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Protein

tRNA-splicing ligase RtcB

Gene

rtcB

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

tRNA-splicing ligase 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

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi103Manganese 1By similarity1
Metal bindingi106Manganese 1By similarity1
Metal bindingi106Manganese 2By similarity1
Metal bindingi692Manganese 1By similarity1
Binding sitei695GMPBy similarity1
Metal bindingi723Manganese 2By similarity1
Metal bindingi818Manganese 2By similarity1
Binding sitei874GMPBy similarity1
Active sitei893GMP-histidine intermediateBy similarity1
Binding sitei969GMPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi818 – 819GMPBy similarity2
Nucleotide bindingi865 – 868GMPBy similarity4
Nucleotide bindingi893 – 896GMPBy similarity4

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Ligase, Nuclease

Keywords - Biological processi

Intron homing, tRNA processing

Keywords - Ligandi

DNA-binding, Manganese, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-splicing ligase RtcB (EC:6.5.1.-)
Cleaved into the following chain:
Gene namesi
Name:rtcB
Ordered Locus Names:PF1615
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000001013 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002325321 – 105tRNA-splicing ligase RtcB, 1st partSequence analysisAdd BLAST105
ChainiPRO_0000232533106 – 586Pfu hyp2 inteinSequence analysisAdd BLAST481
ChainiPRO_0000232534587 – 970tRNA-splicing ligase RtcB, 2nd partSequence analysisAdd BLAST384

Post-translational modificationi

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.Curated

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

Proteomic databases

PRIDEiQ8U0H4.

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

IntActiQ8U0H4. 1 interactor.
STRINGi186497.PF1615.

Structurei

3D structure databases

ProteinModelPortaliQ8U0H4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini256 – 420DOD-type homing endonucleasePROSITE-ProRule annotationAdd BLAST165

Sequence similaritiesi

Belongs to the RtcB family.Curated
Contains 1 DOD-type homing endonuclease domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiarCOG03158. Archaea.
arCOG04246. Archaea.
ENOG4102TCK. Archaea.
COG1372. LUCA.
COG1690. LUCA.
HOGENOMiHOG000296282.
KOiK14415.
OMAiVHNCGVR.

Family and domain databases

Gene3Di2.170.16.10. 3 hits.
3.10.28.10. 2 hits.
InterProiIPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR004860. LAGLIDADG_2.
IPR001233. RtcB.
[Graphical view]
PANTHERiPTHR11118. PTHR11118. 2 hits.
PfamiPF14528. LAGLIDADG_3. 1 hit.
PF01139. RtcB. 1 hit.
[Graphical view]
PRINTSiPR00379. INTEIN.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF103365. SSF103365. 2 hits.
SSF51294. SSF51294. 3 hits.
SSF55608. SSF55608. 1 hit.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q8U0H4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIILRVVNVA VPLKRIDKIR WEIPKFDKRM KVPGRVYADD VLIEKMRQDR
60 70 80 90 100
TLEQAANVAM LPGIYKYSIV MPDGHQGYGF PIGGVAAFDI KEGVISPGGI
110 120 130 140 150
GYDINCLAPG TKVLTEHGYW LKIEEMPEKF KLQRLRLYNI EEGHNDFSRV
160 170 180 190 200
AFVAERNIEK DETAIRIVTE TGTLIEGSED HPVLTPQGYV YLKNIKEGDY
210 220 230 240 250
VIVYPFEGVP YEEKKGIIID ESAFEGEDPQ VIKFLKERNL LPLRWEDPKI
260 270 280 290 300
GTLARILGFA LGDGHLGEMG GRLVLAFYGR EETLRELKKD LESLGIKANL
310 320 330 340 350
YVREKNYRIK TESGEYSGKT VLAELRVSSR SFALLLEKLG MPRGEKTKKA
360 370 380 390 400
YRIPVWIMEA PLWVKRNFLA GFFGADGSIV EFKGTTPLPI HLTQAKDVAL
410 420 430 440 450
EENLKEFLYD ISRILEEFGV KTTIYKVNSK KSVTYRLSIV GEENIRNFLG
460 470 480 490 500
KINYEYDPKK KAKGLIAYAY LKFKESVKKE RRKAMEISKK IYEETGNIDR
510 520 530 540 550
AYKAVKDIVN RRFVERTIYE GERNPRVPKN FLTFEEFAKE RGYEGGFVAE
560 570 580 590 600
KVVKVERIKP EYDRFYDIGV YHEAHNFIAN GIVVHNCGVR LIRTNLTEKD
610 620 630 640 650
VRPKIKQLVD TLFKNVPSGV GSQGKVRLHW TQIDDVLVDG AKWAVDQGYG
660 670 680 690 700
WERDLERLEE GGRMEGADPD AVSQRAKQRG APQLGSLGSG NHFLEVQVVD
710 720 730 740 750
KIFDEEIAKA YGLFEGQVVV MVHTGSRGLG HQVASDYLRI MERAIRKYGI
760 770 780 790 800
PWPDRELVSV PFQSEEGQRY FSAMKAAANF AWANRQMITH WVRESFQEVF
810 820 830 840 850
RQDPEGDLGM EIVYDVAHNI GKVEEHEVDG KKVKVIVHRK GATRAFPPGH
860 870 880 890 900
EAIPKIYRDV GQPVLIPGSM GTASYVLAGT EGAMAETFGS TCHGAGRVLS
910 920 930 940 950
RAAATRQYRG DRIRDELLRR GIYVRAASMR VVAEEAPGAY KNVDNVVKVV
960 970
SEAGIAKLVA RMRPIGVAKG
Length:970
Mass (Da):109,712
Last modified:June 1, 2002 - v1
Checksum:iCC0AEE4573CFE7C2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81739.1.

Genome annotation databases

EnsemblBacteriaiAAL81739; AAL81739; PF1615.
KEGGipfu:PF1615.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81739.1.

3D structure databases

ProteinModelPortaliQ8U0H4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ8U0H4. 1 interactor.
STRINGi186497.PF1615.

Proteomic databases

PRIDEiQ8U0H4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL81739; AAL81739; PF1615.
KEGGipfu:PF1615.

Phylogenomic databases

eggNOGiarCOG03158. Archaea.
arCOG04246. Archaea.
ENOG4102TCK. Archaea.
COG1372. LUCA.
COG1690. LUCA.
HOGENOMiHOG000296282.
KOiK14415.
OMAiVHNCGVR.

Family and domain databases

Gene3Di2.170.16.10. 3 hits.
3.10.28.10. 2 hits.
InterProiIPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR004860. LAGLIDADG_2.
IPR001233. RtcB.
[Graphical view]
PANTHERiPTHR11118. PTHR11118. 2 hits.
PfamiPF14528. LAGLIDADG_3. 1 hit.
PF01139. RtcB. 1 hit.
[Graphical view]
PRINTSiPR00379. INTEIN.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF103365. SSF103365. 2 hits.
SSF51294. SSF51294. 3 hits.
SSF55608. SSF55608. 1 hit.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRTCB_PYRFU
AccessioniPrimary (citable) accession number: Q8U0H4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: June 1, 2002
Last modified: October 5, 2016
This is version 82 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Ligation 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. Intein-containing proteins
    List of intein-containing protein entries
  2. 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.