Chromodomain-helicase-DNA-binding protein 4

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Q6PDQ2 (CHD4_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 88. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Chromodomain-helicase-DNA-binding protein 4
Short name=CHD-4
EC=3.6.4.12

Gene names

Name:

Chd4

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	1915 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Ref.4
Catalytic activity	ATP + H₂O = ADP + phosphate.
Subunit structure	Central component of the nucleosome remodeling and histone deacetylase (NuRD) repressor complex. Interacts with TRIM27. Interacts with ZGPAT; the interaction is direct. Part of a complex containing ATR and HDAC2. Interacts with PCNT By similarity. Interacts with KLF1; the interaction depends on sumoylation of KLF1, and leads to its transcriptional repression. Interacts directly with IKFZ1 in the NuRD complex. Ref.2 Ref.4
Subcellular location	Nucleus By similarity. Cytoplasm › cytoskeleton › centrosome By similarity. Note: Associates with centrosomes in interphase By similarity.
Sequence similarities	Belongs to the SNF2/RAD54 helicase family. Contains 2 chromo domains. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. Contains 2 PHD-type zinc fingers.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Cytoplasm Cytoskeleton Nucleus
Domain	Repeat Zinc-finger
Ligand	ATP-binding DNA-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Chromatin regulator Helicase Hydrolase
PTM	Acetylation Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	NuRD complex Inferred from direct assay PubMed 22075476. Source: MGI centrosome Inferred from electronic annotation. Source: Compara cytoplasm Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro DNA binding Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
Sox2	Q60I23	3	EBI-3043852,EBI-6120118
Zfp819	Q80V81	4	EBI-3043852,EBI-6394055

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1915

1915

Chromodomain-helicase-DNA-binding protein 4

PRO_0000080229

Regions

Domain

522 – 579

Chromo 1

Domain

615 – 676

Chromo 2

Domain

731 – 915

185

Helicase ATP-binding

Domain

1047 – 1196

150

Helicase C-terminal

Zinc finger

363 – 410

PHD-type 1

Zinc finger

442 – 489

PHD-type 2

Nucleotide binding

744 – 751

ATP Potential

Region

1570 – 1915

346

Required for interaction with PCNT By similarity

Motif

866 – 869

DEAH box

Compositional bias

50 – 126

Lys-rich

Compositional bias

471 – 532

Pro-rich

Compositional bias

1560 – 1671

112

Glu-rich

Amino acid modifications

Modified residue

Phosphoserine By similarity

Modified residue

296

Phosphoserine By similarity

Modified residue

301

Phosphoserine By similarity

Modified residue

302

Phosphoserine By similarity

Modified residue

303

Phosphoserine By similarity

Modified residue

312

Phosphoserine By similarity

Modified residue

421

Phosphoserine Ref.6 Ref.7

Modified residue

508

Phosphoserine By similarity

Modified residue

510

Phosphothreonine By similarity

Modified residue

522

Phosphothreonine By similarity

Modified residue

524

Phosphoserine By similarity

Modified residue

1301

Phosphoserine Ref.3

Modified residue

1342

Phosphoserine By similarity

Modified residue

1524

Phosphoserine By similarity

Modified residue

1528

Phosphoserine By similarity

Modified residue

1530

Phosphoserine By similarity

Modified residue

1533

Phosphothreonine Ref.5

Modified residue

1538

Phosphothreonine Ref.5

Modified residue

1542

Phosphothreonine Ref.5

Modified residue

1546

Phosphothreonine By similarity

Modified residue

1646

N6-acetyllysine By similarity

Modified residue

1656

Phosphothreonine By similarity

Modified residue

1682

Phosphothreonine By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q6PDQ2 [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: CFCB83B419AE6B5A
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FASTA

1,915

217,751

        10         20         30         40         50         60 
MASGLGSPSP CSAGSEEEDM DALLNNSLPP PHPENEEDPD EDLSEAETPK LKKKKKPKKP 

        70         80         90        100        110        120 
RDPKIPKSKR QKKELGDSSG EGPEFVEEEE EVALRSDSEG SDYTPGKKKK KKLGPKKEKK 

       130        140        150        160        170        180 
SKSKRKEEEE EEDEDDDSKE PKSSAQLLED WGMEDIDHVF SEEDYRTLTN YKAFSQFVRP 

       190        200        210        220        230        240 
LIAAKNPKIA VSKMMMVLGA KWREFSTNNP FKGSSGASVA AAAAAAVAVV ESMVTATEVA 

       250        260        270        280        290        300 
PPPPPVEVPI RKAKTKEGKG PNARRKPKGS PRVPDAKKPK PKKVAPLKIK LGGFGSKRKR 

       310        320        330        340        350        360 
SSSEDDDLDV ESDFDDASIN SYSVSDGSTS RSSRSRKKLR TAKKKKKGEE EVTAVDGYET 

       370        380        390        400        410        420 
DHQDYCEVCQ QGGEIILCDT CPRAYHMVCL DPDMEKAPEG KWSCPHCEKE GIQWEAKEDN 

