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Protein

Lysine-specific demethylase 5B

Gene

KDM5B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:24952722, PubMed:27214403, PubMed:28262558). Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5 (PubMed:24952722). In contrast, may act as a tumor suppressor for melanoma. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity).By similarity9 Publications

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity

Activity regulationi

Several specific inhibitors are being developed and tested (PubMed:27214403, PubMed:26741168). The inhibitor KDOAM-25 inhibits its demethylase activity, resulting to cell cycle arrest in myeloma cells (PubMed:28262558).3 Publications

Kineticsi

Kcat are 1.9 min(-1) and 2.0 min(-1) for 2-oxoglutarate and histone H3K4me3, respectively.1 Publication
  1. KM=9 µM for 2-oxoglutarate1 Publication
  2. KM=4 µM for histone H3K4me31 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei4252-oxoglutarateBy similarity1
    Metal bindingi499Iron; catalytic3 Publications1
    Metal bindingi501Iron; catalytic3 Publications1
    Binding sitei5072-oxoglutarateBy similarity1
    Binding sitei5092-oxoglutarateBy similarity1
    Binding sitei5172-oxoglutarateBy similarity1
    Metal bindingi587Iron; catalytic3 Publications1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Zinc fingeri309 – 359PHD-type 1Combined sources1 PublicationAdd BLAST51
    Zinc fingeri692 – 744C5HC23 PublicationsAdd BLAST53
    Zinc fingeri1176 – 1224PHD-type 2PROSITE-ProRule annotationAdd BLAST49
    Zinc fingeri1484 – 1538PHD-type 3Combined sourcesAdd BLAST55

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionChromatin regulator, Dioxygenase, Oxidoreductase, Repressor
    Biological processBiological rhythms, Transcription, Transcription regulation
    LigandIron, Metal-binding, Zinc

    Enzyme and pathway databases

    ReactomeiR-HSA-3214842 HDMs demethylate histones
    R-HSA-8866911 TFAP2 (AP-2) family regulates transcription of cell cycle factors
    SIGNORiQ9UGL1

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Lysine-specific demethylase 5B (EC:1.14.11.-)
    Alternative name(s):
    Cancer/testis antigen 31
    Short name:
    CT31
    Histone demethylase JARID1B
    Jumonji/ARID domain-containing protein 1B
    PLU-1
    Retinoblastoma-binding protein 2 homolog 1
    Short name:
    RBP2-H1
    Gene namesi
    Name:KDM5B
    Synonyms:JARID1B, PLU1, RBBP2H1
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 1

    Organism-specific databases

    EuPathDBiHostDB:ENSG00000117139.16
    HGNCiHGNC:18039 KDM5B
    MIMi605393 gene
    neXtProtiNX_Q9UGL1

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi308D → A: Slightly decreases interaction with histone H3. Decreases by 21% demethylase activity and repression of tumor suppressor genes expression. 1 Publication1
    Mutagenesisi309L → A: No effect on interaction with histone H3. 1 Publication1
    Mutagenesisi310Y → A: Slightly decreases interaction with histone H3. 1 Publication1
    Mutagenesisi310Y → F: No effect on interaction with histone H3. 1 Publication1
    Mutagenesisi311V → A: No effect on interaction with histone H3. 1 Publication1
    Mutagenesisi321E → A: Decreases interaction with histone H3. 1 Publication1
    Mutagenesisi322D → A: No effect on interaction with histone H3. 1 Publication1
    Mutagenesisi324L → A: No effect on interaction with histone H3. 1 Publication1
    Mutagenesisi325L → A: Abolishes interaction with histone H3. Decreases by 44% demethylase activity and repression of tumor suppressor genes expression; when associated with A-328. 1 Publication1
    Mutagenesisi326L → A: No effect on interaction with histone H3. 1 Publication1
    Mutagenesisi328D → A: Almost abolishes interaction with histone H3. Decreases by 44% demethylase activity and repression of tumor suppressor genes expression; when associated with A-325. 1 Publication1
    Mutagenesisi332D → A: No effect on interaction with histone H3. 1 Publication1
    Mutagenesisi333S → A: No effect on interaction with histone H3. 1 Publication1
    Mutagenesisi334Y → A: No effect on interaction with histone H3. 1 Publication1
    Mutagenesisi335H → A: Slightly impairs transcription repression ability. 1 Publication1
    Mutagenesisi345D → A: No effect on interaction with histone H3. 1 Publication1
    Mutagenesisi351W → A: Abolishes interaction with histone H3. Decreases by 28% demethylase activity and repression of tumor suppressor genes expression. 1 Publication1
    Mutagenesisi499 – 501HIE → AIA: Abolishes lysine-specific histone demethylase activity. 1 Publication3
    Mutagenesisi499H → Y: Abolishes lysine-specific histone demethylase activity. 1 Publication1
    Mutagenesisi1200H → A: Impairs transcription repression ability and interaction with HDAC4. 1 Publication1

