MYSM1_DANRE
ID MYSM1_DANRE Reviewed; 822 AA.
AC Q5RGA4; A3KPA5;
DT 05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 05-MAY-2009, sequence version 2.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Histone H2A deubiquitinase MYSM1;
DE Short=2A-DUB;
DE EC=3.4.19.-;
DE AltName: Full=Myb-like, SWIRM and MPN domain-containing protein 1;
GN Name=mysm1; ORFNames=si:ch211-59d15.8;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-457.
RC TISSUE=Embryo;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Metalloprotease that specifically deubiquitinates
CC monoubiquitinated histone H2A, a specific tag for epigenetic
CC transcriptional repression, thereby acting as a coactivator.
CC Preferentially deubiquitinates monoubiquitinated H2A in hyperacetylated
CC nucleosomes. Deubiquitination of histone H2A leads to facilitate the
CC phosphorylation and dissociation of histone H1 from the nucleosome.
CC Acts as a coactivator by participating in the initiation and elongation
CC steps of androgen receptor (AR)-induced gene activation (By
CC similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00624}.
CC -!- DOMAIN: Binds double-stranded DNA via the SANT domain. The SWIRM domain
CC does not bind double-stranded DNA (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the peptidase M67A family. MYSM1 subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAI34240.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAI34240.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
CC Sequence=CAI12031.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; BX942841; CAI12031.1; ALT_SEQ; Genomic_DNA.
DR EMBL; BC134239; AAI34240.1; ALT_SEQ; mRNA.
DR RefSeq; NP_001157501.1; NM_001164029.1.
DR AlphaFoldDB; Q5RGA4; -.
DR SMR; Q5RGA4; -.
DR STRING; 7955.ENSDARP00000107103; -.
DR MEROPS; M67.005; -.
DR PaxDb; Q5RGA4; -.
DR PRIDE; Q5RGA4; -.
DR Ensembl; ENSDART00000125133; ENSDARP00000107103; ENSDARG00000034693.
DR GeneID; 561225; -.
DR KEGG; dre:561225; -.
DR CTD; 114803; -.
DR ZFIN; ZDB-GENE-041014-28; mysm1.
DR eggNOG; KOG1279; Eukaryota.
DR eggNOG; KOG1555; Eukaryota.
DR GeneTree; ENSGT00940000157721; -.
DR HOGENOM; CLU_018854_0_0_1; -.
DR InParanoid; Q5RGA4; -.
DR OMA; SWRTDNS; -.
DR OrthoDB; 590811at2759; -.
DR PhylomeDB; Q5RGA4; -.
DR TreeFam; TF324811; -.
DR Reactome; R-DRE-5689901; Metalloprotease DUBs.
DR PRO; PR:Q5RGA4; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 20.
DR Bgee; ENSDARG00000034693; Expressed in early embryo and 20 other tissues.
DR ExpressionAtlas; Q5RGA4; baseline.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0042393; F:histone binding; ISS:UniProtKB.
DR GO; GO:0070122; F:isopeptidase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0140492; F:metal-dependent deubiquitinase activity; ISS:UniProtKB.
DR GO; GO:0003713; F:transcription coactivator activity; ISS:UniProtKB.
DR GO; GO:0006338; P:chromatin remodeling; ISS:UniProtKB.
DR GO; GO:1904888; P:cranial skeletal system development; IMP:ZFIN.
DR GO; GO:0035522; P:monoubiquitinated histone H2A deubiquitination; ISS:UniProtKB.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISS:UniProtKB.
DR CDD; cd00167; SANT; 1.
DR Gene3D; 1.10.10.10; -; 1.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR000555; JAMM/MPN+_dom.
DR InterPro; IPR037518; MPN.
DR InterPro; IPR017930; Myb_dom.
DR InterPro; IPR033497; MYSM1.
DR InterPro; IPR001005; SANT/Myb.
DR InterPro; IPR017884; SANT_dom.
DR InterPro; IPR007526; SWIRM.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR PANTHER; PTHR12802:SF67; PTHR12802:SF67; 2.
DR Pfam; PF01398; JAB; 1.
DR Pfam; PF00249; Myb_DNA-binding; 1.
