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Q9DBR1

- XRN2_MOUSE

UniProt

Q9DBR1 - XRN2_MOUSE

Protein

5'-3' exoribonuclease 2

Gene

Xrn2

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 1 (01 Jun 2001)
      Previous versions | rss
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    Functioni

    Possesses 5'->3' exoribonuclease activity. May promote the termination of transcription by RNA polymerase II. During transcription termination, cleavage at the polyadenylation site liberates a 5' fragment which is subsequently processed to form the mature mRNA and a 3' fragment which remains attached to the elongating polymerase. The processive degradation of this 3' fragment by this protein may promote termination of transcription By similarity.By similarity

    Catalytic activityi

    Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri262 – 27817CCHC-typeAdd
    BLAST

    GO - Molecular functioni

    1. 5'-3' exonuclease activity Source: UniProtKB
    2. 5'-3' exoribonuclease activity Source: UniProtKB
    3. nucleic acid binding Source: InterPro
    4. protein binding Source: MGI
    5. zinc ion binding Source: InterPro

    GO - Biological processi

    1. cell growth Source: UniProtKB
    2. DNA catabolic process, exonucleolytic Source: UniProtKB
    3. DNA recombination Source: UniProtKB
    4. DNA repair Source: UniProtKB
    5. DNA-templated transcription, termination Source: UniProtKB-KW
    6. microtubule-based process Source: UniProtKB
    7. mRNA processing Source: UniProtKB-KW
    8. regulation of transcription, DNA-templated Source: UniProtKB-KW
    9. RNA metabolic process Source: UniProtKB
    10. RNA phosphodiester bond hydrolysis, exonucleolytic Source: GOC
    11. spermatogenesis Source: UniProtKB

    Keywords - Molecular functioni

    Exonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    mRNA processing, Transcription, Transcription regulation, Transcription termination

    Keywords - Ligandi

    Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    5'-3' exoribonuclease 2 (EC:3.1.13.-)
    Alternative name(s):
    Protein Dhm1
    Gene namesi
    Name:Xrn2
    Synonyms:Dhm1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 2

    Organism-specific databases

    MGIiMGI:894687. Xrn2.

    Subcellular locationi

    Nucleusnucleolus By similarity

    GO - Cellular componenti

    1. aggresome Source: Ensembl
    2. nucleolus Source: UniProtKB
    3. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 9519515'-3' exoribonuclease 2PRO_0000071397Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei286 – 2861N6-acetyllysine1 Publication
    Modified residuei439 – 4391PhosphothreonineBy similarity
    Modified residuei448 – 4481Phosphoserine2 Publications
    Modified residuei471 – 4711PhosphoserineBy similarity
    Modified residuei473 – 4731PhosphoserineBy similarity
    Modified residuei475 – 4751PhosphoserineBy similarity
    Modified residuei499 – 4991Phosphoserine3 Publications
    Modified residuei501 – 5011Phosphoserine3 Publications

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiQ9DBR1.
    PaxDbiQ9DBR1.
    PRIDEiQ9DBR1.

    PTM databases

    PhosphoSiteiQ9DBR1.

    Expressioni

    Tissue specificityi

    Expressed in the spleen, testis, heart, brain, lung, liver, skeletal muscle, and kidney.1 Publication

    Gene expression databases

    BgeeiQ9DBR1.
    CleanExiMM_XRN2.
    GenevestigatoriQ9DBR1.

    Interactioni

    Protein-protein interaction databases

    BioGridi204910. 2 interactions.
    IntActiQ9DBR1. 3 interactions.
    MINTiMINT-4140454.
    STRINGi10090.ENSMUSP00000028921.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9DBR1.
    SMRiQ9DBR1. Positions 1-430, 502-785.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Contains 1 CCHC-type zinc finger.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri262 – 27817CCHC-typeAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG5049.
    GeneTreeiENSGT00670000098098.
    HOGENOMiHOG000205514.
    HOVERGENiHBG036677.
    InParanoidiQ9DBR1.
    KOiK12619.
    OMAiMMVEIFK.
    OrthoDBiEOG7S7SCW.
    PhylomeDBiQ9DBR1.
    TreeFamiTF105977.

    Family and domain databases

    InterProiIPR027073. 5_3_exoribonuclease.
    IPR017151. 5_3_exoribonuclease_2.
    IPR004859. Put_53exo.
    IPR001878. Znf_CCHC.
    [Graphical view]
    PANTHERiPTHR12341. PTHR12341. 1 hit.
    PfamiPF03159. XRN_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037239. Exonuclease_Xrn2. 1 hit.
    SMARTiSM00343. ZnF_C2HC. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9DBR1-1) [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