    Organism-specific databases

    DisGeNETi10765
    MalaCardsiKDM5B
    OpenTargetsiENSG00000117139
    Orphaneti178469 Autosomal dominant non-syndromic intellectual disability
    PharmGKBiPA164721626

    Chemistry databases

    ChEMBLiCHEMBL3774295
    GuidetoPHARMACOLOGYi2681

    Polymorphism and mutation databases

    BioMutaiKDM5B
    DMDMi296439317

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002924121 – 1544Lysine-specific demethylase 5BAdd BLAST1544

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Cross-linki148Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Cross-linki204Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Cross-linki209Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Cross-linki242Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Cross-linki274Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Cross-linki278Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Cross-linki769Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Modified residuei832N6-acetyllysineBy similarity1
    Modified residuei986PhosphoserineCombined sources1
    Modified residuei1328PhosphoserineCombined sources1
    Cross-linki1450Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
    Modified residuei1456PhosphoserineCombined sources1

    Keywords - PTMi

    Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    EPDiQ9UGL1
    PaxDbiQ9UGL1
    PeptideAtlasiQ9UGL1
    PRIDEiQ9UGL1
    ProteomicsDBi84231
    84232 [Q9UGL1-2]

    PTM databases

    iPTMnetiQ9UGL1
    PhosphoSitePlusiQ9UGL1

    Expressioni

    Tissue specificityi

    Ubiquitously expressed, with highest levels in testis. Down-regulated in melanoma and glioblastoma. Up-regulated in breast cancer (at protein level).5 Publications

    Gene expression databases

    BgeeiENSG00000117139 Expressed in 213 organ(s), highest expression level in sperm
    CleanExiHS_JARID1B
    ExpressionAtlasiQ9UGL1 baseline and differential
    GenevisibleiQ9UGL1 HS

    Organism-specific databases

    HPAiCAB068193
    HPA027179
    HPA053723

    Interactioni

    Subunit structurei

    Interacts with FOXG1B, PAX9, MYC, MYCN and RB1. Interacts with HDAC1, HDAC4, HDAC5 and HDAC7. Interacts (via PHD-type 1 zinc finger) with histone H3 unmodified at 'Lys-4'; the interaction is inhibited when histone H3 is methylated at 'Arg-2' or 'Lys-4' (PubMed:24952722).6 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CTCFP497118EBI-2514978,EBI-932887

    GO - Molecular functioni

    Protein-protein interaction databases

    BioGridi115984, 64 interactors
    CORUMiQ9UGL1
    DIPiDIP-53652N
    IntActiQ9UGL1, 4 interactors
    STRINGi9606.ENSP00000356234

    Chemistry databases

    BindingDBiQ9UGL1

    Structurei

    Secondary structure

    11544
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    DisProtiDP00712
    ProteinModelPortaliQ9UGL1
    SMRiQ9UGL1
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini32 – 73JmjNPROSITE-ProRule annotationAdd BLAST42
    Domaini97 – 187ARIDPROSITE-ProRule annotationAdd BLAST91
    Domaini453 – 619JmjCPROSITE-ProRule annotationAdd BLAST167

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi1434 – 1439Poly-Lys6

    Domaini

    Both the JmjC domain and the JmjN domain are required for enzymatic activity. However ARID and PHD-type 1 domain are not required for activity per se but contributed to recognition of the H3(1-21)K4me2 substrate peptide.1 Publication
    The 2 first PHD-type zinc finger domains are required for transcription repression activity.

