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A2RUC4

- TYW5_HUMAN

UniProt

A2RUC4 - TYW5_HUMAN

Protein

tRNA wybutosine-synthesizing protein 5

Gene

TYW5

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 67 (01 Oct 2014)
      Sequence version 1 (06 Mar 2007)
      Previous versions | rss
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    Functioni

    tRNA hydroxylase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the hydroxylation of 7-(a-amino-a-carboxypropyl)wyosine (yW-72) into undermodified hydroxywybutosine (OHyW*). OHyW* being further transformed into hydroxywybutosine (OHyW) by LCMT2/TYW4. OHyW is a derivative of wybutosine found in higher eukaryotes.1 Publication

    Catalytic activityi

    7-(3-amino-3-carboxypropyl)wyosine(37) in tRNA(Phe) + 2-oxoglutarate + O2 = 7-(2-hydroxy-3-amino-3-carboxypropyl)wyosine(37) in tRNA(Phe) + succinate + CO2.

    Cofactori

    Binds 1 Fe2+ ion per subunit.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei106 – 10612-oxoglutarate1 Publication
    Metal bindingi160 – 1601Iron; catalytic
    Metal bindingi162 – 1621Iron; catalytic
    Binding sitei166 – 16612-oxoglutarate1 Publication
    Binding sitei175 – 17512-oxoglutarate1 Publication
    Metal bindingi235 – 2351Iron; catalytic

    GO - Molecular functioni

    1. iron ion binding Source: UniProtKB
    2. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors Source: UniProtKB
    3. protein homodimerization activity Source: UniProtKB
    4. tRNA binding Source: UniProtKB

    GO - Biological processi

    1. wybutosine biosynthetic process Source: UniProtKB

    Keywords - Molecular functioni

    Dioxygenase, Oxidoreductase

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    UniPathwayiUPA00375.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    tRNA wybutosine-synthesizing protein 5 (EC:1.14.11.42)
    Short name:
    hTYW5
    Alternative name(s):
    tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-C(2))-hydroxylase
    Gene namesi
    Name:TYW5
    Synonyms:C2orf60
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 2

    Organism-specific databases

    HGNCiHGNC:26754. TYW5.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi108 – 1081R → A: Abolishes enzyme activity and ability to bind tRNA. 1 Publication
    Mutagenesisi149 – 1491R → A: Abolishes enzyme activity and ability to bind tRNA. 1 Publication

    Organism-specific databases

    PharmGKBiPA162379298.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 315315tRNA wybutosine-synthesizing protein 5PRO_0000309274Add
    BLAST

    Proteomic databases

    MaxQBiA2RUC4.
    PaxDbiA2RUC4.
    PRIDEiA2RUC4.

    PTM databases

    PhosphoSiteiA2RUC4.

    Expressioni

    Gene expression databases

    ArrayExpressiA2RUC4.
    BgeeiA2RUC4.
    CleanExiHS_C2orf60.
    GenevestigatoriA2RUC4.

    Organism-specific databases

    HPAiHPA045803.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi9606.ENSP00000346627.

    Structurei

    Secondary structure

    1
    315
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi10 – 134
    Helixi16 – 227
    Helixi24 – 263
    Beta strandi30 – 345
    Helixi40 – 434
    Helixi46 – 538
    Beta strandi57 – 626
    Beta strandi76 – 816
    Helixi82 – 909
    Beta strandi106 – 1083
    Turni114 – 1163
    Helixi121 – 1244
    Helixi126 – 1294
    Helixi140 – 1423
    Beta strandi143 – 1519
    Beta strandi156 – 1605
    Beta strandi163 – 1708
    Beta strandi175 – 1806
    Helixi182 – 1887
    Beta strandi194 – 1963
    Beta strandi200 – 2023
    Turni205 – 2073
    Helixi211 – 2133
    Beta strandi216 – 2216
    Beta strandi226 – 2294
    Beta strandi234 – 2418
    Beta strandi243 – 2508
    Helixi255 – 2573
    Beta strandi263 – 2653
    Helixi270 – 28617
    Helixi291 – 30818

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3AL5X-ray2.50A/B/C/D1-315[»]
    3AL6X-ray2.80A/B/C/D1-315[»]
    ProteinModelPortaliA2RUC4.
    SMRiA2RUC4. Positions 1-311.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini102 – 267166JmjCPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the TYW5 family.Curated
    Contains 1 JmjC domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG276154.
    HOVERGENiHBG096249.
    InParanoidiA2RUC4.
    KOiK18066.
    OMAiRMVLRIQ.
    OrthoDBiEOG7X3QRF.
    PhylomeDBiA2RUC4.
    TreeFamiTF332364.

    Family and domain databases

    InterProiIPR003347. JmjC_dom.
    IPR029612. TYW5.
    [Graphical view]
    PANTHERiPTHR12461:SF24. PTHR12461:SF24. 1 hit.
    SMARTiSM00558. JmjC. 1 hit.
    [Graphical view]
    PROSITEiPS51184. JMJC. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: A2RUC4-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MAGQHLPVPR LEGVSREQFM QHLYPQRKPL VLEGIDLGPC TSKWTVDYLS    50
    QVGGKKEVKI HVAAVAQMDF ISKNFVYRTL PFDQLVQRAA EEKHKEFFVS 100
    EDEKYYLRSL GEDPRKDVAD IRKQFPLLKG DIKFPEFFKE EQFFSSVFRI 150
    SSPGLQLWTH YDVMDNLLIQ VTGKKRVVLF SPRDAQYLYL KGTKSEVLNI 200
    DNPDLAKYPL FSKARRYECS LEAGDVLFIP ALWFHNVISE EFGVGVNIFW 250
    KHLPSECYDK TDTYGNKDPT AASRAAQILD RALKTLAELP EEYRDFYARR 300
    MVLHIQDKAY SKNSE 315
    Length:315
    Mass (Da):36,548
    Last modified:March 6, 2007 - v1
    Checksum:iF291C48E8CA729FE
    GO
    Isoform 2 (identifier: A2RUC4-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-163: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:152
    Mass (Da):17,526
    Checksum:i3FF012BC9E0CAED4
    GO

