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Q8TUS2

- RTCB_METKA

UniProt

Q8TUS2 - RTCB_METKA

Protein

tRNA-splicing ligase RtcB

Gene

rtcB

Organism
Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 73 (01 Oct 2014)
      Sequence version 1 (01 Jun 2002)
      Previous versions | rss
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    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 Probable.1 Publication

    Cofactori

    Binds 2 manganese ions per subunit.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi98 – 981Manganese 1By similarity
    Metal bindingi101 – 1011Manganese 1By similarity
    Metal bindingi101 – 1011Manganese 2By similarity
    Metal bindingi700 – 7001Manganese 1By similarity
    Binding sitei703 – 7031GMPBy similarity
    Metal bindingi732 – 7321Manganese 2By similarity
    Metal bindingi833 – 8331Manganese 2By similarity
    Binding sitei892 – 8921GMPBy similarity
    Active sitei911 – 9111GMP-histidine intermediateBy similarity
    Binding sitei987 – 9871GMPBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi833 – 8342GMPBy similarity
    Nucleotide bindingi883 – 8864GMPBy similarity
    Nucleotide bindingi911 – 9144GMPBy 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: UniProtKB

    GO - Biological processi

    1. intein-mediated protein splicing Source: InterPro
    2. intron homing Source: UniProtKB-KW
    3. tRNA splicing, via endonucleolytic cleavage and ligation Source: UniProtKB

    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:MK1682
    OrganismiMethanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
    Taxonomic identifieri190192 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaMethanopyriMethanopyralesMethanopyraceaeMethanopyrus
    ProteomesiUP000001826: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 100100tRNA-splicing ligase RtcB, 1st partSequence AnalysisPRO_0000232526Add
    BLAST
    Chaini101 – 582482Mka hyp2 inteinSequence AnalysisPRO_0000232527Add
    BLAST
    Chaini583 – 988406tRNA-splicing ligase RtcB, 2nd partSequence AnalysisPRO_0000232528Add
    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

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    STRINGi190192.MK1682.

    Structurei

    3D structure databases

    ProteinModelPortaliQ8TUS2.
    SMRiQ8TUS2. Positions 7-101, 582-988.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini251 – 415165DOD-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. 2 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.
    PS01288. UPF0027. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q8TUS2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAPKSMLKHI RNNVVWELPE DYKGCMKVPG RIYATEKLID GMEKGVFDQV    50
    ANVACLPGIY GYSIALPDAH YGYGFPIGGV AAFDVEEGVV SPGGVGYDIN 100
    CLAPGTKILT EHGCWVKVED LPKMLTDQKL KVYDVDEGRE DDSEIKFVME 150
    RGIEEDERAV VLVTESGLTI EGSEDHPVLT PEGYVELGEI EEGDLVVVYP 200
    FEGVEYEEKE GTILDESDFE DVDPQVLRYL EERDLIPLRW SDPKVGTLAR 250
    ILGFAMGDGH LGEQAGRLTL SFYGDERTLR ELKRDLESLG VKANLHVRKR 300
    RYEIETASGR YEGEATSVEL RVASRSFALL MEKLGMPRGR KVETPYKVPD 350
    WIKEAPLWVK RNFLAGLFAA DGSVVKFKRY TPLPINLTQA KVEELEENLR 400
    EFMNDVAKLL REFGIETTLY EVKSKKNVVY KLAIVGEENI KRFLGKVGYE 450
    YDPEKKVEGL AAYAYLKLKE RVKKDRKEAA ETAAEVYEET GSITKAHEAV 500
    ADVVNRRFVE RVVYDGGISS VRVPEDFPTF ERFKEERVLA GGFVIEEVVE 550
    VKGVEPEYDR FYDIGVCHGA HNFIADGVVV HNCGVRVMKT DLTEDDVRPK 600
    LRELLETIFR NVPAGLGSRH RRVRLSTQEL RQVMLYGAEW AVEEGFGFDE 650
    DLDHIESRGN MTHAYETIGW EEYGPRDDVA SKRAIERGRP QLGTLGSGNH 700
    FLEVQVVDEI YDKEAAEKMG IREEGQVTIM VHTGSRGFGH QVCSDHLRIM 750
    ERSMRDVERR FGVRIPDRQL ACAAMGTDEA KRYFNAMNAA ANYAFANRQM 800
    ISHWTRESFV EVFGDEYGDA DDMGIEVIYD IAHNMAKIEK HPVDGEERWL 850
    VVHRKGATRA FSEEALKKHG EPVPFEGLPQ PVLIPGDMGT GSYILIGTEK 900
    AMEETWGSTC HGAGRTMSRA AAKRKFWGED VARELERQGI LVKAASMPVV 950
    AEEAPPAYKD VDEVVRAVAE AGISDPVVRL RPIGVVKG 988
    Length:988
    Mass (Da):110,989
    Last modified:June 1, 2002 - v1
    Checksum:iC24DAC047EAC3132
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009439 Genomic DNA. Translation: AAM02895.1.
    RefSeqiNP_614965.1. NC_003551.1.

    Genome annotation databases

    EnsemblBacteriaiAAM02895; AAM02895; MK1682.
    GeneIDi1478277.
    KEGGimka:MK1682.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009439 Genomic DNA. Translation: AAM02895.1 .
    RefSeqi NP_614965.1. NC_003551.1.

    3D structure databases

    ProteinModelPortali Q8TUS2.
    SMRi Q8TUS2. Positions 7-101, 582-988.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 190192.MK1682.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAM02895 ; AAM02895 ; MK1682 .
    GeneIDi 1478277.
    KEGGi mka:MK1682.

    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. 2 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.
    PS01288. UPF0027. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938.
    2. "Archaeal 3'-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation."
      Englert M., Sheppard K., Aslanian A., Yates J.R. III, Soll D.
      Proc. Natl. Acad. Sci. U.S.A. 108:1290-1295(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, SUBUNIT.
      Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938.

    Entry informationi

    Entry nameiRTCB_METKA
    AccessioniPrimary (citable) accession number: Q8TUS2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 18, 2006
    Last sequence update: June 1, 2002
    Last modified: October 1, 2014
    This is version 73 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