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fredag 29 juni 2018

OTUD4 (4q31.12) DUBA6, HSHIN1, HIN1

OTUD4 (4q31.21)
Vaihtoehtoisesti silmukoituneita transkriptivariantteja löydetään tästä geenistä. Tätä lyhyttä proteiini-isoformia on havaittavissa vain HIV-1 retroviruksella infektoituneissa soluissa. Geenillä on synonyyminimiä HIN1, DUBA6, HSHIN1. Jo vuonna 1992 tutkijat tekivät havainnon proteiinista, jota muodostui vain HIV1 viruksella infektoituneista soluista. (”HIV-1 promotor insertion revealed by selective detection of chimeric provirus-host-gene transcripts). Pitemmässä variantissa on 1049 aminohappoa. Vaihtoehtoisnimi proteiinille on HIV-1 viruksen indusoima proteiini HIN-1. Suositeltu nimi on  OTU-domeenin sisältävä proteiini 4. OTUD4 pidetään  varsinaisesti  K48 deubikitinaasina, mutta fosfoaktivoitu OTUD4  paljastaa sen latentin   K63-deubikitinaasipiirteen, joka säätelee MyD88:sta riippuvaa järjestelmää. (MyD99 proteiini on tärkeänä adaptorina järjestelmässä, joka tunnistaa soluun tulevia patogeenejä Tollin reseptoreilla). https://www.researchgate.net/figure/Signal-transduction-downstream-of-MYD88-dependent-and-independent-pathways-Activation-of_fig1_264866332.
OTUD4 osallistuu DNA:n alkylaatiovaurion korjaukseen toimimalla alustana tai rekrytoijana toisille DUB-perheen jäsenille ( USP7/HAUSP ja USP9X), jotka edistävät DNA:n alkylaatiovauriota korjaavien demetylaasien (hAlkBH2 ja hAlkBH3) dealkyloivia toimia - kun ne irrottavat DNA:n puriinista N1-asemaN ALKYYLIÄ  tai pyrimidiinistä N3 - aseman alkyylia. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475402/

(Laajemman käsityksen DNA:n korjaukseen osllistuvista DUB- entsyymeistä saa Springerlinkistä. 

PubMed tietoa  OTUD GEENISTÄ (4q31.12)
  • https://www.ncbi.nlm.nih.gov/gene/54726 
  • Also known as HIN1; DUBA6; HSHIN1
  • Summary. Alternatively spliced transcript variants have been found for this gene. The smaller protein isoform encoded by the shorter transcript variant is found only in HIV-1 infected cells. [provided by RefSeq, Jul 2010]
  • Expression. Ubiquitous expression in testis (RPKM 19.7), bone marrow (RPKM 11.0) and 25 other tissues See more
  • Preferred Names OTU domain-containing protein 4
  • Names: HIV-1 induced protein HIN-1
Related articles in PubMed
  1. This shows for the first time that HIV-1 can activate transcription of host cellular genes by promotor insertion in a fashion similar to slow-transforming avian and murine retroviruses.
  2. OTUD4 Is a Phospho-Activated K63 Deubiquitinase that Regulates MyD88-Dependent Signaling. Zhao Y, et al. Mol Cell, 2018 Feb 1. PMID 29395066 Ubiquitination is a major mechanism that regulates numerous cellular processes, including autophagy, DNA damage signaling, and inflammation. While hundreds of ubiquitin ligases exist to conjugate ubiquitin onto substrates, approximately 100 deubiquitinases (DUBs) are encoded by the human genome. Thus, deubiquitinases are likely regulated by unidentified mechanisms to target distinct substrates and cellular functions. Here, we demonstrate that the deubiquitinase OTUD4, which nominally encodes a K48-specific deubiquitinase, is phosphorylated near its catalytic domain, activating a latent K63-specific deubiquitinase. Besides phosphorylation, this latter activity requires an adjacent ubiquitin-interacting motif, which increases the affinity of OTUD4 for K63-linked chains. We reveal the Toll-like receptor (TLR)-associated factor MyD88 as a target of this K63 deubiquitinase activity. Consequently, TLR-mediated activation of NF-κB is negatively regulated by OTUD4, and macrophages from Otud4-/- mice exhibit increased inflammatory signaling upon TLR stimulation. Our results reveal insights into how a deubiquitinase may modulate diverse processes through post-translational modification.
  3. Ataxia, dementia, and hypogonadotropism caused by disordered ubiquitination. Margolin DH, et al. N Engl J Med, 2013 May 23. PMID 23656588, Free PMC Article

    (Suom. Seuraa vaikea harvinainen oireyhtymä, jos taustalla on sellainen kombinoitu mutaatio, jossa RBR-tyyppinen RNF proteiini RNF216, E3 ubikitiiniligaasi,  ja OTUD4,deubikitinaasi, ovat molemmat mutatoituneita geenejä )
See all (35) citations in PubMed
 
