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Protein

Chromodomain Y-like protein

Gene

CDYL

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Isoform 2: Chromatin reader protein that recognizes and binds histone H3 trimethylated at 'Lys-9', dimethylated at 'Lys-27' and trimethylated at 'Lys-27' (H3K9me3, H3K27me2 and H3K27me3, respectively) (PubMed:19808672, PubMed:28402439). Part of multimeric repressive chromatin complexes, where it is required for transmission and restoration of repressive histone marks, thereby preserving the epigenetic landscape (PubMed:28402439). Required for chromatin targeting and maximal enzymatic activity of Polycomb repressive complex 2 (PRC2); acts as a positive regulator of PRC2 activity by bridging the pre-existing histone H3K27me3 and newly recruited PRC2 on neighboring nucleosomes (PubMed:22009739). Acts as a corepressor for REST by facilitating histone-lysine N-methyltransferase EHMT2 recruitment and H3K9 dimethylation at REST target genes for repression (PubMed:19061646). Involved X chromosome inactivation in females: recruited to Xist RNA-coated X chromosome and facilitates propagation of H3K9me2 by anchoring EHMT2 (By similarity). Required for neuronal migration during brain development by repressing expression of RHOA (By similarity). In addition to act as a chromatin reader, acts as a hydro-lyase (PubMed:28803779). Shows crotonyl-coA hydratase activity by mediating the conversion of crotonyl-CoA ((2E)-butenoyl-CoA) to beta-hydroxybutyryl-CoA (3-hydroxybutanoyl-CoA), thereby acting as a negative regulator of histone crotonylation (PubMed:28803779). Histone crotonylation is required during spermatogenesis; down-regulation of histone crotonylation by CDYL regulates the reactivation of sex chromosome-linked genes in round spermatids and histone replacement in elongating spermatids (By similarity).By similarity5 Publications
Isoform 1: Not able to recognize and bind histone H3K9me3, histone H3K27me2 and histone H3K27me3, due to the presence of a N-terminal extension that inactivates the chromo domain (PubMed:19808672).1 Publication
Isoform 3: Not able to recognize and bind histone H3K9me3, histone H3K27me2 and histone H3K27me3, due to the absence of the chromo domain (PubMed:19808672). Acts as a negative regulator of isoform 2 by displacing isoform 2 from chromatin.1 Publication

Catalytic activityi

3-hydroxybutanoyl-CoA = (2E)-butenoyl-CoA + H2O.1 Publication

Kineticsi

  1. KM=73.75 µM for (2E)-butenoyl-CoA1 Publication

    GO - Molecular functioni

    • lyase activity Source: UniProtKB-KW
    • methylated histone binding Source: UniProtKB
    • protein binding, bridging Source: UniProtKB
    • transcription corepressor activity Source: UniProtKB

    GO - Biological processi

    Keywordsi

    Molecular functionLyase, Repressor
    Biological processDifferentiation, Spermatogenesis, Transcription, Transcription regulation

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Chromodomain Y-like protein1 Publication
    Short name:
    CDY-like1 Publication
    Alternative name(s):
    Crotonyl-CoA hydratase1 Publication (EC:4.2.1.-1 Publication)
    Gene namesi
    Name:CDYL1 PublicationImported
    Synonyms:CDYL11 Publication
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 6

    Organism-specific databases

    EuPathDBiHostDB:ENSG00000153046.17.
    HGNCiHGNC:1811. CDYL.

    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

    Chromosome, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi521S → A: Abolishes CoA-binding and ability to inhibit histone crotonylation. 1 Publication1

    Organism-specific databases

    DisGeNETi9425.
    OpenTargetsiENSG00000153046.
    PharmGKBiPA26356.

    Polymorphism and mutation databases

    BioMutaiCDYL.
    DMDMi150421527.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000802211 – 598Chromodomain Y-like proteinAdd BLAST598

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei88PhosphoserineCombined sources1
    Modified residuei135N6,N6,N6-trimethyllysine; by EHMT2; alternate1 Publication1
    Modified residuei135N6,N6-dimethyllysine; by EHMT2; alternate1 Publication1
    Modified residuei135N6-methyllysine; by EHMT2; alternate1 Publication1
    Modified residuei170PhosphoserineCombined sources1
    Modified residuei201PhosphoserineCombined sources1
    Modified residuei216PhosphoserineCombined sources1

    Keywords - PTMi

    Methylation, Phosphoprotein

    Proteomic databases

    EPDiQ9Y232.
    PaxDbiQ9Y232.
    PeptideAtlasiQ9Y232.
    PRIDEiQ9Y232.

