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Protein

Chromodomain Y-like protein

Gene

Cdyl

Organism
Mus musculus (Mouse)
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:12947414). Part of multimeric repressive chromatin complexes, where it is required for transmission and restoration of repressive histone marks, thereby preserving the epigenetic landscape (PubMed:12947414). 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 (By similarity). Acts as a corepressor for REST by facilitating histone-lysine N-methyltransferase EHMT2 recruitment and H3K9 dimethylation at REST target genes for repression (By similarity). Involved X chromosome inactivation in females: recruited to Xist RNA-coated X chromosome and facilitates propagation of H3K9me2 by anchoring EHMT2 (PubMed:24144980). Required for neuronal migration during brain development by repressing expression of RHOA (PubMed:28076783). In addition to act as a chromatin reader, acts as a hydro-lyase (By similarity). 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 (By similarity). 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 (PubMed:28803779). May have histone acetyltransferase activity; such activity is however unsure in vivo (PubMed:12072557).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.By similarity

Miscellaneous

Interaction with HDAC1 or HDAC2 prevents coenzyme A binding.1 Publication

Catalytic activityi

Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N6-acetyl-L-lysine.1 Publication
3-hydroxybutanoyl-CoA = (2E)-butenoyl-CoA + H2O.By similarity

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionAcyltransferase, Lyase, Repressor, Transferase
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 hydrataseBy similarity (EC:4.2.1.-By similarity)
Putative histone acetyltransferase CdylCurated (EC:2.3.1.481 Publication)
Gene namesi
Name:Cdyl1 PublicationImported
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:1339956. 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

Disruption phenotypei

Mice show no overt differences in body weight, but males display a substantial decrease in the size and weight of the testis and show reduced fertility. Males show decreased epididymal sperm counts, sperm cell motility, and sperm velocity and a marked increase in cell apoptosis in the testis.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi516S → A: Abolishes CoA-binding. No effect on transcriptional repressor activity. 1 Publication1
Mutagenesisi588 – 589RK → AA: Abolishes CoA-binding. No effect on transcriptional repressor activity. 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000802221 – 593Chromodomain Y-like proteinAdd BLAST593

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei83PhosphoserineCombined sources1
Modified residuei130N6,N6,N6-trimethyllysine; by EHMT2; alternateBy similarity1
Modified residuei130N6,N6-dimethyllysine; by EHMT2; alternateBy similarity1
Modified residuei130N6-methyllysine; by EHMT2; alternateBy similarity1
Modified residuei211PhosphoserineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

PaxDbiQ9WTK2.
PeptideAtlasiQ9WTK2.
PRIDEiQ9WTK2.

PTM databases

iPTMnetiQ9WTK2.
PhosphoSitePlusiQ9WTK2.

Expressioni

Tissue specificityi

Highly expressed in testis (at protein level) (PubMed:10192397). Isoform 1: Expressed as 2 transcripts encoding the same protein, a ubiquitous transcript and a highly expressed testis-specific transcript (PubMed:10192397).1 Publication

Developmental stagei

Highly expressed in elongating spermatids during histone hyperacetylation.2 Publications

Gene expression databases

BgeeiENSMUSG00000059288.
CleanExiMM_CDYL.
GenevisibleiQ9WTK2. MM.

Interactioni

Subunit structurei

Forms multimers and multimerization is required for stable binding to chromatin (By similarity). Interacts with HDAC1 and HDAC2 via its C-terminal acetyl-CoA-binding domain (PubMed:12947414). Interacts with EZH2, EED, SUZ12, REST, EHMT1 and EHMT2 (By similarity). Part of a complex containing at least CDYL, REST, WIZ, SETB1, EHMT1 and EHMT2 (By similarity). Part of a complex containing at least CDYL, MIER1, MIER2, HDAC1 and HDAC2 (By similarity). Interacts with CHAF1A and CHAF1B; bridging the CAF-1 complex to the MCM2-7 (MCM) complex (By similarity). Interacts with MCM3 and MCM5; bridging the CAF-1 complex to the MCM2-7 (MCM) complex (By similarity).By similarity1 Publication

GO - Molecular functioni

Protein-protein interaction databases

IntActiQ9WTK2. 1 interactor.
MINTiMINT-4090565.
STRINGi10090.ENSMUSP00000074707.

Structurei

3D structure databases

ProteinModelPortaliQ9WTK2.
SMRiQ9WTK2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini56 – 116ChromoPROSITE-ProRule annotationAdd BLAST61

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni56 – 304Interaction with EZH2By similarityAdd BLAST249
Regioni357 – 589Acetyl-CoA-binding domainSequence analysisAdd BLAST233

Domaini

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

Phylogenomic databases

eggNOGiKOG0016. Eukaryota.
KOG1911. Eukaryota.
COG1024. LUCA.
GeneTreeiENSGT00890000139344.
HOGENOMiHOG000111507.
HOVERGENiHBG006723.
InParanoidiQ9WTK2.
KOiK00653.
OMAiHDFNRRH.
OrthoDBiEOG091G0T5I.
PhylomeDBiQ9WTK2.
TreeFamiTF313375.