    Sequence cautioni

    The sequence AAH63502.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti50 – 501S → G.
    Corresponds to variant rs10497844 [ dbSNP | Ensembl ].
    VAR_036926

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 163163Missing in isoform 2. 1 PublicationVSP_029106Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK095272 mRNA. Translation: BAC04517.1.
    AK298977 mRNA. Translation: BAG61071.1.
    AC097717 Genomic DNA. Translation: AAY24162.1.
    CH471063 Genomic DNA. Translation: EAW70191.1.
    BC063502 mRNA. Translation: AAH63502.1. Different initiation.
    BC132835 mRNA. Translation: AAI32836.1.
    BC136837 mRNA. Translation: AAI36838.1.
    CCDSiCCDS42795.1. [A2RUC4-1]
    RefSeqiNP_001034782.1. NM_001039693.2. [A2RUC4-1]
    UniGeneiHs.204619.

    Genome annotation databases

    EnsembliENST00000354611; ENSP00000346627; ENSG00000162971. [A2RUC4-1]
    GeneIDi129450.
    KEGGihsa:129450.
    UCSCiuc002uvi.4. human. [A2RUC4-1]
    uc002uvj.4. human. [A2RUC4-2]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK095272 mRNA. Translation: BAC04517.1 .
    AK298977 mRNA. Translation: BAG61071.1 .
    AC097717 Genomic DNA. Translation: AAY24162.1 .
    CH471063 Genomic DNA. Translation: EAW70191.1 .
    BC063502 mRNA. Translation: AAH63502.1 . Different initiation.
    BC132835 mRNA. Translation: AAI32836.1 .
    BC136837 mRNA. Translation: AAI36838.1 .
    CCDSi CCDS42795.1. [A2RUC4-1 ]
    RefSeqi NP_001034782.1. NM_001039693.2. [A2RUC4-1 ]
    UniGenei Hs.204619.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3AL5 X-ray 2.50 A/B/C/D 1-315 [» ]
    3AL6 X-ray 2.80 A/B/C/D 1-315 [» ]
    ProteinModelPortali A2RUC4.
    SMRi A2RUC4. Positions 1-311.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 9606.ENSP00000346627.

    PTM databases

    PhosphoSitei A2RUC4.

    Proteomic databases

    MaxQBi A2RUC4.
    PaxDbi A2RUC4.
    PRIDEi A2RUC4.

    Protocols and materials databases

    DNASUi 129450.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000354611 ; ENSP00000346627 ; ENSG00000162971 . [A2RUC4-1 ]
    GeneIDi 129450.
    KEGGi hsa:129450.
    UCSCi uc002uvi.4. human. [A2RUC4-1 ]
    uc002uvj.4. human. [A2RUC4-2 ]

    Organism-specific databases

    CTDi 129450.
    GeneCardsi GC02M200794.
    H-InvDB HIX0002719.
    HGNCi HGNC:26754. TYW5.
    HPAi HPA045803.
    neXtProti NX_A2RUC4.
    PharmGKBi PA162379298.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG276154.
    HOVERGENi HBG096249.
    InParanoidi A2RUC4.
    KOi K18066.
    OMAi RMVLRIQ.
    OrthoDBi EOG7X3QRF.
    PhylomeDBi A2RUC4.
    TreeFami TF332364.

    Enzyme and pathway databases

    UniPathwayi UPA00375 .

    Miscellaneous databases

    GenomeRNAii 129450.
    NextBioi 82587.
    PROi A2RUC4.

    Gene expression databases

    ArrayExpressi A2RUC4.
    Bgeei A2RUC4.
    CleanExi HS_C2orf60.
    Genevestigatori A2RUC4.

    Family and domain databases

    InterProi IPR003347. JmjC_dom.
    IPR029612. TYW5.
    [Graphical view ]
    PANTHERi PTHR12461:SF24. PTHR12461:SF24. 1 hit.
    SMARTi SM00558. JmjC. 1 hit.
    [Graphical view ]
    PROSITEi PS51184. JMJC. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
      Tissue: Tongue.
    2. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
      Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
      , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
      Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Brain and Retinoblastoma.
    5. "Expanding role of the jumonji C domain as an RNA hydroxylase."
      Noma A., Ishitani R., Kato M., Nagao A., Nureki O., Suzuki T.
      J. Biol. Chem. 285:34503-34507(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, PATHWAY.
    6. "Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification."
      Kato M., Araiso Y., Noma A., Nagao A., Suzuki T., Ishitani R., Nureki O.
      Nucleic Acids Res. 39:1576-1585(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 4-311 IN COMPLEX WITH 2-OXOGLUTARATE AND NICKEL ION, PATHWAY, COFACTOR, SUBUNIT, MUTAGENESIS OF ARG-108 AND ARG-149.

    Entry informationi

    Entry nameiTYW5_HUMAN
    AccessioniPrimary (citable) accession number: A2RUC4
    Secondary accession number(s): B2RNE3, Q8N1R2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 13, 2007
    Last sequence update: March 6, 2007
    Last modified: October 1, 2014
    This is version 67 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 2
      Human chromosome 2: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3