See citations in PubMed for homologs of this gene provided by HomoloGene
GeneRIFWhat's a GeneRIF?s: Gene References Into Functions
  1. OTUD4 is a positive regulator of ALKBH2 and ALKBH3, two DNA demethylases critical for alkylation repair. Repair of DNA alkylation damage is critical for genomic stability and involves multiple conserved enzymatic pathways. Alkylation damage resistance, which is critical in cancer chemotherapy, depends on the overexpression of alkylation repair proteins. However, the mechanisms responsible for this upregulation are unknown. Here, we show that an OTU domain deubiquitinase, OTUD4, is a positive regulator of ALKBH2 and ALKBH3, two DNA demethylases critical for alkylation repair. Remarkably, we find that OTUD4 catalytic activity is completely dispensable for this function. Rather, OTUD4 is a scaffold for USP7 and USP9X, two deubiquitinases that act directly on the AlkB proteins. Moreover, we show that loss of OTUD4, USP7, or USP9X in tumor cells makes them significantly more sensitive to alkylating agents. Taken together, this work reveals a novel, noncanonical mechanism by which an OTU family deubiquitinase regulates its substrates, and provides multiple new targets for alkylation chemotherapy sensitization of tumors.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475402/
Peptide history and structure:
 OTU domain-containing protein 4 isoform 3 [Homo sapiens]
NCBI Reference Sequence: NP_001096123.1
Identical Proteins FASTA Graphics
LOCUS       NP_001096123            1049 aa            linear   PRI 24-JUN-2018
DEFINITION  OTU domain-containing protein 4 isoform 3 [Homo sapiens].
ACCESSION   NP_001096123
VERSION     NP_001096123.1
DBSOURCE    REFSEQ: accession NM_001102653.1
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (residues 1 to 1049)
  AUTHORS   Zhao Y, Mudge MC, Soll JM, Rodrigues RB, Byrum AK, Schwarzkopf EA,
            Bradstreet TR, Gygi SP, Edelson BT and Mosammaparast N.
  TITLE     OTUD4 Is a Phospho-Activated K63 Deubiquitinase that Regulates
            MyD88-Dependent Signaling
  JOURNAL   Mol. Cell 69 (3), 505-516 (2018)
   PUBMED   29395066
REFERENCE   2  (residues 1 to 1049)
  AUTHORS   Louis M, Hofmann K and Broemer M.
  TITLE     Evolutionary Loss of Activity in De-Ubiquitylating Enzymes of the
            OTU Family
  JOURNAL   PLoS ONE 10 (11), e0143227 (2015)
   PUBMED   26588485
  REMARK    GeneRIF: There is an evolutionary loss of activity in
            de-ubiquitylating enzymes of the OTU family, OTUD4, otu, and
            CG3251.
            Publication Status: Online-Only
REFERENCE   3  (residues 1 to 1049)
  AUTHORS   Zhao Y, Majid MC, Soll JM, Brickner JR, Dango S and Mosammaparast
            N.
  TITLE     Noncanonical regulation of alkylation damage resistance by the
            OTUD4 deubiquitinase
  JOURNAL   EMBO J. 34 (12), 1687-1703 (2015)
   PUBMED   25944111
  REMARK    GeneRIF: OTUD4 is a positive regulator of ALKBH2 and ALKBH3, two
            DNA demethylases critical for alkylation repair.
REFERENCE   4  (residues 1 to 1049)
  AUTHORS   Mevissen TE, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M,
            Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SM,
            Ovaa H and Komander D.
  TITLE     OTU deubiquitinases reveal mechanisms of linkage specificity and
            enable ubiquitin chain restriction analysis
  JOURNAL   Cell 154 (1), 169-184 (2013)
   PUBMED   23827681
REFERENCE   5  (residues 1 to 1049)
  AUTHORS   Margolin DH, Kousi M, Chan YM, Lim ET, Schmahmann JD,
            Hadjivassiliou M, Hall JE, Adam I, Dwyer A, Plummer L, Aldrin SV,
            O'Rourke J, Kirby A, Lage K, Milunsky A, Milunsky JM, Chan J,
            Hedley-Whyte ET, Daly MJ, Katsanis N and Seminara SB.
  TITLE     Ataxia, dementia, and hypogonadotropism caused by disordered
            ubiquitination
  JOURNAL   N. Engl. J. Med. 368 (21), 1992-2003 (2013)
   PUBMED   23656588
  REMARK    GeneRIF: The syndrome of hypogonadotropic hypogonadism, ataxia, and
            dementia can be caused by inactivating mutations in RNF216 or by
            the combination of mutations in RNF216 and OTUD4
REFERENCE   6  (residues 1 to 1049)
  AUTHORS   Beausoleil SA, Villen J, Gerber SA, Rush J and Gygi SP.
  TITLE     A probability-based approach for high-throughput protein
            phosphorylation analysis and site localization
  JOURNAL   Nat. Biotechnol. 24 (10), 1285-1292 (2006)
   PUBMED   16964243
REFERENCE   7  (residues 1 to 1049)
  AUTHORS   Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, Zhang H, Zha XM,
            Polakiewicz RD and Comb MJ.
  TITLE     Immunoaffinity profiling of tyrosine phosphorylation in cancer
            cells
  JOURNAL   Nat. Biotechnol. 23 (1), 94-101 (2005)
   PUBMED   15592455
REFERENCE   8  (residues 1 to 1049)
  AUTHORS   Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li
            J, Cohn MA, Cantley LC and Gygi SP.
  TITLE     Large-scale characterization of HeLa cell nuclear phosphoproteins
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 101 (33), 12130-12135 (2004)
   PUBMED   15302935
REFERENCE   9  (residues 1 to 1049)
  AUTHORS   Brill LM, Salomon AR, Ficarro SB, Mukherji M, Stettler-Gill M and
            Peters EC.
  TITLE     Robust phosphoproteomic profiling of tyrosine phosphorylation sites
            from human T cells using immobilized metal affinity chromatography
            and tandem mass spectrometry
  JOURNAL   Anal. Chem. 76 (10), 2763-2772 (2004)
   PUBMED   15144186
REFERENCE   10 (residues 1 to 1049)
  AUTHORS   Raineri I and Senn HP.
  TITLE     HIV-1 promotor insertion revealed by selective detection of
            chimeric provirus-host gene transcripts
  JOURNAL   Nucleic Acids Res. 20 (23), 6261-6266 (1992)
   PUBMED   1475186
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB446926.2, BC118572.1 and
            AC096757.3.
            This sequence is a reference standard in the RefSeqGene project.
            