    MGVPAFFRWL SRKYPSIIVN CVEEKPKECN GVKIPVDASK PNPNDVEFDN    50
    LYLDMNGIIH PCTHPEDKPA PKNEDEMMVA IFEYIDRLFN IVRPRRLLYM 100
    AIDGVAPRAK MNQQRSRRFR ASKEGMEAAV EKQRVREEIL AKGGFLPPEE 150
    IKERFDSNCI TPGTEFMDNL AKCLRYYIAD RLNNDPGWKN LTVILSDASA 200
    PGEGEHKIMD YIRRQRAQPN HDPNTHHCLC GADADLIMLG LATHEPNFTI 250
    IREEFKPNKP KPCALCNQFG HEVKDCEGLP REKKGKHDEL ADSLPCAEGE 300
    FIFLRLNVLR EYLERELTMA SLPFPFDVER SIDDWVFMCF FVGNDFLPHL 350
    PSLEIREGAI DRLVNIYKNV VHKTGGYLTE SGYVNLQRVQ MIMLAVGEVE 400
    DSIFKKRKDD EDSFRRRQKE KRKRMKRDQP AFTPSGILTP HALGSRNSPG 450
    CQVASNPRQA AYEMRMQRNS SPSISPNTSF ASDGSPSPLG GIKRKAEDSD 500
    SEPEPEDNVR LWEAGWKQRY YKNKFDVDAA DEKFRRKVVQ SYVEGLCWVL 550
    RYYYQGCASW KWYYPFHYAP FASDFEGIAD MSSEFEKGTK PFKPLEQLMG 600
    VFPAASGNFL PPTWRKLMSD PDSSIIDFYP EDFAIDLNGK KYAWQGVALL 650
    PFVDERRLRA ALEEVYPDLT PEENRRNSLG GDVLFVGKLH PLRDFILELY 700
    QTGSTEPVDV PPELCHGIQG TFSLDEEAIL PDQTVCSPVP MLRDLTQNTA 750
    VSINFKDPQF AEDYVFKAAM LPGARKPATV LKPGDWEKSS NGRQWKPQLG 800
    FNRDRRPVHL DQAAFRTLGH VTPRGSGTSV YTNTALPPAN YQGNNYRPLL 850
    RGQAQIPKLM SNMRPQDSWR GPPPLFQQHR FERSVGAEPL LPWNRMIQNQ 900
    NAAFQPNQYQ MLGGPGGYPP RRDDHRGGRQ GYPREGRKYP LPPPSGRYSW 950
    N 951
    Length:951
    Mass (Da):108,687
    Last modified:June 1, 2001 - v1
    Checksum:iCF57479291DD18B9
    GO
    Isoform 2 (identifier: Q9DBR1-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         931-951: GYPREGRKYPLPPPSGRYSWN → VISTMWAVEGKQHTAHC

    Note: No experimental confirmation available. May result from the retention of an intron in the cDNA.

    Show »
    Length:947
    Mass (Da):108,108
    Checksum:iD07EDE545BB57F24
    GO

    Sequence cautioni

    The sequence AAH04028.1 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti122 – 1243SKE → IKG in BAA07524. (PubMed:7885830)Curated
    Sequence conflicti221 – 2211H → Q in BAA07524. (PubMed:7885830)Curated
    Sequence conflicti306 – 3061L → P in BAE40020. (PubMed:16141072)Curated
    Sequence conflicti332 – 3321I → N in BAA07524. (PubMed:7885830)Curated
    Sequence conflicti336 – 3361V → E in BAA07524. (PubMed:7885830)Curated
    Sequence conflicti440 – 4401P → H in BAE40020. (PubMed:16141072)Curated
    Sequence conflicti449 – 4491P → Q in BAE40020. (PubMed:16141072)Curated
    Sequence conflicti493 – 4931K → R in BAA07524. (PubMed:7885830)Curated
    Sequence conflicti563 – 5631Y → L in BAA07524. (PubMed:7885830)Curated
    Sequence conflicti712 – 7121P → H in BAC27318. (PubMed:16141072)Curated
    Sequence conflicti734 – 7341T → K in BAC27318. (PubMed:16141072)Curated
    Sequence conflicti837 – 8371P → L in BAA07524. (PubMed:7885830)Curated
    Sequence conflicti866 – 8661Q → K in BAA07524. (PubMed:7885830)Curated
    Sequence conflicti889 – 8891P → H in BAC27318. (PubMed:16141072)Curated
    Sequence conflicti923 – 9231D → G in BAE40020. (PubMed:16141072)Curated
    Sequence conflicti930 – 9301Q → QV in BAC27318. (PubMed:16141072)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei931 – 95121GYPRE…RYSWN → VISTMWAVEGKQHTAHC in isoform 2. 1 PublicationVSP_007235Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D38517 mRNA. Translation: BAA07524.1.
    AK004800 mRNA. Translation: BAB23573.1.
    AK031247 mRNA. Translation: BAC27318.1.
    AK053643 mRNA. Translation: BAC35458.1.
    AK133654 mRNA. Translation: BAE21766.1.
    AK167019 mRNA. Translation: BAE39193.1.
    AK168037 mRNA. Translation: BAE40020.1.
    BC004028 mRNA. Translation: AAH04028.1. Different initiation.
    BC054743 mRNA. Translation: AAH54743.1.
    CCDSiCCDS38258.1. [Q9DBR1-1]
    PIRiI49635.
    RefSeqiNP_036047.2. NM_011917.2. [Q9DBR1-1]
    UniGeneiMm.3065.