    Sequence similaritiesi

    Belongs to the JARID1 histone demethylase family.Curated

    Zinc finger

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Zinc fingeri309 – 359PHD-type 1Combined sources1 PublicationAdd BLAST51
    Zinc fingeri692 – 744C5HC23 PublicationsAdd BLAST53
    Zinc fingeri1176 – 1224PHD-type 2PROSITE-ProRule annotationAdd BLAST49
    Zinc fingeri1484 – 1538PHD-type 3Combined sourcesAdd BLAST55

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiKOG1246 Eukaryota
    ENOG410XR9J LUCA
    GeneTreeiENSGT00530000063118
    HOGENOMiHOG000290719
    InParanoidiQ9UGL1
    KOiK11446
    OMAiHWDDKAR
    OrthoDBiEOG091G0RFR
    PhylomeDBiQ9UGL1
    TreeFamiTF106476

    Family and domain databases

    Gene3Di1.10.150.60, 1 hit
    3.30.40.10, 2 hits
    InterProiView protein in InterPro
    IPR001606 ARID_dom
    IPR036431 ARID_dom_sf
    IPR003347 JmjC_dom
    IPR003349 JmjN
    IPR013637 Lys_sp_deMease-like_dom
    IPR019786 Zinc_finger_PHD-type_CS
    IPR004198 Znf_C5HC2
    IPR011011 Znf_FYVE_PHD
    IPR001965 Znf_PHD
    IPR019787 Znf_PHD-finger
    IPR013083 Znf_RING/FYVE/PHD
    PfamiView protein in Pfam
    PF01388 ARID, 1 hit
    PF02373 JmjC, 1 hit
    PF02375 JmjN, 1 hit
    PF00628 PHD, 3 hits
    PF08429 PLU-1, 1 hit
    PF02928 zf-C5HC2, 1 hit
    SMARTiView protein in SMART
    SM00501 BRIGHT, 1 hit
    SM00558 JmjC, 1 hit
    SM00545 JmjN, 1 hit
    SM00249 PHD, 3 hits
    SUPFAMiSSF46774 SSF46774, 1 hit
    SSF57903 SSF57903, 3 hits
    PROSITEiView protein in PROSITE
    PS51011 ARID, 1 hit
    PS51184 JMJC, 1 hit
    PS51183 JMJN, 1 hit
    PS01359 ZF_PHD_1, 2 hits
    PS50016 ZF_PHD_2, 3 hits

    Sequences (2+)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

    This entry has 2 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

    Isoform 1 (identifier: Q9UGL1-1) [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
            10         20         30         40         50
    MEAATTLHPG PRPALPLGGP GPLGEFLPPP ECPVFEPSWE EFADPFAFIH
    60 70 80 90 100
    KIRPIAEQTG ICKVRPPPDW QPPFACDVDK LHFTPRIQRL NELEAQTRVK
    110 120 130 140 150
    LNFLDQIAKY WELQGSTLKI PHVERKILDL FQLNKLVAEE GGFAVVCKDR
    160 170 180 190 200
    KWTKIATKMG FAPGKAVGSH IRGHYERILN PYNLFLSGDS LRCLQKPNLT
    210 220 230 240 250
    TDTKDKEYKP HDIPQRQSVQ PSETCPPARR AKRMRAEAMN IKIEPEETTE
    260 270 280 290 300
    ARTHNLRRRM GCPTPKCENE KEMKSSIKQE PIERKDYIVE NEKEKPKSRS
    310 320 330 340 350
    KKATNAVDLY VCLLCGSGND EDRLLLCDGC DDSYHTFCLI PPLHDVPKGD
    360 370 380 390 400
    WRCPKCLAQE CSKPQEAFGF EQAARDYTLR TFGEMADAFK SDYFNMPVHM
    410 420 430 440 450
    VPTELVEKEF WRLVSTIEED VTVEYGADIA SKEFGSGFPV RDGKIKLSPE
    460 470 480 490 500
    EEEYLDSGWN LNNMPVMEQS VLAHITADIC GMKLPWLYVG MCFSSFCWHI
    510 520 530 540 550
    EDHWSYSINY LHWGEPKTWY GVPGYAAEQL ENVMKKLAPE LFVSQPDLLH
    560 570 580 590 600
    QLVTIMNPNT LMTHEVPVYR TNQCAGEFVI TFPRAYHSGF NQGFNFAEAV
    610 620 630 640 650
    NFCTVDWLPL GRQCVEHYRL LHRYCVFSHD EMICKMASKA DVLDVVVAST
    660 670 680 690 700
    VQKDMAIMIE DEKALRETVR KLGVIDSERM DFELLPDDER QCVKCKTTCF
    710 720 730 740 750
    MSAISCSCKP GLLVCLHHVK ELCSCPPYKY KLRYRYTLDD LYPMMNALKL
    760 770 780 790 800
    RAESYNEWAL NVNEALEAKI NKKKSLVSFK ALIEESEMKK FPDNDLLRHL
    810 820 830 840 850
    RLVTQDAEKC ASVAQQLLNG KRQTRYRSGG GKSQNQLTVN ELRQFVTQLY
    860 870 880 890 900
    ALPCVLSQTP LLKDLLNRVE DFQQHSQKLL SEETPSAAEL QDLLDVSFEF
    910 920 930 940 950
    DVELPQLAEM RIRLEQARWL EEVQQACLDP SSLTLDDMRR LIDLGVGLAP
    960 970 980 990 1000
    YSAVEKAMAR LQELLTVSEH WDDKAKSLLK ARPRHSLNSL ATAVKEIEEI
    1010 1020 1030 1040 1050
    PAYLPNGAAL KDSVQRARDW LQDVEGLQAG GRVPVLDTLI ELVTRGRSIP
    1060 1070 1080 1090 1100
    VHLNSLPRLE TLVAEVQAWK ECAVNTFLTE NSPYSLLEVL CPRCDIGLLG
    1110 1120 1130 1140 1150
    LKRKQRKLKE PLPNGKKKST KLESLSDLER ALTESKETAS AMATLGEARL
    1160 1170 1180 1190 1200
    REMEALQSLR LANEGKLLSP LQDVDIKICL CQKAPAAPMI QCELCRDAFH
    1210 1220 1230 1240 1250
    TSCVAVPSIS QGLRIWLCPH CRRSEKPPLE KILPLLASLQ RIRVRLPEGD
    1260 1270 1280 1290 1300
    ALRYMIERTV NWQHRAQQLL SSGNLKFVQD RVGSGLLYSR WQASAGQVSD
    1310 1320 1330 1340 1350
    TNKVSQPPGT TSFSLPDDWD NRTSYLHSPF STGRSCIPLH GVSPEVNELL
    1360 1370 1380 1390 1400
    MEAQLLQVSL PEIQELYQTL LAKPSPAQQT DRSSPVRPSS EKNDCCRGKR
    1410 1420 1430 1440 1450
    DGINSLERKL KRRLEREGLS SERWERVKKM RTPKKKKIKL SHPKDMNNFK
    1460 1470 1480 1490 1500
    LERERSYELV RSAETHSLPS DTSYSEQEDS EDEDAICPAV SCLQPEGDEV
    1510 1520 1530 1540
    DWVQCDGSCN QWFHQVCVGV SPEMAEKEDY ICVRCTVKDA PSRK
    Length:1,544
    Mass (Da):175,658
    Last modified:May 18, 2010 - v3
    Checksum:i70A0738D9A709F61
    GO
    Isoform 2 (identifier: Q9UGL1-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         237-237: E → ERQSLAVLPRLECSGAILAHCNLRLLDSSNSSASASQ