    PTM databases

    iPTMnetiQ9Y232.
    PhosphoSitePlusiQ9Y232.

    Expressioni

    Tissue specificityi

    Ubiquitous (PubMed:19808672). Expressed at moderate levels in all tissues examined (PubMed:19808672). Isoform 2: Most abundantly expressed isoform (PubMed:19808672).1 Publication

    Gene expression databases

    BgeeiENSG00000153046.
    CleanExiHS_CDYL.
    ExpressionAtlasiQ9Y232. baseline and differential.
    GenevisibleiQ9Y232. HS.

    Organism-specific databases

    HPAiCAB012249.
    HPA035577.
    HPA035578.

    Interactioni

    Subunit structurei

    Forms multimers and multimerization is required for stable binding to chromatin (PubMed:19808672). Interacts with HDAC1 and HDAC2 via its C-terminal acetyl-CoA-binding domain (By similarity). Interacts with EZH2, EED, SUZ12, REST, EHMT1 and EHMT2 (PubMed:19061646). Part of a complex containing at least CDYL, REST, WIZ, SETB1, EHMT1 and EHMT2. Part of a complex containing at least CDYL, MIER1, MIER2, HDAC1 and HDAC2 (PubMed:22009739). Interacts with CHAF1A and CHAF1B; bridging the CAF-1 complex to the MCM2-7 (MCM) complex (PubMed:28402439). Interacts with MCM3 and MCM5; bridging the CAF-1 complex to the MCM2-7 (MCM) complex (PubMed:28402439). Recruited to Xist RNA-coated X chromosome (By similarity).By similarity4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    HIST1H3DP684315EBI-1387386,EBI-79722

    GO - Molecular functioni

    • methylated histone binding Source: UniProtKB
    • protein binding, bridging Source: UniProtKB

    Protein-protein interaction databases

    BioGridi114818. 48 interactors.
    CORUMiQ9Y232.
    IntActiQ9Y232. 20 interactors.
    MINTiMINT-2829840.
    STRINGi9606.ENSP00000380718.

    Structurei

    Secondary structure

    1598
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi66 – 71Combined sources6
    Beta strandi77 – 81Combined sources5
    Helixi88 – 90Combined sources3
    Beta strandi92 – 95Combined sources4
    Turni96 – 98Combined sources3
    Helixi103 – 113Combined sources11
    Beta strandi342 – 349Combined sources8
    Beta strandi352 – 357Combined sources6
    Beta strandi360 – 363Combined sources4
    Helixi369 – 384Combined sources16
    Beta strandi390 – 397Combined sources8
    Helixi405 – 414Combined sources10
    Helixi416 – 436Combined sources21
    Beta strandi441 – 445Combined sources5
    Helixi452 – 455Combined sources4
    Helixi457 – 459Combined sources3
    Beta strandi460 – 466Combined sources7
    Beta strandi470 – 472Combined sources3
    Turni475 – 479Combined sources5
    Helixi486 – 494Combined sources9
    Helixi496 – 505Combined sources10
    Helixi511 – 516Combined sources6
    Beta strandi521 – 524Combined sources4
    Helixi526 – 528Combined sources3
    Helixi529 – 541Combined sources13
    Helixi545 – 556Combined sources12
    Turni557 – 559Combined sources3
    Helixi560 – 579Combined sources20
    Turni581 – 584Combined sources4
    Helixi585 – 596Combined sources12

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2DNTNMR-A63-119[»]
    2GTRX-ray1.90A/B/C338-598[»]
    ProteinModelPortaliQ9Y232.
    SMRiQ9Y232.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9Y232.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini61 – 121ChromoPROSITE-ProRule annotationAdd BLAST61

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni61 – 309Interaction with EZH21 PublicationAdd BLAST249
    Regioni362 – 594Acetyl-CoA-binding domainSequence analysisAdd BLAST233

    Domaini

    The chromo domain recognizes and binds histone H3K9me3, histone H3K27me2 and histone H3K27me3.1 Publication
    The acetyl-CoA-binding domain mediates crotonyl-coA hydratase activity.1 Publication

    Phylogenomic databases

    eggNOGiKOG0016. Eukaryota.
    KOG1911. Eukaryota.
    COG1024. LUCA.
    GeneTreeiENSGT00890000139344.
    HOVERGENiHBG006723.
    InParanoidiQ9Y232.
    KOiK00653.
    OMAiHDFNRRH.
    OrthoDBiEOG091G0T5I.
    PhylomeDBiQ9Y232.
    TreeFamiTF313375.

