RSBN1_HUMAN
ID RSBN1_HUMAN Reviewed; 802 AA.
AC Q5VWQ0; A8K937; Q6AI21; Q8TC33; Q9HA80; Q9NUP6;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-SEP-2009, sequence version 2.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Lysine-specific demethylase 9 {ECO:0000250|UniProtKB:Q80T69};
DE Short=KDM9 {ECO:0000250|UniProtKB:Q80T69};
DE EC=1.14.11.- {ECO:0000250|UniProtKB:Q80T69};
DE AltName: Full=Round spermatid basic protein 1;
GN Name=RSBN1;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Embryo, and Placenta;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16710414; DOI=10.1038/nature04727;
RA Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A.,
RA Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C.,
RA Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.,
RA Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C.,
RA Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W.,
RA Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J.,
RA Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J.,
RA Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y.,
RA Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J.,
RA Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
RA Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
RA Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
RA Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S.,
RA Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K.,
RA Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R.,
RA Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M.,
RA Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S.,
RA Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J.,
RA Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W.,
RA McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
RA Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
RA Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
RA Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
RA Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S.,
RA Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M.,
RA White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H.,
RA Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E.,
RA Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G.,
RA Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.;
RT "The DNA sequence and biological annotation of human chromosome 1.";
RL Nature 441:315-321(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 39-802 (ISOFORM 4).
RC TISSUE=Testis;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 47-802 (ISOFORM 1).
RC TISSUE=Liver tumor;
RX PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D.,
RA Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A.,
RA Wiemann S., Schupp I.;
RT "The full-ORF clone resource of the German cDNA consortium.";
RL BMC Genomics 8:399-399(2007).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-81, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full phosphorylation
RT site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [7]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-781, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25772364; DOI=10.1016/j.celrep.2015.02.033;
RA Hendriks I.A., Treffers L.W., Verlaan-de Vries M., Olsen J.V.,
RA Vertegaal A.C.;
RT "SUMO-2 orchestrates chromatin modifiers in response to DNA damage.";
RL Cell Rep. 10:1778-1791(2015).
RN [8]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-290; LYS-313; LYS-740 AND
RP LYS-781, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
CC -!- FUNCTION: Histone demethylase that specifically demethylates
CC dimethylated 'Lys-20' of histone H4 (H4K20me2), thereby modulating
CC chromosome architecture. {ECO:0000250|UniProtKB:Q80T69}.
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q80T69};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:Q9GRZ3};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q5VWQ0-1; Sequence=Displayed;
CC Name=4;
CC IsoId=Q5VWQ0-4; Sequence=VSP_027656;
CC -!- PTM: Phosphorylated by PKA. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the round spermatid basic protein 1 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH26155.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=BAA92075.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=BAB13974.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=CAH10493.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAH10493.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};
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DR EMBL; AK002082; BAA92075.1; ALT_INIT; mRNA.
DR EMBL; AK292552; BAF85241.1; -; mRNA.
DR EMBL; AK022166; BAB13974.1; ALT_INIT; mRNA.
DR EMBL; AL137856; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AL365321; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC026155; AAH26155.1; ALT_INIT; mRNA.
DR EMBL; CR627402; CAH10493.1; ALT_SEQ; mRNA.
DR CCDS; CCDS862.1; -. [Q5VWQ0-1]
DR RefSeq; NP_060834.2; NM_018364.4. [Q5VWQ0-1]
DR RefSeq; XP_016857007.1; XM_017001518.1. [Q5VWQ0-4]
DR AlphaFoldDB; Q5VWQ0; -.
DR SMR; Q5VWQ0; -.
DR BioGRID; 120094; 159.
DR IntAct; Q5VWQ0; 57.
DR STRING; 9606.ENSP00000261441; -.
DR iPTMnet; Q5VWQ0; -.
DR PhosphoSitePlus; Q5VWQ0; -.
DR BioMuta; RSBN1; -.
DR DMDM; 257050986; -.
DR EPD; Q5VWQ0; -.
DR jPOST; Q5VWQ0; -.
DR MassIVE; Q5VWQ0; -.
DR MaxQB; Q5VWQ0; -.
DR PaxDb; Q5VWQ0; -.
DR PeptideAtlas; Q5VWQ0; -.
DR PRIDE; Q5VWQ0; -.
DR ProteomicsDB; 65552; -. [Q5VWQ0-1]
DR ProteomicsDB; 65553; -. [Q5VWQ0-4]
DR Antibodypedia; 46942; 108 antibodies from 20 providers.
DR DNASU; 54665; -.
DR Ensembl; ENST00000261441.9; ENSP00000261441.5; ENSG00000081019.14. [Q5VWQ0-1]
DR Ensembl; ENST00000612242.4; ENSP00000479490.1; ENSG00000081019.14. [Q5VWQ0-1]
DR GeneID; 54665; -.
DR KEGG; hsa:54665; -.
DR MANE-Select; ENST00000261441.9; ENSP00000261441.5; NM_018364.5; NP_060834.2.
DR UCSC; uc001edq.4; human. [Q5VWQ0-1]
DR CTD; 54665; -.
