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Protein

Chromo domain-containing protein 1

Gene

CHD1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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) complexes SAGA and SLIK. It recognizes H3K4me. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Acts in opposition to the FACT complex in regulating polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the pol 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.11 Publications

Kineticsi

  1. KM=10.2 nM for ATP1 Publication

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi401 – 408ATPPROSITE-ProRule annotation8

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • chromatin DNA binding Source: SGD
    • DNA binding Source: SGD
    • DNA-dependent ATPase activity Source: SGD
    • helicase activity Source: UniProtKB-KW
    • methylated histone binding Source: SGD
    • nucleosome-dependent ATPase activity Source: SGD
    • rDNA binding Source: SGD
    • transcription regulatory region DNA binding Source: SGD

    GO - Biological processi

    • ATP-dependent chromatin remodeling Source: SGD
    • histone H2B conserved C-terminal lysine ubiquitination Source: SGD
    • negative regulation of DNA-dependent DNA replication Source: SGD
    • negative regulation of histone exchange Source: SGD
    • negative regulation of histone H3-K14 acetylation Source: SGD
    • negative regulation of histone H3-K9 acetylation Source: SGD
    • nucleosome mobilization Source: SGD
    • nucleosome organization Source: SGD
    • nucleosome positioning Source: SGD
    • regulation of chromatin organization Source: SGD
    • regulation of nucleosome density Source: SGD
    • regulation of transcriptional start site selection at RNA polymerase II promoter Source: SGD
    • termination of RNA polymerase II transcription Source: SGD
    • termination of RNA polymerase I transcription Source: SGD
    • transcription elongation from RNA polymerase II promoter Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Chromatin regulator, Helicase, Hydrolase

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    ATP-binding, DNA-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30325-MONOMER.
    SABIO-RKP32657.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Chromo domain-containing protein 1 (EC:3.6.4.-)
    Alternative name(s):
    ATP-dependent helicase CHD1
    Gene namesi
    Name:CHD1
    Ordered Locus Names:YER164W
    ORF Names:SYGP-ORF4
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome V

    Organism-specific databases

    EuPathDBiFungiDB:YER164W.
    SGDiS000000966. CHD1.

    Subcellular locationi

    GO - Cellular componenti

    • nuclear chromatin Source: SGD
    • nucleolar chromatin Source: SGD
    • SAGA complex Source: SGD
    • SLIK (SAGA-like) complex Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi220E → L or W: No interaction with methylated histone H3 'K-4'. 2 Publications1
    Mutagenesisi222H → Y: Confers interaction with methylated histone H3 'K-4'. 1 Publication1
    Mutagenesisi314L → Y: No effect on interaction with methylated histone H3 'K-4'. 1 Publication1
    Mutagenesisi316Y → E: Disrupts interaction with methylated histone H3 'K-4'; abrogates histone acetylation activity of SLIK. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000802371 – 1468Chromo domain-containing protein 1Add BLAST1468

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei36PhosphoserineCombined sources1
    Modified residuei72PhosphoserineCombined sources1
    Modified residuei987PhosphoserineCombined sources1
    Modified residuei989PhosphoserineCombined sources1
    Cross-linki1144Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Modified residuei1336PhosphoserineCombined sources1
    Modified residuei1364PhosphoserineCombined sources1
    Modified residuei1372PhosphoserineCombined sources1

    Keywords - PTMi

    Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP32657.
    PRIDEiP32657.

    PTM databases

    iPTMnetiP32657.

    Interactioni

    Subunit structurei

    Component of the 1.8 MDa SAGA complex, which consists of at least of TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1. TAF5, TAF6, TAF9, TAF19, TAF12 and ADA1 seem to be present in 2 copies. SAGA is built of 5 distinct domains with specialized functions. Domain I (containing TRA1) probably represents the activator interaction surface. Domain II (containing TAF5 and TAF6, and probably TAF9 and TAF10), domain III (containing GCN5, TAF10, SPT7, TAF5 and ADA1, and probably ADA2, ADA3 and TAF12), and domain IV (containing HFI1/ADA1 and TAF6, and probably TAF9) are believed to play primarily an architectural role. Domain III also harbors the HAT activity. Domain V (containing SPT3 and SPT20, and probably SPT8) represents the TBP-interacting module, which may be associated transiently with SAGA. Component of the SLIK complex, which consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10 and TAF9. Interacts with RTF1, SPT5 and with the FACT subunits POB3 and SPT16.6 Publications

    GO - Molecular functioni

    • methylated histone binding Source: SGD

    Protein-protein interaction databases

    BioGridi36917. 234 interactors.
    DIPiDIP-6362N.
    IntActiP32657. 39 interactors.
    MINTiMINT-618890.

