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Protein

Chromodomain Y-like protein

Gene

Cdyl

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -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). Part of multimeric repressive chromatin complexes, where it is required for transmission and restoration of repressive histone marks, thereby preserving the epigenetic landscape. 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. 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 (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. 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 (By similarity). Displays acetyltransferase activity toward tubulin in vitro; such activity is however unsure in vivo and additional evidences would be required to confirm this result (PubMed:28681565).By similarity1 Publication
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

Caution

Acetyltransferase activity toward tubulin in vitro is unclear (PubMed:28681565). Crystallographic studies with the human protein demonstrated that it does not share any similarity with other acetyltranferases and instead forms a crotonase-like fold.1 Publication

Catalytic activityi

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 proteinBy similarity
Short name:
CDY-likeBy similarity
Alternative name(s):
Putative tubulin acetyltransferase CdylCurated (EC:2.3.1.-1 Publication)
Gene namesi
Name:CdylImported
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 17

Organism-specific databases

RGDi1549745 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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002921381 – 589Chromodomain Y-like proteinAdd BLAST589

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei82PhosphoserineCombined sources1
Modified residuei129N6,N6,N6-trimethyllysine; by EHMT2; alternateBy similarity1
Modified residuei129N6,N6-dimethyllysine; by EHMT2; alternateBy similarity1
Modified residuei129N6-methyllysine; by EHMT2; alternateBy similarity1
Modified residuei164PhosphoserineBy similarity1
Modified residuei195PhosphoserineBy similarity1
Modified residuei210PhosphoserineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

PaxDbiQ6AYK9
PRIDEiQ6AYK9

PTM databases

iPTMnetiQ6AYK9
PhosphoSitePlusiQ6AYK9

Expressioni

Gene expression databases

BgeeiENSRNOG00000032215
GenevisibleiQ6AYK9 RN

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 (By similarity). Interacts with EZH2, EED, SUZ12, REST, EHMT1 and EHMT2. 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. Interacts with CHAF1A and CHAF1B; bridging the CAF-1 complex to the MCM2-7 (MCM) complex. Interacts with MCM3 and MCM5; bridging the CAF-1 complex to the MCM2-7 (MCM) complex (By similarity). Recruited to Xist RNA-coated X chromosome (By similarity).By similarity

GO - Molecular functioni

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000048651

Structurei

3D structure databases

ProteinModelPortaliQ6AYK9
SMRiQ6AYK9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini55 – 115ChromoPROSITE-ProRule annotationAdd BLAST61

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni55 – 300Interaction with EZH2By similarityAdd BLAST246
Regioni353 – 585Acetyl-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
InParanoidiQ6AYK9
KOiK00653
OMAiHDFNRRH
OrthoDBiEOG091G0T5I
PhylomeDBiQ6AYK9
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
IPR001753 Enoyl-CoA_hydra/iso
IPR014748 enoyl-CoA_hydra_C
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: Q6AYK9-1) [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
MGLGSSQPST KEAEPCTLQE KEEHPVDDTR QQNNAVPATV SDPDQVSPAV
60 70 80 90 100
QDAETQVESI VDKRKNKKGK TEYLVRWKGY DSEDDTWEPE QHLVNCEEYI
110 120 130 140 150
HDFNRRHNER QKEGTLARAN RASPSNARKQ ISRSTHSALS KTNPKALVVG
160 170 180 190 200
KDHESKTNQL LATSQKFRKN TAPSLANRKN MDLAKSGIKI LVPKSPIKGR
210 220 230 240 250
TSIDGFHGES PEKLDQGAED TVTPEVTAEK PTGALLGPGA ERARMGSRPR
260 270 280 290 300
IHSLVPQVSG PVTAAMATTL AVNGKGTSPF MDALTANGTV TIQTSVTGVT
310 320 330 340 350
AGKRKFIDDR RDQPFDKRLR FSVRQTESAY RYRDIVVRKQ DGFTHILLST
360 370 380 390 400
KSSENNSLNP EVMKEVQSAL STAAADDSKL VLLSAVGSVF CCGLDFIYFI
410 420 430 440 450
RRLTDDRKRE STKMAEAIRN FVNTFIQFKK PIIVAVNGPA IGLGASILPL
460 470 480 490 500
CDVVWANEKA WFQTPYTTFG QSPDGCSTVM FPKIMGGASA NEMLLSGRKL
510 520 530 540 550
TAQEACGKGL VSQVFWPGTF TQEVMVRIKE LASCNPIVLE ESKALVRCNM
560 570 580
KMELEQANER ECDALKKIWG SAQGMDSMLK YLQRKIDEF
Length:589
Mass (Da):65,031
Last modified:September 13, 2004 - v1
Checksum:i6AE0CBAF89E30A21
GO
Isoform 2 (identifier: Q6AYK9-2) [UniParc]FASTAAdd to basket
Also known as: bBy similarity, CDYL1bBy similarity

The sequence of this isoform differs from the canonical sequence as follows:
     1-56: MGLGSSQPSTKEAEPCTLQEKEEHPVDDTRQQNNAVPATVSDPDQVSPAVQDAETQ → MASEELYE

Show »
Length:541
Mass (Da):60,010
Checksum:i6149DBA0A221CCFE
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0591571 – 56MGLGS…DAETQ → MASEELYE in isoform 2. Add BLAST56

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC117279 Genomic DNA No translation available.
AC140751 Genomic DNA No translation available.
BC079003 mRNA Translation: AAH79003.1
RefSeqiNP_001014167.1, NM_001014145.1 [Q6AYK9-1]
UniGeneiRn.146844

Genome annotation databases

EnsembliENSRNOT00000048757; ENSRNOP00000048651; ENSRNOG00000032215 [Q6AYK9-1]
GeneIDi361237
KEGGirno:361237
UCSCiRGD:1549745 rat [Q6AYK9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiCDYL_RAT
AccessioniPrimary (citable) accession number: Q6AYK9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: September 13, 2004
Last modified: May 23, 2018
This is version 106 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health