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Q9V168

- RTCB_PYRAB

UniProt

Q9V168 - RTCB_PYRAB

Protein

tRNA-splicing ligase RtcB

Gene

rtcB

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 78 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      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 By similarity.By similarity

    Cofactori

    Binds 2 manganese ions per subunit.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi95 – 951Manganese 1By similarity
    Metal bindingi98 – 981Manganese 1By similarity
    Metal bindingi98 – 981Manganese 2By similarity
    Metal bindingi639 – 6391Manganese 1By similarity
    Binding sitei642 – 6421GMPBy similarity
    Metal bindingi670 – 6701Manganese 2By similarity
    Metal bindingi764 – 7641Manganese 2By similarity
    Binding sitei820 – 8201GMPBy similarity
    Active sitei839 – 8391GMP-histidine intermediateBy similarity
    Binding sitei915 – 9151GMPBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi764 – 7652GMPBy similarity
    Nucleotide bindingi811 – 8144GMPBy similarity
    Nucleotide bindingi839 – 8424GMPBy 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

    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:PYRAB05600
    ORF Names:PAB0383
    OrganismiPyrococcus abyssi (strain GE5 / Orsay)
    Taxonomic identifieri272844 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000000810: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 9797tRNA-splicing ligase RtcB, 1st partSequence AnalysisPRO_0000232529Add
    BLAST
    Chaini98 – 533436Pab hyp2 inteinSequence AnalysisPRO_0000232530Add
    BLAST
    Chaini534 – 916383tRNA-splicing ligase RtcB, 2nd partSequence AnalysisPRO_0000232531Add
    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.By similarity

    Protein-protein interaction databases

    STRINGi272844.PAB0383.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9V168.
    SMRiQ9V168. Positions 3-98, 533-916.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini248 – 409162DOD-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. 2 hits.
    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.

    Q9V168-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTVPLKRIDK IRWEIPKFDK RMRVPGRVYA DDVLLEKMKS DRTLEQAANV    50
    AMLPGIYKYS IVMPDGHQGY GFPIGGVAAF DVNEGVISPG GIGYDINCLA 100
    PGSKVLTEHG YWLKVEELPE KFKLQGVKVY NLDEGHNDTS NVAFVAEREV 150
    ETGEMAVRVT TESGRIIEGS EDHPVLTPEG YVYLGNLKEG NLVIVYPFEG 200
    VEYEERKGVI LDEDAFKDED PQVLSFLREK GLVPLRWDDP RIGTIARILG 250
    FAFGDGYLGE MGGRLTLTFY GKEETLRELK KDLERLGISA NLYVRESIET 300
    TSGHSEGKSL SIELRVTSRS FALFLEKLGM PRGKKTEKAY RVPGWILEAP 350
    LWVKRNFLAG LFAADGSIVE FKGNTPLPIN LTQSKSDELA ENLVEFLGDV 400
    AKLLAEFGIE TTLYEVKSKK GVTYRLSIVG EDSIRTFVER INYEYDPEKK 450
    VKGLIAAAYL KLKERIVKEA HEAVKDDFPT FEEFAKERGY EGGFVAEKVV 500
    KVERVKPEYT KFYDIGVYHE AHNFIANGIV VHNCGVRLIR TNLTEKDVRP 550
    RIKQLVDTLF KNVPSGVGSQ GRVRLHWTQI DDVLVDGAKW AVDNGYGWEE 600
    DLERLEEGGR MEGADPDAVS QRAKQRGAPQ LGSLGSGNHF LEVQVVDKIF 650
    DPEVAKVYGL FEGQVVVMVH TGSRGLGHQV ASDYLRIMER AIRKYRIPWP 700
    DRELVSVPFQ SEEGQRYFSA MKAAANFAWA NRQMITHWVR ESFQEVFRQD 750
    PEDLGMSIVY DVAHNIGKVE EHEVDGKKVK VIVHRKGATR AFPPGHEAIP 800
    KIYRDVGQPV LIPGSMGTAS YVLAGTEGAM KETFGSTCHG AGRVLSRKAA 850
    TRQYRGDRIR QELLNRGIYV RAASMRVVAE EAPGAYKNVD NVVKVVSEAG 900
    IAKLVARMRP IGVAKG 916
    Length:916
    Mass (Da):102,456
    Last modified:May 1, 2000 - v1
    Checksum:i32DB1F28BE85155A
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ248284 Genomic DNA. Translation: CAB49482.1.
    HE613800 Genomic DNA. Translation: CCE69950.1.
    PIRiC75175.
    RefSeqiNP_126251.1. NC_000868.1.
    WP_010867684.1. NC_000868.1.

    Genome annotation databases

    EnsemblBacteriaiCAB49482; CAB49482; PAB0383.
    GeneIDi1495463.
    KEGGipab:PAB0383.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ248284 Genomic DNA. Translation: CAB49482.1 .
    HE613800 Genomic DNA. Translation: CCE69950.1 .
    PIRi C75175.
    RefSeqi NP_126251.1. NC_000868.1.
    WP_010867684.1. NC_000868.1.

    3D structure databases

    ProteinModelPortali Q9V168.
    SMRi Q9V168. Positions 3-98, 533-916.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 272844.PAB0383.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB49482 ; CAB49482 ; PAB0383 .
    GeneIDi 1495463.
    KEGGi pab:PAB0383.

    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. 2 hits.
    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: GE5 / Orsay.
    2. "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638."
      Gao J., Wang J.
      Curr. Microbiol. 64:118-129(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENOME REANNOTATION.
      Strain: GE5 / Orsay.

    Entry informationi

    Entry nameiRTCB_PYRAB
    AccessioniPrimary (citable) accession number: Q9V168
    Secondary accession number(s): G8ZJ23
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 18, 2006
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 78 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

    Documents

    1. Intein-containing proteins
      List of intein-containing protein entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3