       430        440        450        460        470        480 
SEGEEILEEV GGDPEEEDDH HMEFCRVCKD GGELLCCDTC PSSYHIHCLN PPLPEIPNGE 

       490        500        510        520        530        540 
WLCPRCTCPA LKGKVQKILI WKWGQPPSPT PVPRPPDADP NTPSPKPLEG RPERQFFVKW 

       550        560        570        580        590        600 
QGMSYWHCSW VSELQLELHC QVMFRNYQRK NDMDEPPSGD FGGDEEKSRK RKNKDPKFAE 

       610        620        630        640        650        660 
MEERFYRYGI KPEWMMIHRI LNHSVDKKGH VHYLIKWRDL PYDQASWESE DVEIQDYDLF 

       670        680        690        700        710        720 
KQSYWNHREL MRGEEGRPGK KLKKVKLRKL ERPPETPTVD PTVKYERQPE YLDATGGTLH 

       730        740        750        760        770        780 
PYQMEGLNWL RFSWAQGTDT ILADEMGLGK TVQTAVFLYS LYKEGHSKGP FLVSAPLSTI 

       790        800        810        820        830        840 
INWEREFEMW APDMYVVTYV GDKDSRAIIR ENEFSFEDNA IRGGKKASRM KKEASVKFHV 

       850        860        870        880        890        900 
LLTSYELITI DMAILGSIDW ACLIVDEAHR LKNNQSKFFR VLNGYSLQHK LLLTGTPLQN 

       910        920        930        940        950        960 
NLEELFHLLN FLTPERFHNL EGFLEEFADI AKEDQIKKLH DMLGPHMLRR LKADVFKNMP 

       970        980        990       1000       1010       1020 
SKTELIVRVE LSPMQKKYYK YILTRNFEAL NARGGGNQVS LLNVVMDLKK CCNHPYLFPV 

      1030       1040       1050       1060       1070       1080 
AAMEAPKMPN GMYDGSALIR ASGKLLLLQK MLKNLKEGGH RVLIFSQMTK MLDLLEDFLE 

      1090       1100       1110       1120       1130       1140 
HEGYKYERID GGITGNMRQE AIDRFNAPGA QQFCFLLSTR AGGLGINLAT ADTVIIYDSD 

      1150       1160       1170       1180       1190       1200 
WNPHNDIQAF SRAHRIGQNK KVMIYRFVTR ASVEERITQV AKKKMMLTHL VVRPGLGSKT 

      1210       1220       1230       1240       1250       1260 
GSMSKQELDD ILKFGTEELF KDEATDGGGD NKEGEDSSVI HYDDKAIERL LDRNQDETED 

      1270       1280       1290       1300       1310       1320 
TELQGMNEYL SSFKVAQYVV REEEMGEEEE VEREIIKQEE SVDPDYWEKL LRHHYEQQQE 

      1330       1340       1350       1360       1370       1380 
DLARNLGKGK RIRKQVNYND GSQEDRDWQD DQSDNQSDYS VASEEGDEDF DERSEAPRRP 

      1390       1400       1410       1420       1430       1440 
SRKGLRNDKD KPLPPLLARV GGNIEVLGFN ARQRKAFLNA IMRYGMPPQD AFTTQWLVRD 

      1450       1460       1470       1480       1490       1500 
LRGKSEKEFK AYVSLFMRHL CEPGADGAET FADGVPREGL SRQHVLTRIG VMSLIRKKVQ 

      1510       1520       1530       1540       1550       1560 
EFEHVNGRWS MPELAEVEEN KKMSQPGSPS PKTPTPSTPG DTQPNTPAPV PPAEDGIKIE 

      1570       1580       1590       1600       1610       1620 
ENSLKEEEST EGEKEVKSTA PEATVECAQP PAPAPATAPA TATAPEDDKA PAEPPEGEEK 

      1630       1640       1650       1660       1670       1680 
VEKAEVKERT EEPMETEAKG TTEVEKVEEK SAVDLTPIVV EDKEEKKEEE EKKDVMLQNG 

      1690       1700       1710       1720       1730       1740 
ETPKDLSDEK QKKNSKQRFM FNIADGGFTE LHSLWQNEER AATVTKKTYE IWHRRHDYWL 

      1750       1760       1770       1780       1790       1800 
LAGIINHGYA RWQDIQNDPR YAILNEPFKG EMNRGNFLEI KNKFLARRFK LLEQALVIEE 

      1810       1820       1830       1840       1850       1860 
QLRRAAYLNM SEDPSHPSMA LNTRFAEVEC LAESHQHLSK ESMAGNKPAN AVLHKVLKQL 