    Genome annotation databases

    EnsembliENSMUST00000028921; ENSMUSP00000028921; ENSMUSG00000027433. [Q9DBR1-1]
    GeneIDi24128.
    KEGGimmu:24128.
    UCSCiuc008msq.1. mouse. [Q9DBR1-2]
    uc008msr.1. mouse. [Q9DBR1-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D38517 mRNA. Translation: BAA07524.1 .
    AK004800 mRNA. Translation: BAB23573.1 .
    AK031247 mRNA. Translation: BAC27318.1 .
    AK053643 mRNA. Translation: BAC35458.1 .
    AK133654 mRNA. Translation: BAE21766.1 .
    AK167019 mRNA. Translation: BAE39193.1 .
    AK168037 mRNA. Translation: BAE40020.1 .
    BC004028 mRNA. Translation: AAH04028.1 . Different initiation.
    BC054743 mRNA. Translation: AAH54743.1 .
    CCDSi CCDS38258.1. [Q9DBR1-1 ]
    PIRi I49635.
    RefSeqi NP_036047.2. NM_011917.2. [Q9DBR1-1 ]
    UniGenei Mm.3065.

    3D structure databases

    ProteinModelPortali Q9DBR1.
    SMRi Q9DBR1. Positions 1-430, 502-785.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 204910. 2 interactions.
    IntActi Q9DBR1. 3 interactions.
    MINTi MINT-4140454.
    STRINGi 10090.ENSMUSP00000028921.

    PTM databases

    PhosphoSitei Q9DBR1.

    Proteomic databases

    MaxQBi Q9DBR1.
    PaxDbi Q9DBR1.
    PRIDEi Q9DBR1.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000028921 ; ENSMUSP00000028921 ; ENSMUSG00000027433 . [Q9DBR1-1 ]
    GeneIDi 24128.
    KEGGi mmu:24128.
    UCSCi uc008msq.1. mouse. [Q9DBR1-2 ]
    uc008msr.1. mouse. [Q9DBR1-1 ]

    Organism-specific databases

    CTDi 22803.
    MGIi MGI:894687. Xrn2.

    Phylogenomic databases

    eggNOGi COG5049.
    GeneTreei ENSGT00670000098098.
    HOGENOMi HOG000205514.
    HOVERGENi HBG036677.
    InParanoidi Q9DBR1.
    KOi K12619.
    OMAi MMVEIFK.
    OrthoDBi EOG7S7SCW.
    PhylomeDBi Q9DBR1.
    TreeFami TF105977.

    Miscellaneous databases

    ChiTaRSi XRN2. mouse.
    NextBioi 304163.
    PROi Q9DBR1.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q9DBR1.
    CleanExi MM_XRN2.
    Genevestigatori Q9DBR1.

    Family and domain databases

    InterProi IPR027073. 5_3_exoribonuclease.
    IPR017151. 5_3_exoribonuclease_2.
    IPR004859. Put_53exo.
    IPR001878. Znf_CCHC.
    [Graphical view ]
    PANTHERi PTHR12341. PTHR12341. 1 hit.
    Pfami PF03159. XRN_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037239. Exonuclease_Xrn2. 1 hit.
    SMARTi SM00343. ZnF_C2HC. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Characterization of cDNA encoding mouse homolog of fission yeast dhp1+ gene: structural and functional conservation."
      Shobuike T., Sugano S., Yamashita T., Ikeda H.
      Nucleic Acids Res. 23:357-361(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), TISSUE SPECIFICITY.
      Tissue: Testis.
    2. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-417 (ISOFORMS 1/2).
      Strain: C57BL/6J.
      Tissue: Embryo, Eye, Forelimb, Lung and Pituitary.
    3. "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).
      Strain: C57BL/6 and Czech II.
      Tissue: Brain and Mammary gland.
    4. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-448; SER-499 AND SER-501, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Liver.
    5. "Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis."
      Zhou H., Ye M., Dong J., Han G., Jiang X., Wu R., Zou H.
      J. Proteome Res. 7:3957-3967(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Liver.
    6. "The phagosomal proteome in interferon-gamma-activated macrophages."
      Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
      Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-448; SER-499 AND SER-501, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    7. "Large scale localization of protein phosphorylation by use of electron capture dissociation mass spectrometry."
      Sweet S.M., Bailey C.M., Cunningham D.L., Heath J.K., Cooper H.J.
      Mol. Cell. Proteomics 8:904-912(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-499 AND SER-501, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Embryonic fibroblast.
    8. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
      Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
      Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-286, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Embryonic fibroblast.

    Entry informationi

    Entry nameiXRN2_MOUSE
    AccessioniPrimary (citable) accession number: Q9DBR1
    Secondary accession number(s): Q3TI26
    , Q3TKF2, Q3UZT9, Q61489, Q99KS7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 23, 2003
    Last sequence update: June 1, 2001
    Last modified: October 1, 2014
    This is version 104 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3