DR DisGeNET; 54665; -.
DR GeneCards; RSBN1; -.
DR HGNC; HGNC:25642; RSBN1.
DR HPA; ENSG00000081019; Low tissue specificity.
DR MIM; 615858; gene.
DR neXtProt; NX_Q5VWQ0; -.
DR OpenTargets; ENSG00000081019; -.
DR PharmGKB; PA134869532; -.
DR VEuPathDB; HostDB:ENSG00000081019; -.
DR eggNOG; KOG4425; Eukaryota.
DR GeneTree; ENSGT00390000001969; -.
DR InParanoid; Q5VWQ0; -.
DR OMA; SNMDCDL; -.
DR OrthoDB; 930910at2759; -.
DR PhylomeDB; Q5VWQ0; -.
DR TreeFam; TF323256; -.
DR PathwayCommons; Q5VWQ0; -.
DR SignaLink; Q5VWQ0; -.
DR BioGRID-ORCS; 54665; 17 hits in 1090 CRISPR screens.
DR ChiTaRS; RSBN1; human.
DR GenomeRNAi; 54665; -.
DR Pharos; Q5VWQ0; Tbio.
DR PRO; PR:Q5VWQ0; -.
DR Proteomes; UP000005640; Chromosome 1.
DR RNAct; Q5VWQ0; protein.
DR Bgee; ENSG00000081019; Expressed in caput epididymis and 204 other tissues.
DR ExpressionAtlas; Q5VWQ0; baseline and differential.
DR Genevisible; Q5VWQ0; HS.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0035575; F:histone H4-methyl-lysine-20 demethylase activity; IEA:Ensembl.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR InterPro; IPR026306; RSBN1/Dpy-21.
DR PANTHER; PTHR13354; PTHR13354; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chromatin regulator; Dioxygenase; Iron;
KW Isopeptide bond; Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein;
KW Reference proteome; Ubl conjugation.
FT CHAIN 1..802
FT /note="Lysine-specific demethylase 9"
FT /id="PRO_0000299412"
FT REGION 65..244
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 252..263
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT COMPBIAS 65..81
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 125..160
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 197..221
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 579
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:Q9GRZ3"
FT BINDING 582
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q9GRZ3"
FT BINDING 584
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q9GRZ3"
FT BINDING 676
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:Q9GRZ3"
FT BINDING 684
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q9GRZ3"
FT MOD_RES 81
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:20068231"
FT CROSSLNK 290
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 313
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 740
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 781
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:25772364,
FT ECO:0007744|PubMed:28112733"
FT VAR_SEQ 460..802
FT /note="Missing (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_027656"
FT CONFLICT 39..40
FT /note="GP -> SG (in Ref. 3; AAH26155)"
FT /evidence="ECO:0000305"
FT CONFLICT 106
FT /note="E -> G (in Ref. 1; BAF85241)"
FT /evidence="ECO:0000305"
FT CONFLICT 120
FT /note="Q -> R (in Ref. 1; BAA92075)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 802 AA; 90072 MW; 78F229AB6A0FABD1 CRC64;
MFISGRRTAD KWRAEERLQC PAGSARAALA RCADGGAVGP FKCVFVGEMA AQVGAVRVVR
AVAAQEEPDK EGKEKPHAGV SPRGVKRQRR SSSGGSQEKR GRPSQEPPLA PPHRRRRSRQ
HPGPLPPTNA APTVPGPVEP LLLPPPPPPS LAPAGPAVAA PLPAPSTSAL FTFSPLTVSA
AGPKHKGHKE RHKHHHHRGP DGDPSSCGTD LKHKDKQENG ERTGGVPLIK APKRETPDEN
GKTQRADDFV LKKIKKKKKK KHREDMRGRR LKMYNKEVQT VCAGLTRISK EILTQGQINS
TSGLNKESFR YLKDEQLCRL NLGMQEYRVP QGVQTPFMTH QEHSIRRNFL KTGTKFSNFI
HEEHQSNGGA LVLHAYMDEL SFLSPMEMER FSEEFLALTF SENEKNAAYY ALAIVHGAAA
YLPDFLDYFA FNFPNTPVKM EILGKKDIET TTISNFHTQV NRTYCCGTYR AGPMRQISLV
GAVDEEVGDY FPEFLDMLEE SPFLKMTLPW GTLSSLRLQC RSQSDDGPIM WVRPGEQMIP
TADMPKSPFK RRRSMNEIKN LQYLPRTSEP REVLFEDRTR AHADHVGQGF DWQSTAAVGV
LKAVQFGEWS DQPRITKDVI CFHAEDFTDV VQRLQLDLHE PPVSQCVQWV DEAKLNQMRR
EGIRYARIQL CDNDIYFIPR NVIHQFKTVS AVCSLAWHIR LKQYHPVVEA TQNTESNSNM
DCGLTGKREL EVDSQCVRIK TESEEACTEI QLLTTASSSF PPASELNLQQ DQKTQPIPVL
KVESRLDSDQ QHNLQEHSTT SV