DR Pfam; PF04433; SWIRM; 1.
DR SMART; SM00232; JAB_MPN; 1.
DR SMART; SM00717; SANT; 1.
DR SUPFAM; SSF46689; SSF46689; 2.
DR PROSITE; PS50249; MPN; 1.
DR PROSITE; PS51293; SANT; 1.
DR PROSITE; PS50934; SWIRM; 1.
PE 2: Evidence at transcript level;
KW Activator; Chromatin regulator; DNA-binding; Hydrolase; Metal-binding;
KW Metalloprotease; Nucleus; Protease; Reference proteome; Transcription;
KW Transcription regulation; Ubl conjugation pathway; Zinc.
FT CHAIN 1..822
FT /note="Histone H2A deubiquitinase MYSM1"
FT /id="PRO_0000373925"
FT DOMAIN 97..148
FT /note="SANT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00624"
FT DOMAIN 313..411
FT /note="SWIRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00247"
FT DOMAIN 517..651
FT /note="MPN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT REGION 189..221
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 235..267
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 775..822
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 596..609
FT /note="JAMM motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT COMPBIAS 196..215
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 246..261
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 784..814
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 596
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 598
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT BINDING 609
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01182"
FT CONFLICT 38
FT /note="R -> K (in Ref. 1; AAI34240)"
FT /evidence="ECO:0000305"
FT CONFLICT 41
FT /note="S -> G (in Ref. 1; AAI34240)"
FT /evidence="ECO:0000305"
FT CONFLICT 208
FT /note="R -> C (in Ref. 1; AAI34240)"
FT /evidence="ECO:0000305"
FT CONFLICT 221
FT /note="R -> S (in Ref. 1; AAI34240)"
FT /evidence="ECO:0000305"
FT CONFLICT 242
FT /note="A -> V (in Ref. 1; AAI34240)"
FT /evidence="ECO:0000305"
FT CONFLICT 246
FT /note="F -> I (in Ref. 1; AAI34240)"
FT /evidence="ECO:0000305"
FT CONFLICT 295
FT /note="A -> G (in Ref. 1; AAI34240)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 822 AA; 92803 MW; D6F0BB5E0266BA5A CRC64;
MADELDVVDI EGDECDEIVG DLSSAEILQD QYLQSAWRTN SSVLPWTLDS SISDENRQVI
ESMLLEEQYY FASKKAPKVA WTNEKTKVKK PLVKSSAAQT RWAEEEKELF EKGLAQFGRR
WTKIAKLIGT RTVLQVKSYA KQYFKNKPKA EPAAEVTSAN VTSVSSIQPH VSALTNAVRI
ERLSDDEDVD ITDDFSDSEL QSKKQPERSV SPDCNHHGEL RPSLSDALLH LPSESTAADG
QADPDFSEDT EIHHSEIDSE AVEESGNPFI NLDSPSKHSL TGEEETELAD KCESAECLEE
EVEDQEEDEE EELRAPEQEV ELDLNTITEE EKQAISEFFE GRPSKTPERY LKIRNYILDQ
WRRSKPKYLN KTSVRPGLKN CGDVNCIGRI HTYLELIGAI NFNCDQAIYN RPRLVDRSRL
KESKDSLEAY HLAQRLQSMR TRKRRIRDVW GNWCDAKDLE GQTYEHLSAE ELAIRREEMK
KKGPRPSKLP KQRGSFDPFQ LIPCKTFGEE RQEPYSVIVC AEALIVMDIH AHVSMGEVIG
LLGGTYEEED KVLKICSAEP CNSLSTGLQC EMDPVSQTQA SEVLGVKGLS VVGWYHSHPA
FDPNPSLRDI DTQAKYQSYF SRGGAPFIGM IVSPYNPSNS SPQSQSTCLL VQEEPGPSGS
HKFPYQFNMQ CSAEPPDWSE VMRRAEWVVF KYRLCHGSVP MDRLFRRDSS LTCLEKMLLS
IRTVLERLSE VDIETFLVQL ESLFNTHFLS ETGSSSTHLY ETATQPQLLS FLSSEPISSS
ATEETSDGHD EPNTTGPDKL EQSCVEEEHD ETVMQSTSAE TV