    Show »
    Length:1,580
    Mass (Da):179,409
    Checksum:i61B03B8A7EE16B3C
    GO

    Computationally mapped potential isoform sequencesi

    There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
    EntryEntry nameProtein names
    Gene namesLengthAnnotation
    B3KV94B3KV94_HUMAN
    Jumonji, AT rich interactive domain...
    KDM5B JARID1B, hCG_2027322
    1,275Annotation score:
    R4GN45R4GN45_HUMAN
    Lysine-specific demethylase 5B
    KDM5B
    77Annotation score:

    Sequence cautioni

    The sequence CAB63108 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti78V → G in CAB63108 (PubMed:10878660).Curated1
    Sequence conflicti585 – 589AYHSG → VPQW in AAD16061 (PubMed:10616211).Curated5
    Sequence conflicti708C → W in AAD16061 (PubMed:10616211).Curated1
    Sequence conflicti759A → P in AAD16061 (PubMed:10616211).Curated1
    Sequence conflicti771N → T in AAD16061 (PubMed:10616211).Curated1
    Sequence conflicti771N → T in CAB63108 (PubMed:10878660).Curated1
    Sequence conflicti1182Q → R in AAD16061 (PubMed:10616211).Curated1
    Sequence conflicti1293A → P in AAD16061 (PubMed:10616211).Curated1
    Sequence conflicti1307P → L in AAD16061 (PubMed:10616211).Curated1
    Sequence conflicti1331S → ST in AAD16061 (PubMed:10616211).Curated1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_026408237E → ERQSLAVLPRLECSGAILAH CNLRLLDSSNSSASASQ in isoform 2. 1 Publication1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ132440 mRNA Translation: CAB43532.1
    AF087481 mRNA Translation: AAD16061.1
    AJ243706 mRNA Translation: CAB63108.1 Different initiation.
    AC098934 Genomic DNA No translation available.
    AC104463 Genomic DNA No translation available.
    CCDSiCCDS30974.1 [Q9UGL1-1]
    CCDS81417.1 [Q9UGL1-2]
    RefSeqiNP_001300971.1, NM_001314042.1 [Q9UGL1-2]
    NP_006609.3, NM_006618.4 [Q9UGL1-1]
    UniGeneiHs.18891
    Hs.443650

    Genome annotation databases

    EnsembliENST00000367264; ENSP00000356233; ENSG00000117139 [Q9UGL1-2]
    ENST00000367265; ENSP00000356234; ENSG00000117139 [Q9UGL1-1]
    GeneIDi10765
    KEGGihsa:10765
    UCSCiuc001gyf.4 human [Q9UGL1-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Similar proteinsi

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ132440 mRNA Translation: CAB43532.1
    AF087481 mRNA Translation: AAD16061.1
    AJ243706 mRNA Translation: CAB63108.1 Different initiation.
    AC098934 Genomic DNA No translation available.
    AC104463 Genomic DNA No translation available.
    CCDSiCCDS30974.1 [Q9UGL1-1]
    CCDS81417.1 [Q9UGL1-2]
    RefSeqiNP_001300971.1, NM_001314042.1 [Q9UGL1-2]
    NP_006609.3, NM_006618.4 [Q9UGL1-1]
    UniGeneiHs.18891
    Hs.443650

