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Q9YBF1

- ENDA_AERPE

UniProt

Q9YBF1 - ENDA_AERPE

Protein

tRNA-splicing endonuclease

Gene

endA

Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Status
Reviewed - Annotation score: 2 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 73 (01 Oct 2014)
      Sequence version 2 (26 Jun 2007)
      Previous versions | rss
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    Functioni

    Endonuclease that removes tRNA introns. Cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-OH termini. Recognizes a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp.UniRule annotation

    Catalytic activityi

    PretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei125 – 1251UniRule annotation
    Active sitei133 – 1331UniRule annotation
    Active sitei164 – 1641UniRule annotation

    GO - Molecular functioni

    1. lyase activity Source: UniProtKB-KW
    2. nucleic acid binding Source: InterPro
    3. tRNA-intron endonuclease activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. tRNA splicing, via endonucleolytic cleavage and ligation Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    tRNA processing

    Enzyme and pathway databases

    BioCyciAPER272557:GJD6-1118-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    tRNA-splicing endonucleaseUniRule annotation (EC:4.6.1.16UniRule annotation)
    Alternative name(s):
    tRNA-intron endonucleaseUniRule annotation
    Gene namesi
    Name:endAUniRule annotation
    Ordered Locus Names:APE_1646.1
    OrganismiAeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
    Taxonomic identifieri272557 [NCBI]
    Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeAeropyrum
    ProteomesiUP000002518: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 186186tRNA-splicing endonucleasePRO_0000109469Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer; although the tetramer contains four active sites, only two participate in the cleavage. Therefore, it should be considered as a dimer of dimers.UniRule annotation

    Protein-protein interaction databases

    STRINGi272557.APE_1646.1.

    Structurei

    Secondary structure

    1
    186
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi10 – 156
    Beta strandi18 – 214
    Helixi24 – 329
    Beta strandi37 – 415
    Beta strandi54 – 574
    Helixi58 – 669
    Beta strandi69 – 735
    Helixi82 – 909
    Helixi93 – 10715
    Beta strandi111 – 1144
    Helixi116 – 1183
    Beta strandi120 – 1278
    Turni129 – 1313
    Beta strandi132 – 1343
    Beta strandi136 – 1416
    Helixi150 – 15910
    Turni160 – 1623
    Beta strandi164 – 1729
    Beta strandi175 – 1839

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3AJVX-ray1.70B/D1-186[»]
    3P1YX-ray2.05A/B/C/D39-53[»]
    3P1ZX-ray2.80B/D/F/H/J/L1-186[»]
    ProteinModelPortaliQ9YBF1.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9YBF1.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the tRNA-intron endonuclease family. Archaeal short subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG1676.
    HOGENOMiHOG000107823.
    KOiK01170.

    Family and domain databases

    Gene3Di3.40.1350.10. 1 hit.
    HAMAPiMF_01833. EndA_short.
    InterProiIPR011856. tRNA_endonuc-like_dom.
    IPR006677. tRNA_intron_Endonuc_cat-like.
    IPR006678. tRNA_intron_Endonuc_N.
    IPR006676. tRNA_splic.
    IPR016442. tRNA_splic_arch_short.
    [Graphical view]
    PfamiPF01974. tRNA_int_endo. 1 hit.
    PF02778. tRNA_int_endo_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005285. tRNA_splic_archaea. 1 hit.
    SUPFAMiSSF53032. SSF53032. 1 hit.
    SSF55267. SSF55267. 1 hit.
    TIGRFAMsiTIGR00324. endA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q9YBF1-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGDRCAPIKA SGVLIGDSVL VTDVEQARSL YSCGYYGQPL DVEKPRGADF    50
    EGPLRLSLIE SLYLAEKGVL EVAKPDGSSV GVEDLRTAVR GNPRFSMLYN 100
    IYRDLRERGF VVRSGLKFGS DFAVYRLGPG IDHAPFIVHA YSPEDNIDPV 150
    EIVRAGRLSH SVRKKFVFAV TRGGDVSYLM IDWFRP 186
    Length:186
    Mass (Da):20,602
    Last modified:June 26, 2007 - v2
    Checksum:i3377457A91F479B9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000002 Genomic DNA. Translation: BAA80647.2.
    PIRiB72545.
    RefSeqiNP_148074.2. NC_000854.2.

    Genome annotation databases

    EnsemblBacteriaiBAA80647; BAA80647; APE_1646.1.
    GeneIDi1446148.
    KEGGiape:APE_1646.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000002 Genomic DNA. Translation: BAA80647.2 .
    PIRi B72545.
    RefSeqi NP_148074.2. NC_000854.2.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3AJV X-ray 1.70 B/D 1-186 [» ]
    3P1Y X-ray 2.05 A/B/C/D 39-53 [» ]
    3P1Z X-ray 2.80 B/D/F/H/J/L 1-186 [» ]
    ProteinModelPortali Q9YBF1.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 272557.APE_1646.1.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAA80647 ; BAA80647 ; APE_1646.1 .
    GeneIDi 1446148.
    KEGGi ape:APE_1646.1.

    Phylogenomic databases

    eggNOGi COG1676.
    HOGENOMi HOG000107823.
    KOi K01170.

    Enzyme and pathway databases

    BioCyci APER272557:GJD6-1118-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q9YBF1.

    Family and domain databases

    Gene3Di 3.40.1350.10. 1 hit.
    HAMAPi MF_01833. EndA_short.
    InterProi IPR011856. tRNA_endonuc-like_dom.
    IPR006677. tRNA_intron_Endonuc_cat-like.
    IPR006678. tRNA_intron_Endonuc_N.
    IPR006676. tRNA_splic.
    IPR016442. tRNA_splic_arch_short.
    [Graphical view ]
    Pfami PF01974. tRNA_int_endo. 1 hit.
    PF02778. tRNA_int_endo_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF005285. tRNA_splic_archaea. 1 hit.
    SUPFAMi SSF53032. SSF53032. 1 hit.
    SSF55267. SSF55267. 1 hit.
    TIGRFAMsi TIGR00324. endA. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1.

    Entry informationi

    Entry nameiENDA_AERPE
    AccessioniPrimary (citable) accession number: Q9YBF1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 11, 2004
    Last sequence update: June 26, 2007
    Last modified: October 1, 2014
    This is version 73 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3