            Summary: Alternatively spliced transcript variants have been found
            for this gene. The smaller protein isoform encoded by the shorter
            transcript variant is found only in HIV-1 infected cells. [provided
            by RefSeq, Jul 2010].
            
            Transcript Variant: This variant (3) represents the longer
            transcript and encodes the longer isoform (3).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because no single transcript was available
            for the full length of the gene. The extent of this transcript is
            supported by transcript alignments.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK302581.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000350]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1049
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /chromosome="4"
                     /map="4q31.21"
     Protein         1..1049
                     /product="OTU domain-containing protein 4 isoform 3"
                     /EC_number="3.4.19.12"
                     /note="OTU domain-containing protein 4; HIV-1 induced
                     protein HIN-1"
                     /calculated_mol_wt=116951
     Region          <3 ..="">56
                     /region_name="OTU"
                     /note="OTU-like cysteine protease; cl19932"
                     /db_xref="CDD:303090"
     CDS             1..1049
                     /gene="OTUD4"
                     /gene_synonym="DUBA6; HIN1; HSHIN1"
                     /coded_by="NM_001102653.1:139..3288"
                     /note="isoform 3 is encoded by transcript variant 3"
                     /db_xref="CCDS:CCDS47139.1"
                     /db_xref="GeneID:54726"
                     /db_xref="HGNC:HGNC:24949"
                     /db_xref="MIM:611744"
ORIGIN      
        1 macihylren rekfeafieg sfeeylkrle npqewvgqve isalslmyrk dfiiyrepnv
       61 spsqvtennf pekvllcfsn gnhydivypi kykessamcq sllyellyek vfktdvskiv
      121 meldtlevad ednseisdse ddscksktaa aaadvngfkp lsgneqlknn gnstslplsr
      181 kvlkslnpav yrnveyeiwl kskqaqqkrd ysiaaglqye vgdkcqvrld hngkflnadv
      241 qgihsengpv lveelgkkht sknlkapppe swntvsgkkm kkpstsgqnf hsdvdyrgpk
      301 npskpikaps alpprlqhps gvrqhafssh ssgsqsqkfs sehknlsrtp sqiirkpdre
      361 rvedfdhtsr esnyfglspe errekqaiee srllyeiqnr deqafpalss ssvnqsasqs
      421 snpcvqrkss hvgdrkgsrr rmdteerkdk dsihghsqld krpepstlen itddkyatvs
      481 spskskklec pspaeqkpae hvslsnpapl lvspevhltp avpslpatvp awpsepttfg
      541 ptgvpapipv lsvtqtlttg pdsavsqahl tpspvpvsiq avnqplmplp qtlslyqdpl
      601 ypgfpcnekg draivppysl cqtgedlpkd knilrfffnl gvkayscpmw aphsylyplh
      661 qaylaacrmy pkvpvpvyph npwfqeapaa qnesdctctd ahfpmqteas vngqmpqpei
      721 gpptfssplv ippsqvsesh gqlsyqadle setpgqllha dyeeslsgkn mfpqpsfgpn
      781 pflgpvpiap pffphvwygy pfqgfienpv mrqnivlpsd ekgeldlsle nldlskdcgs
      841 vstvdefpea rgehvhslpe asvsskpdeg rteqssqtrk adtalasipp vaegkahppt
      901 qilnreretv pvelepkrti qslkektekv kdpktaadvv spgansvdsr vqrpkeesse
      961 denevsnilr sgrskqfynq tygsrkyksd wgysgrggyq hvrseeswkg qpsrsrdegy
     1021 qyhrnvrgrp frgdrrrsgm gdghrgqht
//

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