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2MA5NMR-A1487-1544[»]
    2MNYNMR-A306-360[»]
    2MNZNMR-A306-360[»]
    5A1FX-ray2.10A26-770[»]
    5A3NX-ray2.00A26-101[»]
    A374-772[»]
    5A3PX-ray2.01A26-101[»]
    A374-770[»]
    5A3TX-ray1.90A26-101[»]
    A374-772[»]
    5A3WX-ray2.00A26-101[»]
    A374-772[»]
    5FPLX-ray2.35A26-101[»]
    A374-772[»]
    5FPUX-ray2.24A26-101[»]
    A374-772[»]
    5FUNX-ray2.30A26-101[»]
    A374-772[»]
    5FUPX-ray2.15A26-101[»]
    A374-770[»]
    5FV3X-ray2.37A26-101[»]
    A374-770[»]
    5FY4X-ray2.10A26-101[»]
    A374-770[»]
    5FY5X-ray2.47A26-101[»]
    A374-770[»]
    5FY9X-ray2.03A26-101[»]
    A374-770[»]
    5FYBX-ray1.87A26-101[»]
    A374-770[»]
    5FYSX-ray1.89A26-101[»]
    A374-770[»]
    5FYTX-ray1.87A26-101[»]
    A374-770[»]
    5FYUX-ray2.06A26-101[»]
    A374-770[»]
    5FYVX-ray1.87A26-101[»]
    A374-770[»]
    5FYYX-ray2.18A26-101[»]
    A374-770[»]
    5FYZX-ray1.75A26-101[»]
    A374-770[»]
    5FZ0X-ray2.42A26-101[»]
    A374-770[»]
    5FZ1X-ray2.39A26-101[»]
    A374-770[»]
    5FZ3X-ray2.50A26-101[»]
    A374-770[»]
    5FZ4X-ray2.07A26-101[»]
    A374-770[»]
    5FZ6X-ray2.33A26-101[»]
    A374-770[»]
    5FZ7X-ray2.30A26-101[»]
    A374-770[»]
    5FZ8X-ray1.86A26-101[»]
    A374-770[»]
    5FZ9X-ray2.06A26-101[»]
    A374-770[»]
    5FZAX-ray2.10A26-101[»]
    A374-770[»]
    5FZBX-ray2.18A26-101[»]
    A374-770[»]
    5FZCX-ray2.05A26-101[»]
    A374-770[»]
    5FZDX-ray2.05A26-101[»]
    A374-770[»]
    5FZEX-ray2.02A26-101[»]
    A374-770[»]
    5FZFX-ray1.97A26-101[»]
    A374-770[»]
    5FZGX-ray1.96A26-101[»]
    A374-770[»]
    5FZHX-ray2.09A26-101[»]
    A374-442[»]
    A444-770[»]
    5FZIX-ray1.95A26-101[»]
    A374-770[»]
    5FZKX-ray2.05A26-101[»]
    A374-770[»]
    5FZLX-ray2.55A26-101[»]
    A374-770[»]
    5FZMX-ray2.49A26-101[»]
    A376-770[»]
    5LW9X-ray2.30A26-99[»]
    A374-772[»]
    5LWBX-ray2.39A26-101[»]
    A374-772[»]
    6EINX-ray2.11A26-101[»]
    A374-772[»]
    6EIUX-ray1.88A26-100[»]
    A374-754[»]
    6EIYX-ray2.15A26-100[»]
    A374-754[»]
    6EJ0X-ray2.06A26-98[»]
    A375-754[»]
    6EJ1X-ray2.07A26-98[»]
    A375-754[»]
    6EK6X-ray2.05A347-754[»]
    DisProtiDP00712
    ProteinModelPortaliQ9UGL1
    SMRiQ9UGL1
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi115984, 64 interactors
    CORUMiQ9UGL1
    DIPiDIP-53652N
    IntActiQ9UGL1, 4 interactors
    STRINGi9606.ENSP00000356234

    Chemistry databases

    BindingDBiQ9UGL1
    ChEMBLiCHEMBL3774295
    GuidetoPHARMACOLOGYi2681

    PTM databases

    iPTMnetiQ9UGL1
    PhosphoSitePlusiQ9UGL1

    Polymorphism and mutation databases

    BioMutaiKDM5B
    DMDMi296439317

    Proteomic databases

    EPDiQ9UGL1
    PaxDbiQ9UGL1
    PeptideAtlasiQ9UGL1
    PRIDEiQ9UGL1
    ProteomicsDBi84231
    84232 [Q9UGL1-2]