Family and domain databases

CDDicd00024. CHROMO. 1 hit.
Gene3Di1.10.12.10. 1 hit.
InterProiView protein in InterPro
IPR000953. Chromo/chromo_shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR029045. ClpP/crotonase-like_dom.
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 (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q9WTK2-1) [UniParc]FASTAAdd to basket
Also known as: aBy similarity, CDYL1aBy similarity

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
MGIGNSQPNS QEAQLCTLPE KAEQPTDDNT CQQNNVVPAT VSEPDQASPA
60 70 80 90 100
IQDAETQVES IVDKRKNKKG KTEYLVRWKG YDSEDDTWEP EQHLVNCEEY
110 120 130 140 150
IHDFNRRHNE RQKEGSLARA SRASPSNARK QISRSTHSTL SKTNSKALVV
160 170 180 190 200
GKDHESKSSQ LLAASQKFRK NPAPSLANRK NMDLAKSGIK ILVPKSPVKG
210 220 230 240 250
RTSVDGFQGE SPEKLDPVDQ GAEDTVAPEV TAEKPTGALL GPGAERARMG
260 270 280 290 300
SRPRIHPLVP QVSGPVTAAM ATGLAVNGKG TSPFMDALAA NGTVTIQTSV
310 320 330 340 350
TGVTAGKRKF IDDRRDQPFD KRLRFSVRQT ESAYRYRDIV VRKQDGFTHI
360 370 380 390 400
LLSTKSSENN SLNPEVMKEV QSALSTAAAD DSKLVLLSAV GSVFCCGLDF
410 420 430 440 450
IYFIRRLTDD RKRESTKMAD AIRNFVNTFI QFKKPIIVAV NGPAIGLGAS
460 470 480 490 500
ILPLCDVVWA NEKAWFQTPY TTFGQSPDGC STVMFPKIMG GASANEMLFS
510 520 530 540 550
GRKLTAQEAC GKGLVSQVFW PGTFTQEVMV RIKELASCNP VVLEESKALV
560 570 580 590
RCNMKMELEQ ANERECEVLK KIWGSAQGMD SMLKYLQRKI DEF
Length:593
Mass (Da):65,211
Last modified:November 1, 1999 - v1
Checksum:i470D5B97D7E52CCA
GO
Isoform 2 (identifier: Q9WTK2-2) [UniParc]FASTAAdd to basket
Also known as: bBy similarity, CDYL1bBy similarity

The sequence of this isoform differs from the canonical sequence as follows:
     1-49: Missing.
     50-57: AIQDAETQ → MASEELYE

Show »
Length:544
Mass (Da):60,142
Checksum:iB8E3B85969ED9103
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti489M → I in BAE33739 (PubMed:16141072).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0263851 – 49Missing in isoform 2. 2 PublicationsAdd BLAST49
Alternative sequenceiVSP_02638650 – 57AIQDAETQ → MASEELYE in isoform 2. 2 Publications8

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF081260 mRNA. Translation: AAD22736.1.
AF081261 mRNA. Translation: AAD22737.1.
AK156509 mRNA. Translation: BAE33739.1.
BC055103 mRNA. Translation: AAH55103.1.
BC062123 mRNA. Translation: AAH62123.1.
CCDSiCCDS49235.1. [Q9WTK2-1]
CCDS49236.1. [Q9WTK2-2]
RefSeqiNP_001116858.1. NM_001123386.1. [Q9WTK2-2]
NP_034011.1. NM_009881.3. [Q9WTK2-1]
UniGeneiMm.29002.

Genome annotation databases

EnsembliENSMUST00000075220; ENSMUSP00000074707; ENSMUSG00000059288. [Q9WTK2-1]
ENSMUST00000163595; ENSMUSP00000131784; ENSMUSG00000059288. [Q9WTK2-2]
GeneIDi12593.
KEGGimmu:12593.
UCSCiuc007qce.2. mouse. [Q9WTK2-1]
uc007qcg.2. mouse. [Q9WTK2-2]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiCDYL_MOUSE
AccessioniPrimary (citable) accession number: Q9WTK2
Secondary accession number(s): Q3U0W2, Q6P6N3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2003
Last sequence update: November 1, 1999
Last modified: October 25, 2017
This is version 128 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

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:12947414). Moreover, crystallographic studies in human demonstrated that it does not share any similarity with other acetyltranferases and instead forms a crotonase-like fold.By similarity2 Publications

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot