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A1YVX4

- KDM5C_PIG

UniProt

A1YVX4 - KDM5C_PIG

Protein

Lysine-specific demethylase 5C

Gene

KDM5C

Organism
Sus scrofa (Pig)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 46 (01 Oct 2014)
      Sequence version 1 (06 Feb 2007)
      Previous versions | rss
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    Functioni

    Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements By similarity.By similarity

    Cofactori

    Alpha-ketoglutarate.By similarity
    Binds 1 Fe2+ ion per subunit.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi473 – 4731Iron; catalyticPROSITE-ProRule annotation
    Metal bindingi476 – 4761Iron; catalyticPROSITE-ProRule annotation
    Metal bindingi561 – 5611Iron; catalyticPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri283 – 33351PHD-type 1PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri1144 – 120966PHD-type 2PROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. DNA binding Source: InterPro
    2. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors Source: InterPro
    3. zinc ion binding Source: InterPro

    GO - Biological processi

    1. chromatin modification Source: UniProtKB-KW
    2. regulation of transcription, DNA-templated Source: UniProtKB-KW
    3. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Chromatin regulator, Dioxygenase, Oxidoreductase

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    Iron, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Lysine-specific demethylase 5C (EC:1.14.11.-)
    Alternative name(s):
    Histone demethylase JARID1C
    Jumonji/ARID domain-containing protein 1C
    Protein SmcX
    Gene namesi
    Name:KDM5C
    Synonyms:JARID1C, SMCX
    OrganismiSus scrofa (Pig)
    Taxonomic identifieri9823 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaSuinaSuidaeSus
    ProteomesiUP000008227: Unplaced

    Subcellular locationi

    Nucleus PROSITE-ProRule annotation

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 15161516Lysine-specific demethylase 5CPRO_0000292417Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei276 – 2761PhosphoserineBy similarity
    Modified residuei1318 – 13181PhosphoserineBy similarity

    Keywords - PTMi

    Phosphoprotein

    Interactioni

    Subunit structurei

    Part of two distinct complexes, one containing E2F6, and the other containing REST.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliA1YVX4.
    SMRiA1YVX4. Positions 22-147, 278-353.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini14 – 5542JmjNPROSITE-ProRule annotationAdd
    BLAST
    Domaini24 – 128105ARIDPROSITE-ProRule annotationAdd
    BLAST
    Domaini427 – 593167JmjCPROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi1413 – 14175Poly-Arg
    Compositional biasi1450 – 14578Poly-Glu

    Domaini

    The first PHD-type zinc finger domain recognizes and binds H3-K9Me3.By similarity
    Both the JmjC domain and the JmjN domain are required for enzymatic activity.By similarity

    Sequence similaritiesi

    Belongs to the JARID1 histone demethylase family.Curated
    Contains 1 ARID domain.PROSITE-ProRule annotation
    Contains 1 JmjC domain.PROSITE-ProRule annotation
    Contains 1 JmjN domain.PROSITE-ProRule annotation
    Contains 2 PHD-type zinc fingers.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri283 – 33351PHD-type 1PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri1144 – 120966PHD-type 2PROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiNOG327026.
    KOiK11446.

    Family and domain databases

    Gene3Di1.10.150.60. 1 hit.
    3.30.40.10. 2 hits.
    InterProiIPR001606. ARID/BRIGHT_DNA-bd.
    IPR003347. JmjC_dom.
    IPR013637. Lys_sp_deMease_like_dom.
    IPR003349. TF_JmjN.
    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.
    [Graphical view]
    PfamiPF01388. ARID. 1 hit.
    PF02373. JmjC. 1 hit.
    PF02375. JmjN. 1 hit.
    PF00628. PHD. 1 hit.
    PF08429. PLU-1. 1 hit.
    PF02928. zf-C5HC2. 1 hit.
    [Graphical view]
    SMARTiSM00558. JmjC. 1 hit.
    SM00545. JmjN. 1 hit.
    SM00249. PHD. 2 hits.
    [Graphical view]
    SUPFAMiSSF46774. SSF46774. 1 hit.
    SSF57903. SSF57903. 2 hits.
    PROSITEiPS51011. ARID. 1 hit.
    PS51184. JMJC. 1 hit.
    PS51183. JMJN. 1 hit.
    PS01359. ZF_PHD_1. 2 hits.
    PS50016. ZF_PHD_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    A1YVX4-1 [UniParc]FASTAAdd to Basket

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    MEPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA     50
    DWQPPFAVEV DNFRFTPRIQ RLNELEIVVE EGGYEAICKD RRWARVAQRL 100
    NYPPGKNIGS LLRSHYERIV YPYEMYQSGA NLVQCNTRPF DNEEKDKEYK 150
    PHSIPLRQSV QPSKFNSYGR RAKRLQPDPE PTEEDIEKNP ELKKLQIYGA 200
    GPKMMGLGLM AKDKTLRKKD KEGPECPPTV VVKEESGGDV KVESTSPKTF 250
    LESKEELSHS PEPCTKMTMR LRRNHSNAQF IESYVCRMCS RGDEDDKLLL 300
    CDGCDDNYHI FCLLPPLPEI PKGVWRCPKC VMAECKRPPE AFGFEQATRE 350
    YTLQSFGEMA DSFKADYSNM PVHMVPTELV EKEFWRLVNS IEEDVTVEYG 400
    ADIHSKEFGS GFPVSDSKRH LTPEEEEYAT SGWNLNVMPV LEQSVLCHIN 450
    ADISGMKVPW LYVGMVFSAF CWHIEDHWSY SINYLHWGEP KTWYGVPSLA 500
    AEHLEEVMKK LTPELFDSQP DLLHQLVTLM NPNTLMSHGV PVVRTNQCAG 550
    EFVITFPRAY HSGFNQGYNF AEAVNFCTAD WLPAGRQCIE HYRRLRRYCV 600
    FSHEELICKM AACPEKLDLN LAAAVHKEMF IMVQEERRLR KALLEKGITE 650
    AEREAFELLP DDERQCIKCK TTCFLSALAC YDCPDGLVCL SHINDLCKCS 700
    SSRQYLRYRY TLDELPAMLH KLKVRAESFD TWANKVRVAL EVEDGRKRSL 750
    EELRALESEA RERRFPNSEL LQRLKNCLSE AEACVSRALG LVSGQEAGPH 800
    RVAGLQMTLA ELRAFLDQMN NLPCAMHQIG DVKGILEQVE AYQAEAREAL 850
    ASLPSSPGLL QSLLERGRQL GVEVPEAQQL QRQVEQARWL DEVKRTLAPS 900
    ARRGTLAVMR GLLVAGASVA PSPAVDKAQA ELQELLTIAE RWEEKAHLCL 950
    EARQKHPPAT LEAIIHEAEN IPVHLPNIQA LKEALAKARA WIADVDEIQN 1000
    GDHYPCLDDL EGLVAVGRDL PVGLEELRQL ELQVLTAHSW REKASKTFLK 1050
    KNSCYTLLEV LCPCADAGSD STKRSRWMEK ELGLYKSDTE LLGLSAQDLR 1100
    DPGSVIVAFK EGEQKEKEGI LQLRRTNSAK PSPLASPNTS SSATSICVCG 1150
    QVPAGVGALQ CDLCQDWFHG RCVSVPRLLS SPRPSPTSSP LLAWWEWDTK 1200
    FLCPLCMRSR RPRLETILAL LVALQRLPVR LPEGEALQCL TERAISWQGR 1250
    ARQALAFEDV TALLGRLAEL RQRLQAEPRP EEPPTYPSTP AFDPLREGSG 1300
    KDMPKVQGLL ENGDSVTSPE KVAPGEGSDL ELLSSLLPQL TGPVLELPEA 1350
    TRAPLEELML EGDLLEVTLD ENHSIWQLLQ AGKPPDLARI RTLLELEKAE 1400
    RHGSRARGRA LERRRRRKVD RGGEGDDPAR EELEPKRVRS SWPEAEEAHE 1450
    EEELEEETGG EGPPQPLPAT GSPSTQENQN GLEPALGASS GSSVPFSTLT 1500
    PRLHMSCPQQ PPQQQL 1516
    Length:1,516
    Mass (Da):170,584
    Last modified:February 6, 2007 - v1
    Checksum:i8DE6C52868E3E7E3
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    EF139241 mRNA. Translation: ABL74503.1.
    RefSeqiNP_001090902.1. NM_001097433.1.
    UniGeneiSsc.25162.

    Genome annotation databases

    GeneIDi100037295.
    KEGGissc:100037295.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    EF139241 mRNA. Translation: ABL74503.1 .
    RefSeqi NP_001090902.1. NM_001097433.1.
    UniGenei Ssc.25162.

    3D structure databases

    ProteinModelPortali A1YVX4.
    SMRi A1YVX4. Positions 22-147, 278-353.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 100037295.
    KEGGi ssc:100037295.

    Organism-specific databases

    CTDi 8242.

    Phylogenomic databases

    eggNOGi NOG327026.
    KOi K11446.

    Family and domain databases

    Gene3Di 1.10.150.60. 1 hit.
    3.30.40.10. 2 hits.
    InterProi IPR001606. ARID/BRIGHT_DNA-bd.
    IPR003347. JmjC_dom.
    IPR013637. Lys_sp_deMease_like_dom.
    IPR003349. TF_JmjN.
    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.
    [Graphical view ]
    Pfami PF01388. ARID. 1 hit.
    PF02373. JmjC. 1 hit.
    PF02375. JmjN. 1 hit.
    PF00628. PHD. 1 hit.
    PF08429. PLU-1. 1 hit.
    PF02928. zf-C5HC2. 1 hit.
    [Graphical view ]
    SMARTi SM00558. JmjC. 1 hit.
    SM00545. JmjN. 1 hit.
    SM00249. PHD. 2 hits.
    [Graphical view ]
    SUPFAMi SSF46774. SSF46774. 1 hit.
    SSF57903. SSF57903. 2 hits.
    PROSITEi PS51011. ARID. 1 hit.
    PS51184. JMJC. 1 hit.
    PS51183. JMJN. 1 hit.
    PS01359. ZF_PHD_1. 2 hits.
    PS50016. ZF_PHD_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Yi L., Xu Y.
      Submitted (NOV-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].

    Entry informationi

    Entry nameiKDM5C_PIG
    AccessioniPrimary (citable) accession number: A1YVX4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 26, 2007
    Last sequence update: February 6, 2007
    Last modified: October 1, 2014
    This is version 46 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3