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000367264; ENSP00000356233; ENSG00000117139 [Q9UGL1-2]
    ENST00000367265; ENSP00000356234; ENSG00000117139 [Q9UGL1-1]
    GeneIDi10765
    KEGGihsa:10765
    UCSCiuc001gyf.4 human [Q9UGL1-1]

    Organism-specific databases

    CTDi10765
    DisGeNETi10765
    EuPathDBiHostDB:ENSG00000117139.16
    GeneCardsiKDM5B
    H-InvDBiHIX0001478
    HGNCiHGNC:18039 KDM5B
    HPAiCAB068193
    HPA027179
    HPA053723
    MalaCardsiKDM5B
    MIMi605393 gene
    neXtProtiNX_Q9UGL1
    OpenTargetsiENSG00000117139
    Orphaneti178469 Autosomal dominant non-syndromic intellectual disability
    PharmGKBiPA164721626
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG1246 Eukaryota
    ENOG410XR9J LUCA
    GeneTreeiENSGT00530000063118
    HOGENOMiHOG000290719
    InParanoidiQ9UGL1
    KOiK11446
    OMAiHWDDKAR
    OrthoDBiEOG091G0RFR
    PhylomeDBiQ9UGL1
    TreeFamiTF106476

    Enzyme and pathway databases

    ReactomeiR-HSA-3214842 HDMs demethylate histones
    R-HSA-8866911 TFAP2 (AP-2) family regulates transcription of cell cycle factors
    SIGNORiQ9UGL1

    Miscellaneous databases

    ChiTaRSiKDM5B human
    GeneWikiiJARID1B
    GenomeRNAii10765
    PROiPR:Q9UGL1
    SOURCEiSearch...

    Gene expression databases

    BgeeiENSG00000117139 Expressed in 213 organ(s), highest expression level in sperm
    CleanExiHS_JARID1B
    ExpressionAtlasiQ9UGL1 baseline and differential
    GenevisibleiQ9UGL1 HS

    Family and domain databases

    Gene3Di1.10.150.60, 1 hit
    3.30.40.10, 2 hits
    InterProiView protein in InterPro
    IPR001606 ARID_dom
    IPR036431 ARID_dom_sf
    IPR003347 JmjC_dom
    IPR003349 JmjN
    IPR013637 Lys_sp_deMease-like_dom
    IPR019786 Zinc_finger_PHD-type_CS
    IPR004198 Znf_C5HC2
    IPR011011 Znf_FYVE_PHD
    IPR001965 Znf_PHD
    IPR019787 Znf_PHD-finger
    IPR013083 Znf_RING/FYVE/PHD
    PfamiView protein in Pfam
    PF01388 ARID, 1 hit
    PF02373 JmjC, 1 hit
    PF02375 JmjN, 1 hit
    PF00628 PHD, 3 hits
    PF08429 PLU-1, 1 hit
    PF02928 zf-C5HC2, 1 hit
    SMARTiView protein in SMART
    SM00501 BRIGHT, 1 hit
    SM00558 JmjC, 1 hit
    SM00545 JmjN, 1 hit
    SM00249 PHD, 3 hits
    SUPFAMiSSF46774 SSF46774, 1 hit
    SSF57903 SSF57903, 3 hits
    PROSITEiView protein in PROSITE
    PS51011 ARID, 1 hit
    PS51184 JMJC, 1 hit
    PS51183 JMJN, 1 hit
    PS01359 ZF_PHD_1, 2 hits
    PS50016 ZF_PHD_2, 3 hits
    ProtoNetiSearch...

    Entry informationi

    Entry nameiKDM5B_HUMAN
    AccessioniPrimary (citable) accession number: Q9UGL1
    Secondary accession number(s): O95811, Q15752, Q9Y3Q5
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 26, 2007
    Last sequence update: May 18, 2010
    Last modified: November 7, 2018
    This is version 153 of the entry and version 3 of the sequence. See 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. SIMILARITY comments
      Index of protein domains and families
    2. Human chromosome 1
      Human chromosome 1: entries, gene names and cross-references to MIM
    3. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    4. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health

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