    Structurei

    Secondary structure

    11468
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi179 – 187Combined sources9
    Turni190 – 192Combined sources3
    Helixi193 – 196Combined sources4
    Helixi204 – 210Combined sources7
    Beta strandi211 – 217Combined sources7
    Helixi222 – 224Combined sources3
    Beta strandi226 – 228Combined sources3
    Helixi230 – 233Combined sources4
    Beta strandi234 – 237Combined sources4
    Helixi239 – 249Combined sources11
    Helixi251 – 258Combined sources8
    Helixi264 – 283Combined sources20
    Beta strandi286 – 297Combined sources12
    Beta strandi299 – 301Combined sources3
    Beta strandi303 – 311Combined sources9
    Beta strandi320 – 323Combined sources4
    Helixi324 – 330Combined sources7
    Helixi332 – 338Combined sources7
    Helixi1012 – 1025Combined sources14
    Helixi1029 – 1031Combined sources3
    Helixi1032 – 1037Combined sources6
    Helixi1046 – 1091Combined sources46
    Beta strandi1092 – 1094Combined sources3
    Beta strandi1096 – 1098Combined sources3
    Beta strandi1101 – 1103Combined sources3
    Helixi1104 – 1112Combined sources9
    Beta strandi1119 – 1122Combined sources4
    Beta strandi1125 – 1129Combined sources5
    Helixi1130 – 1150Combined sources21
    Helixi1155 – 1157Combined sources3
    Beta strandi1171 – 1173Combined sources3
    Helixi1177 – 1190Combined sources14
    Helixi1195 – 1200Combined sources6
    Turni1202 – 1204Combined sources3
    Helixi1207 – 1209Combined sources3
    Helixi1250 – 1264Combined sources15
    Turni1265 – 1268Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2DY7NMR-A172-252[»]
    2DY8NMR-A279-347[»]
    2H1EX-ray2.20A/B174-339[»]
    2XB0X-ray2.00X1009-1274[»]
    3MWYX-ray3.70W142-939[»]
    3TEDX-ray2.00A1006-1274[»]
    ProteinModelPortaliP32657.
    SMRiP32657.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP32657.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini195 – 257Chromo 1PROSITE-ProRule annotationAdd BLAST63
    Domaini285 – 350Chromo 2PROSITE-ProRule annotationAdd BLAST66
    Domaini388 – 562Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST175
    Domaini699 – 860Helicase C-terminalPROSITE-ProRule annotationAdd BLAST162

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi513 – 516DEAH box4

    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

    GeneTreeiENSGT00760000119067.
    HOGENOMiHOG000207917.
    InParanoidiP32657.
    KOiK11367.
    OrthoDBiEOG092C1YH4.

    Family and domain databases

    Gene3Di1.10.10.60. 1 hit.
    3.40.50.300. 2 hits.
    InterProiIPR000953. Chromo/shadow_dom.
    IPR023780. Chromo_domain.
    IPR016197. Chromodomain-like.
    IPR023779. Chromodomain_CS.
    IPR025260. DUF4208.
    IPR014001. Helicase_ATP-bd.
    IPR001650. Helicase_C.
    IPR009057. Homeodomain-like.
    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]
    SUPFAMiSSF46689. SSF46689. 1 hit.
    SSF52540. 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.

