ2Q.
PhylomeDBiQ6AYT3.
TreeFamiTF314404.

Miscellaneous databases

NextBioi681535.
PROiQ6AYT3.

Gene expression databases

GenevestigatoriQ6AYT3.

Family and domain databases

HAMAPiMF_03144. RtcB_euk.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning of the rat P55 gene."
    Ding N.-Z., He M., He C.-Q., Chen J.G.
    Submitted (MAR-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: Brown Norway.
    Tissue: Kidney.

Entry informationi

Entry nameiRTCB_RAT
AccessioniPrimary (citable) accession number: Q6AYT3
Secondary accession number(s): Q6PX76
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: September 13, 2004
Last modified: January 7, 2015
This is version 71 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

External Data

Dasty 3

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 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.