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Q8U0H4

- RTCB_PYRFU

UniProt

Q8U0H4 - RTCB_PYRFU

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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: 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi103 – 1031Manganese 1By similarity
Metal bindingi106 – 1061Manganese 1By similarity
Metal bindingi106 – 1061Manganese 2By similarity
Metal bindingi692 – 6921Manganese 1By similarity
Binding sitei695 – 6951GMPBy similarity
Metal bindingi723 – 7231Manganese 2By similarity
Metal bindingi818 – 8181Manganese 2By similarity
Binding sitei874 – 8741GMPBy similarity
Active sitei893 – 8931GMP-histidine intermediateBy similarity
Binding sitei969 – 9691GMPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi818 – 8192GMPBy similarity
Nucleotide bindingi865 – 8684GMPBy similarity
Nucleotide bindingi893 – 8964GMPBy similarity

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. endonuclease activity Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW
  4. RNA ligase activity Source: InterPro

GO - Biological processi

  1. intein-mediated protein splicing Source: InterPro
  2. intron homing Source: UniProtKB-KW
  3. tRNA processing Source: UniProtKB-KW
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
ProteomesiUP000001013: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 105105tRNA-splicing ligase RtcB, 1st partSequence AnalysisPRO_0000232532Add
BLAST
Chaini106 – 586481Pfu hyp2 inteinSequence AnalysisPRO_0000232533Add
BLAST
Chaini587 – 970384tRNA-splicing ligase RtcB, 2nd partSequence AnalysisPRO_0000232534Add
BLAST

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 interaction.
STRINGi186497.PF1615.

Structurei

3D structure databases

ProteinModelPortaliQ8U0H4.
SMRiQ8U0H4. Positions 11-106, 586-970.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini256 – 420165DOD-type homing endonucleasePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1372.
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.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR001233. RtcB.
[Graphical view]
PANTHERiPTHR11118. PTHR11118. 1 hit.
PfamiPF14528. LAGLIDADG_3. 1 hit.
PF01139. RtcB. 2 hits.
[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.
RefSeqiNP_579344.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL81739; AAL81739; PF1615.
GeneIDi1469492.
KEGGipfu:PF1615.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81739.1 .
RefSeqi NP_579344.1. NC_003413.1.

3D structure databases

ProteinModelPortali Q8U0H4.
SMRi Q8U0H4. Positions 11-106, 586-970.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi Q8U0H4. 1 interaction.
STRINGi 186497.PF1615.

Proteomic databases

PRIDEi Q8U0H4.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL81739 ; AAL81739 ; PF1615 .
GeneIDi 1469492.
KEGGi pfu:PF1615.

Phylogenomic databases

eggNOGi COG1372.
HOGENOMi HOG000296282.
KOi K14415.
OMAi VHNCGVR.

Family and domain databases

Gene3Di 2.170.16.10. 3 hits.
3.10.28.10. 2 hits.
InterProi IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR001233. RtcB.
[Graphical view ]
PANTHERi PTHR11118. PTHR11118. 1 hit.
Pfami PF14528. LAGLIDADG_3. 1 hit.
PF01139. RtcB. 2 hits.
[Graphical view ]
PRINTSi PR00379. INTEIN.
SMARTi SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view ]
SUPFAMi SSF103365. SSF103365. 2 hits.
SSF51294. SSF51294. 3 hits.
SSF55608. SSF55608. 1 hit.
TIGRFAMsi TIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEi PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
    Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
    Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.

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: November 26, 2014
This is version 72 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

External Data

Dasty 3