      1870       1880       1890       1900       1910 
EELLSDMKAD VTRLPATIAR IPPVAVRLQM SERNILSRLA NRAPEPPPQQ VAQQQ

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Eye.
[2]	"An ikaros-containing chromatin-remodeling complex in adult-type erythroid cells." O'Neill D.W., Schoetz S.S., Lopez R.A., Castle M., Rabinowitz L., Shor E., Krawchuk D., Goll M.G., Renz M., Seelig H.P., Han S., Seong R.H., Park S.D., Agalioti T., Munshi N., Thanos D., Erdjument-Bromage H., Tempst P., Bank A. Mol. Cell. Biol. 20:7572-7582(2000) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH IKFZ1 IN THE NURD COMPLEX.
[3]	"Protein phosphorylation and expression profiling by Yin-yang multidimensional liquid chromatography (Yin-yang MDLC) mass spectrometry." Dai J., Jin W.-H., Sheng Q.-H., Shieh C.-H., Wu J.-R., Zeng R. J. Proteome Res. 6:250-262(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1301, MASS SPECTROMETRY. Tissue: Liver.
[4]	"Sumoylation of EKLF promotes transcriptional repression and is involved in inhibition of megakaryopoiesis." Siatecka M., Xue L., Bieker J.J. Mol. Cell. Biol. 27:8547-8560(2007) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH KLF1, FUNCTION.
[5]	"Large-scale phosphorylation analysis of mouse liver." Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-1533; THR-1538 AND THR-1542, MASS SPECTROMETRY. Tissue: Liver.
[6]	"Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry." Zanivan S., Gnad F., Wickstroem S.A., Geiger T., Macek B., Cox J., Faessler R., Mann M. J. Proteome Res. 7:5314-5326(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-421, MASS SPECTROMETRY. Tissue: Melanoma.
[7]	"The phagosomal proteome in interferon-gamma-activated macrophages." Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P. Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-421, MASS SPECTROMETRY. Tissue: Macrophage.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BC058578 mRNA. Translation: AAH58578.1.
IPI	IPI00396802.
RefSeq	NP_666091.1. NM_145979.2.
UniGene	Mm.333388.
3D structure databases
ProteinModelPortal	Q6PDQ2.
SMR	Q6PDQ2. Positions 358-494, 517-667, 717-1214.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-59651N.
IntAct	Q6PDQ2. 7 interactions.
PTM databases
PhosphoSite	Q6PDQ2.
Proteomic databases
PaxDb	Q6PDQ2.
PRIDE	Q6PDQ2.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000056889; ENSMUSP00000060054; ENSMUSG00000063870.
GeneID	107932.
KEGG	mmu:107932.
UCSC	uc009dtk.1. mouse.
Organism-specific databases
CTD	1108.
MGI	MGI:1344380. Chd4.
Phylogenomic databases
eggNOG	COG0553.
GeneTree	ENSGT00560000076896.
HOGENOM	HOG000231124.
HOVERGEN	HBG005326.
KO	K11643.
OrthoDB	EOG4WH8JX.
Gene expression databases
ArrayExpress	Q6PDQ2.
Bgee	Q6PDQ2.
CleanEx	MM_CHD4.
Genevestigator	Q6PDQ2.
GermOnline	ENSMUSG00000063870. Mus musculus.
Family and domain databases
Gene3D	3.30.40.10. 2 hits.
InterPro	IPR012957. CHD_C2. IPR012958. CHD_N. IPR023780. Chromo_domain. IPR000953. Chromo_domain/shadow. IPR016197. Chromodomain-like. IPR002464. DNA/RNA_helicase_DEAH_CS. IPR009462. DUF1086. IPR009463. DUF1087. IPR014001. Helicase_ATP-bd. IPR001650. Helicase_C. IPR000330. SNF2_N. IPR019786. Zinc_finger_PHD-type_CS. IPR011011. Znf_FYVE_PHD. IPR001965. Znf_PHD. IPR019787. Znf_PHD-finger. IPR001841. Znf_RING. IPR013083. Znf_RING/FYVE/PHD. [Graphical view]
Pfam	PF08074. CHDCT2. 1 hit. PF08073. CHDNT. 1 hit. PF00385. Chromo. 2 hits. PF06461. DUF1086. 1 hit. PF06465. DUF1087. 1 hit. PF00271. Helicase_C. 1 hit. PF00628. PHD. 2 hits. PF00176. SNF2_N. 1 hit. [Graphical view]
SMART	SM00298. CHROMO. 2 hits. SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. SM00249. PHD. 2 hits. SM00184. RING. 2 hits. [Graphical view]
SUPFAM	SSF54160. Chromodomain-like. 2 hits. SSF57903. FYVE_PHD_ZnF. 2 hits.
PROSITE	PS00598. CHROMO_1. 2 hits. PS50013. CHROMO_2. 2 hits. PS00690. DEAH_ATP_HELICASE. 1 hit. PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS01359. ZF_PHD_1. 2 hits. PS50016. ZF_PHD_2. 2 hits. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	CHD4. mouse.
NextBio	359735.
PMAP-CutDB	Q6PDQ2.
SOURCE	Search...

Entry information

Entry name

CHD4_MOUSE

Accession

Primary (citable) accession number: Q6PDQ2

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 31, 2004
Last sequence update:	July 5, 2004
Last modified:	May 1, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

MGD cross-references

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

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents