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Protein

Chromodomain-helicase-DNA-binding protein 1

Gene

Chd1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3 (By similarity). Required for maintaining open chromatin and pluripotency in embryonic stem cells. Is also associated with histone deacetylase (HDAC) activity.By similarity2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi504 – 511ATPPROSITE-ProRule annotation8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • chromatin binding Source: UniProtKB
  • DNA binding Source: UniProtKB-KW
  • helicase activity Source: UniProtKB
  • methylated histone binding Source: MGI

GO - Biological processi

  • chromatin assembly or disassembly Source: UniProtKB
  • chromatin modification Source: UniProtKB-KW
  • chromatin remodeling Source: MGI
  • positive regulation by host of viral transcription Source: MGI
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Helicase, Hydrolase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Chromodomain-helicase-DNA-binding protein 1 (EC:3.6.4.12)
Short name:
CHD-1
Alternative name(s):
ATP-dependent helicase CHD1
Gene namesi
Name:Chd1
Synonyms:Chd-1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 17

Organism-specific databases

MGIiMGI:88393. Chd1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: MGI
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000802251 – 1711Chromodomain-helicase-DNA-binding protein 1Add BLAST1711

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei214PhosphoserineCombined sources1
Modified residuei215PhosphoserineCombined sources1
Modified residuei235PhosphothreonineBy similarity1
Modified residuei239PhosphoserineBy similarity1
Modified residuei248PhosphothreonineBy similarity1
Modified residuei250PhosphoserineBy similarity1
Modified residuei469PhosphoserineBy similarity1
Modified residuei1023PhosphoserineBy similarity1
Modified residuei1038PhosphoserineBy similarity1
Modified residuei1079PhosphoserineBy similarity1
Modified residuei1094PhosphoserineBy similarity1
Modified residuei1096PhosphoserineBy similarity1
Modified residuei1098PhosphoserineBy similarity1
Modified residuei1100PhosphoserineBy similarity1
Modified residuei1159PhosphoserineBy similarity1
Modified residuei1353PhosphoserineBy similarity1
Modified residuei1355PhosphoserineBy similarity1
Modified residuei1356PhosphoserineBy similarity1
Modified residuei1360PhosphoserineBy similarity1
Modified residuei1363PhosphoserineBy similarity1
Modified residuei1678PhosphoserineBy similarity1
Modified residuei1690PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP40201.
MaxQBiP40201.
PaxDbiP40201.
PeptideAtlasiP40201.
PRIDEiP40201.

PTM databases

iPTMnetiP40201.
PhosphoSitePlusiP40201.

Expressioni

Tissue specificityi

Abundance is higher in cells representing early stages of the B-lymphoid lineage such as pre-B and B-cells, than in cells representing mature plasmacytes or other cell lineages such as fibroblasts.

Gene expression databases

BgeeiENSMUSG00000023852.
CleanExiMM_CHD1.
ExpressionAtlasiP40201. baseline and differential.
GenevisibleiP40201. MM.

Interactioni

Subunit structurei

Component of the SAGA complex (By similarity). Specifically interacts with methylated H3K4me2 and H3K4me3. Interacts with the FACT complex, the PAF complex and the U2 snRNP. Interacts directly with PAF1, SFA3A1, SFA3A2, SFA3A3, SNF2 and SSRP1 (By similarity). Interacts with BCLAF1, NCoR, SRP20 and SAFB.By similarity3 Publications

GO - Molecular functioni

Protein-protein interaction databases

BioGridi198693. 3 interactors.
IntActiP40201. 2 interactors.
MINTiMINT-4090783.
STRINGi10090.ENSMUSP00000024627.

Structurei

3D structure databases

ProteinModelPortaliP40201.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini270 – 362Chromo 1PROSITE-ProRule annotationAdd BLAST93
Domaini387 – 450Chromo 2PROSITE-ProRule annotationAdd BLAST64
Domaini491 – 661Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST171
Domaini790 – 941Helicase C-terminalPROSITE-ProRule annotationAdd BLAST152
Repeati1629 – 163315
Repeati1635 – 163925
Repeati1641 – 164535

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1629 – 16453 X 5 AA repeats of H-S-D-H-RAdd BLAST17

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi612 – 615DEAH box4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1 – 70Ser-richAdd BLAST70
Compositional biasi116 – 136Ser-richAdd BLAST21

Domaini

The 2 chromodomains are involved in the binding to the histone H3 methyllysine at position 4 (H3K4me3).By similarity

Sequence similaritiesi

Belongs to the SNF2/RAD54 helicase family.Curated
Contains 2 chromo domains.PROSITE-ProRule annotation
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0383. Eukaryota.
COG0553. LUCA.
GeneTreeiENSGT00760000119067.
HOGENOMiHOG000207917.
HOVERGENiHBG005325.
InParanoidiP40201.
KOiK11367.
OMAiEITSVKH.
OrthoDBiEOG091G00HF.
TreeFamiTF300674.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR025260. DUF4208.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000330. SNF2_N.
[Graphical view]
PfamiPF00385. Chromo. 2 hits.
PF13907. DUF4208. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00176. SNF2_N. 1 hit.
[Graphical view]
SMARTiSM00298. CHROMO. 2 hits.
SM00487. DEXDc. 1 hit.
SM01176. DUF4208. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
SSF54160. SSF54160. 2 hits.
PROSITEiPS00598. CHROMO_1. 2 hits.
PS50013. CHROMO_2. 2 hits.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P40201-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNGHSDEESV RNGSGESSQS GDDCGSASGS GSGSSSGSSS DGSSSQSGSS
60 70 80 90 100
DSDSGSDSGS QSESESDTSR ENKVQAKPPK VDGAEFWKSS PSILAVQRSA
110 120 130 140 150
MLRKQPQQAQ QQRPASSNSG SEEDSSSSED SDDSSSGAKR KKHNDEDWQM
160 170 180 190 200
SGSGSPSQSG SDSESEEERD KSSCDGTESD YEPKNKVRSR KPQNRSKSKN
210 220 230 240 250
GKKILGQKKR QIDSSEDEDD EDYDNDKRSS RRQATVNVSY KEDEEMKTDS
260 270 280 290 300
DDLLEVCGED VPQPEDEEFE TIERVMDCRV GRKGATGATT TIYAVEADGD
310 320 330 340 350
PNAGFERNKE PGDIQYLIKW KGWSHIHNTW ETEETLKQQN VRGMKKLDNY
360 370 380 390 400
KKKDQETKRW LKNASPEDVE YYNCQQELTD DLHKQYQIVE RIIAHSNQKS
410 420 430 440 450
AAGLPDYYCK WQGLPYSECS WEDGALISKK FQTCIDEYFS RNQSKTTPFK
460 470 480 490 500
DCKVLKQRPR FVALKKQPSY IGGHEGLELR DYQLNGLNWL AHSWCKGNSC
510 520 530 540 550
ILADEMGLGK TIQTISFLNY LFHEHQLYGP FLLVVPLSTL TSWQREIQTW
560 570 580 590 600
ASQMNAVVYL GDINSRNMIR THEWMHPQTK RLKFNILLTT YEILLKDKAF
610 620 630 640 650
LGGLNWAFIG VDEAHRLKND DSLLYKTLID FKSNHRLLIT GTPLQNSLKE
660 670 680 690 700
LWSLLHFIMP EKFSSWEDFE EEHGKGREYG YASLHKELEP FLLRRVKKDV
710 720 730 740 750
EKSLPAKVEQ ILRMEMSALQ KQYYKWILTR NYKALSKGSK GSTSGFLNIM
760 770 780 790 800
MELKKCCNHC YLIKPPDNNE FYNKQEALQH LIRSSGKLIL LDKLLIRLRE
810 820 830 840 850
RGNRVLIFSQ MVRMLDILAE YLKYRQFPFQ RLDGSIKGEL RKQALDHFNA
860 870 880 890 900
EGSEDFCFLL STRAGGLGIN LASADTVVIF DSDWNPQNDL QAQARAHRIG
910 920 930 940 950
QKKQVNIYRL VTKGSVEEDI LERAKKKMVL DHLVIQRMDT TGKTVLHTGS
960 970 980 990 1000
APSSSTPFNK EELSAILKFG AEELFKEPEG EEQEPQEMDI DEILKRAETH
1010 1020 1030 1040 1050
ENEPGPLSVG DELLSQFKVA NFSNMDEDDI ELEPERNSKN WEEIIPEEQR
1060 1070 1080 1090 1100
RRLEEEERQK ELEEIYMLPR MRNCAKQISF NGSEGRRSRS RRYSGSDSDS
1110 1120 1130 1140 1150
ISERKRPKKR GRPRTIPREN IKGFSDAEIR RFIKSYKKFG GPLERLDAIA
1160 1170 1180 1190 1200
RDAELVDKSE TDLRRLGELV HNGCVKALKD SSSGTERAGG RLGKVKGPTF
1210 1220 1230 1240 1250
RISGVQVNAK LVIAHEDELI PLHKSIPSDP EERKQYTIPC HTKAAHFDID
1260 1270 1280 1290 1300
WGKEDDSNLL IGIYEYGYGS WEMIKMDPDL SLTHKILPDD PDKKPQAKQL
1310 1320 1330 1340 1350
QTRADYLIKL LSRDLAKREA QRLCGAGGSK RRKTRAKKSK AMKSIKVKEE
1360 1370 1380 1390 1400
IKSDSSPLPS EKSDEDDDKL NDSKPESKDR SKKSVVSDAP VHITASGEPV
1410 1420 1430 1440 1450
PIAEESEELD QKTFSICKER MRPVKAALKQ LDRPEKGLSE REQLEHTRQC
1460 1470 1480 1490 1500
LIKIGDHITE CLKEYSNPEQ IKQWRKNLWI FVSKFTEFDA RKLHKLYKHA
1510 1520 1530 1540 1550
IKKRQESQQN SDQNSNVATT HVIRNPDMER LKENTNHDDS SRDSYSSDRH
1560 1570 1580 1590 1600
LSQYHDHHKD RHQGDSYKKS DSRKRPYSSF SNGKDHREWD HYRQDSRYYS
1610 1620 1630 1640 1650
DREKHRKLDD HRSREHRPSL EGGLKDRCHS DHRSHSDHRM HSDHRSSSEH
1660 1670 1680 1690 1700
THHKSSRDYR YLSDWQLDHR AASSGPRSPL DQRSPYGSRS PFEHSAEHRS
1710
TPEHTWSSRK T
Length:1,711
Mass (Da):196,385
Last modified:July 27, 2011 - v3
Checksum:i51499636E943A856
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti159S → L in AAB08486 (PubMed:8460153).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L10410 mRNA. Translation: AAB08486.1.
CH466630 Genomic DNA. Translation: EDL20454.1.
BC115822 mRNA. Translation: AAI15823.1.
CCDSiCCDS28416.1.
PIRiA47392.
RefSeqiNP_031716.2. NM_007690.3.
UniGeneiMm.8137.

Genome annotation databases

EnsembliENSMUST00000024627; ENSMUSP00000024627; ENSMUSG00000023852.
GeneIDi12648.
KEGGimmu:12648.
UCSCiuc008aou.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L10410 mRNA. Translation: AAB08486.1.
CH466630 Genomic DNA. Translation: EDL20454.1.
BC115822 mRNA. Translation: AAI15823.1.
CCDSiCCDS28416.1.
PIRiA47392.
RefSeqiNP_031716.2. NM_007690.3.
UniGeneiMm.8137.

3D structure databases

ProteinModelPortaliP40201.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi198693. 3 interactors.
IntActiP40201. 2 interactors.
MINTiMINT-4090783.
STRINGi10090.ENSMUSP00000024627.

PTM databases

iPTMnetiP40201.
PhosphoSitePlusiP40201.

Proteomic databases

EPDiP40201.
MaxQBiP40201.
PaxDbiP40201.
PeptideAtlasiP40201.
PRIDEiP40201.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000024627; ENSMUSP00000024627; ENSMUSG00000023852.
GeneIDi12648.
KEGGimmu:12648.
UCSCiuc008aou.2. mouse.

Organism-specific databases

CTDi1105.
MGIiMGI:88393. Chd1.

Phylogenomic databases

eggNOGiKOG0383. Eukaryota.
COG0553. LUCA.
GeneTreeiENSGT00760000119067.
HOGENOMiHOG000207917.
HOVERGENiHBG005325.
InParanoidiP40201.
KOiK11367.
OMAiEITSVKH.
OrthoDBiEOG091G00HF.
TreeFamiTF300674.

Miscellaneous databases

PROiP40201.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000023852.
CleanExiMM_CHD1.
ExpressionAtlasiP40201. baseline and differential.
GenevisibleiP40201. MM.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR025260. DUF4208.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000330. SNF2_N.
[Graphical view]
PfamiPF00385. Chromo. 2 hits.
PF13907. DUF4208. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00176. SNF2_N. 1 hit.
[Graphical view]
SMARTiSM00298. CHROMO. 2 hits.
SM00487. DEXDc. 1 hit.
SM01176. DUF4208. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
SSF54160. SSF54160. 2 hits.
PROSITEiPS00598. CHROMO_1. 2 hits.
PS50013. CHROMO_2. 2 hits.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCHD1_MOUSE
AccessioniPrimary (citable) accession number: P40201
Secondary accession number(s): Q14BJ0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: July 27, 2011
Last modified: November 2, 2016
This is version 138 of the entry and version 3 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.