    Family and domain databases

    CDDicd00024. CHROMO. 1 hit.
    Gene3Di1.10.12.10. 1 hit.
    InterProiView protein in InterPro
    IPR016197. Chromo-like_dom_sf.
    IPR000953. Chromo/chromo_shadow_dom.
    IPR023780. Chromo_domain.
    IPR023779. Chromodomain_CS.
    IPR029045. ClpP/crotonase-like_dom_sf.
    IPR014748. Crontonase_C.
    IPR001753. Crotonase_core_superfam.
    PfamiView protein in Pfam
    PF00385. Chromo. 1 hit.
    PF00378. ECH_1. 1 hit.
    SMARTiView protein in SMART
    SM00298. CHROMO. 1 hit.
    SUPFAMiSSF52096. SSF52096. 1 hit.
    SSF54160. SSF54160. 1 hit.
    PROSITEiView protein in PROSITE
    PS00598. CHROMO_1. 1 hit.
    PS50013. CHROMO_2. 1 hit.

    Sequences (4)i

    Sequence statusi: Complete.

    This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q9Y232-1) [UniParc]FASTAAdd to basket
    Also known as: a1 Publication, CDYL1a1 Publication

    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
    MTFQASHRSA WGKSRKKNWQ YEGPTQKLFL KRNNVSAPDG PSDPSISVSS
    60 70 80 90 100
    EQSGAQQPPA LQVERIVDKR KNKKGKTEYL VRWKGYDSED DTWEPEQHLV
    110 120 130 140 150
    NCEEYIHDFN RRHTEKQKES TLTRTNRTSP NNARKQISRS TNSNFSKTSP
    160 170 180 190 200
    KALVIGKDHE SKNSQLFAAS QKFRKNTAPS LSSRKNMDLA KSGIKILVPK
    210 220 230 240 250
    SPVKSRTAVD GFQSESPEKL DPVEQGQEDT VAPEVAAEKP VGALLGPGAE
    260 270 280 290 300
    RARMGSRPRI HPLVPQVPGP VTAAMATGLA VNGKGTSPFM DALTANGTTN
    310 320 330 340 350
    IQTSVTGVTA SKRKFIDDRR DQPFDKRLRF SVRQTESAYR YRDIVVRKQD
    360 370 380 390 400
    GFTHILLSTK SSENNSLNPE VMREVQSALS TAAADDSKLV LLSAVGSVFC
    410 420 430 440 450
    CGLDFIYFIR RLTDDRKRES TKMAEAIRNF VNTFIQFKKP IIVAVNGPAI
    460 470 480 490 500
    GLGASILPLC DVVWANEKAW FQTPYTTFGQ SPDGCSTVMF PKIMGGASAN
    510 520 530 540 550
    EMLLSGRKLT AQEACGKGLV SQVFWPGTFT QEVMVRIKEL ASCNPVVLEE
    560 570 580 590
    SKALVRCNMK MELEQANERE CEVLKKIWGS AQGMDSMLKY LQRKIDEF
    Length:598
    Mass (Da):66,482
    Last modified:June 26, 2007 - v2
    Checksum:iA34E7221130626EC
    GO
    Isoform 2 (identifier: Q9Y232-2) [UniParc]FASTAAdd to basket
    Also known as: b1 Publication, CDYL1b1 Publication

    The sequence of this isoform differs from the canonical sequence as follows:
         1-54: Missing.
         55-62: AQQPPALQ → MASEELYE

    Note: Major isoform.1 Publication
    Show »
    Length:544
    Mass (Da):60,609
    Checksum:iD30E1CE197B67FC7
    GO
    Isoform 3 (identifier: Q9Y232-3) [UniParc]FASTAAdd to basket
    Also known as: c1 Publication, CDYL1c1 Publication

    The sequence of this isoform differs from the canonical sequence as follows:
         1-289: Missing.

    Show »
    Length:309
    Mass (Da):34,561
    Checksum:i6033C3171A80CB47
    GO
    Isoform 4 (identifier: Q9Y232-4) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-186: Missing.

    Show »
    Length:412
    Mass (Da):45,135
    Checksum:i6AFC72E69A0462A3
    GO

    Sequence cautioni

    The sequence CAB43304 differs from that shown.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti205S → N in BAF84290 (PubMed:14702039).Curated1
    Sequence conflicti291D → N in BAG59526 (PubMed:14702039).Curated1
    Sequence conflicti443V → L in BAF84290 (PubMed:14702039).Curated1
    Sequence conflicti558N → S in BAG59526 (PubMed:14702039).Curated1
    Sequence conflicti584M → T in AAI19683 (PubMed:15489334).Curated1
    Sequence conflicti591L → M in AAI19683 (PubMed:15489334).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_0329362T → A1 PublicationCorresponds to variant dbSNP:rs3812179Ensembl.1
    Natural variantiVAR_0329379S → P1 PublicationCorresponds to variant dbSNP:rs3812178Ensembl.1
    Natural variantiVAR_03293848V → A1 PublicationCorresponds to variant dbSNP:rs13196069Ensembl.1
    Natural variantiVAR_03293960A → G1 PublicationCorresponds to variant dbSNP:rs28360500Ensembl.1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_0263821 – 289Missing in isoform 3. 1 PublicationAdd BLAST289
    Alternative sequenceiVSP_0410251 – 186Missing in isoform 4. 1 PublicationAdd BLAST186
    Alternative sequenceiVSP_0263831 – 54Missing in isoform 2. 2 PublicationsAdd BLAST54
    Alternative sequenceiVSP_02638455 – 62AQQPPALQ → MASEELYE in isoform 2. 2 Publications8

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF081258 mRNA. Translation: AAD22734.1.
    AF081259 mRNA. Translation: AAD22735.1.
    AK291601 mRNA. Translation: BAF84290.1.
    AK296985 mRNA. Translation: BAG59526.1.
    AL356747, AL022725, AL359643 Genomic DNA. Translation: CAC36888.2.
    AL359643, AL022725, AL356747 Genomic DNA. Translation: CAH73737.1.
    AL022725, AL356747, AL359643 Genomic DNA. Translation: CAI20892.1.
    BC061516 mRNA. Translation: AAH61516.1.
    BC108725 mRNA. Translation: AAI08726.1.
    BC119682 mRNA. Translation: AAI19683.1.
    AL050164 mRNA. Translation: CAB43304.1. Sequence problems.
    CCDSiCCDS4491.2. [Q9Y232-2]
    CCDS47364.1. [Q9Y232-4]
    PIRiT08789.
    RefSeqiNP_001137442.1. NM_001143970.1. [Q9Y232-4]
    NP_001137443.1. NM_001143971.1. [Q9Y232-4]
    NP_004815.3. NM_004824.3. [Q9Y232-2]
    UniGeneiHs.269092.

    Genome annotation databases

    EnsembliENST00000328908; ENSP00000330512; ENSG00000153046. [Q9Y232-1]
    ENST00000343762; ENSP00000340908; ENSG00000153046. [Q9Y232-4]
    ENST00000397588; ENSP00000380718; ENSG00000153046. [Q9Y232-2]
    ENST00000449732; ENSP00000394076; ENSG00000153046. [Q9Y232-4]
    GeneIDi9425.
    KEGGihsa:9425.
    UCSCiuc003mwi.4. human. [Q9Y232-1]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Similar proteinsi

    Entry informationi

    Entry nameiCDYL_HUMAN
    AccessioniPrimary (citable) accession number: Q9Y232
    Secondary accession number(s): A8K6D6
    , B4DLG4, Q0VDG7, Q32NC5, Q5VX99, Q6P7T5, Q9BWZ2, Q9Y424
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2003
    Last sequence update: June 26, 2007
    Last modified: November 22, 2017
    This is version 154 of the entry and version 2 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

    Caution

    Was initially reported to display histone acetyltransferase activity, with a preference for histone H4 (PubMed:12072557). Such activity is however unsure in vivo. Histone acetyltransferase activity would be in contradiction with the function of the protein in corepressor complexes (PubMed:19061646, PubMed:22009739). Moreover, crystallographic studies demonstrated that it does not share any similarity with other acetyltranferases and instead forms a crotonase-like fold (PubMed:19507244).4 Publications

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 6
      Human chromosome 6: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references