    P32657-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAAKDISTEV LQNPELYGLR RSHRAAAHQQ NYFNDSDDED DEDNIKQSRR
    60 70 80 90 100
    KRMTTIEDDE DEFEDEEGEE DSGEDEDEED FEEDDDYYGS PIKQNRSKPK
    110 120 130 140 150
    SRTKSKSKSK PKSQSEKQST VKIPTRFSNR QNKTVNYNID YSDDDLLESE
    160 170 180 190 200
    DDYGSEEALS EENVHEASAN PQPEDFHGID IVINHRLKTS LEEGKVLEKT
    210 220 230 240 250
    VPDLNNCKEN YEFLIKWTDE SHLHNTWETY ESIGQVRGLK RLDNYCKQFI
    260 270 280 290 300
    IEDQQVRLDP YVTAEDIEIM DMERERRLDE FEEFHVPERI IDSQRASLED
    310 320 330 340 350
    GTSQLQYLVK WRRLNYDEAT WENATDIVKL APEQVKHFQN RENSKILPQY
    360 370 380 390 400
    SSNYTSQRPR FEKLSVQPPF IKGGELRDFQ LTGINWMAFL WSKGDNGILA
    410 420 430 440 450
    DEMGLGKTVQ TVAFISWLIF ARRQNGPHII VVPLSTMPAW LDTFEKWAPD
    460 470 480 490 500
    LNCICYMGNQ KSRDTIREYE FYTNPRAKGK KTMKFNVLLT TYEYILKDRA
    510 520 530 540 550
    ELGSIKWQFM AVDEAHRLKN AESSLYESLN SFKVANRMLI TGTPLQNNIK
    560 570 580 590 600
    ELAALVNFLM PGRFTIDQEI DFENQDEEQE EYIHDLHRRI QPFILRRLKK
    610 620 630 640 650
    DVEKSLPSKT ERILRVELSD VQTEYYKNIL TKNYSALTAG AKGGHFSLLN
    660 670 680 690 700
    IMNELKKASN HPYLFDNAEE RVLQKFGDGK MTRENVLRGL IMSSGKMVLL
    710 720 730 740 750
    DQLLTRLKKD GHRVLIFSQM VRMLDILGDY LSIKGINFQR LDGTVPSAQR
    760 770 780 790 800
    RISIDHFNSP DSNDFVFLLS TRAGGLGINL MTADTVVIFD SDWNPQADLQ
    810 820 830 840 850
    AMARAHRIGQ KNHVMVYRLV SKDTVEEEVL ERARKKMILE YAIISLGVTD
    860 870 880 890 900
    GNKYTKKNEP NAGELSAILK FGAGNMFTAT DNQKKLEDLN LDDVLNHAED
    910 920 930 940 950
    HVTTPDLGES HLGGEEFLKQ FEVTDYKADI DWDDIIPEEE LKKLQDEEQK
    960 970 980 990 1000
    RKDEEYVKEQ LEMMNRRDNA LKKIKNSVNG DGTAANSDSD DDSTSRSSRR
    1010 1020 1030 1040 1050
    RARANDMDSI GESEVRALYK AILKFGNLKE ILDELIADGT LPVKSFEKYG
    1060 1070 1080 1090 1100
    ETYDEMMEAA KDCVHEEEKN RKEILEKLEK HATAYRAKLK SGEIKAENQP
    1110 1120 1130 1140 1150
    KDNPLTRLSL KKREKKAVLF NFKGVKSLNA ESLLSRVEDL KYLKNLINSN
    1160 1170 1180 1190 1200
    YKDDPLKFSL GNNTPKPVQN WSSNWTKEED EKLLIGVFKY GYGSWTQIRD
    1210 1220 1230 1240 1250
    DPFLGITDKI FLNEVHNPVA KKSASSSDTT PTPSKKGKGI TGSSKKVPGA
    1260 1270 1280 1290 1300
    IHLGRRVDYL LSFLRGGLNT KSPSADIGSK KLPTGPSKKR QRKPANHSKS
    1310 1320 1330 1340 1350
    MTPEITSSEP ANGPPSKRMK ALPKGPAALI NNTRLSPNSP TPPLKSKVSR
    1360 1370 1380 1390 1400
    DNGTRQSSNP SSGSAHEKEY DSMDEEDCRH TMSAIRTSLK RLRRGGKSLD
    1410 1420 1430 1440 1450
    RKEWAKILKT ELTTIGNHIE SQKGSSRKAS PEKYRKHLWS YSANFWPADV
    1460
    KSTKLMAMYD KITESQKK
    Length:1,468
    Mass (Da):168,241
    Last modified:October 1, 1993 - v1
    Checksum:i78BDB74C7FEC6BE5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18917 Genomic DNA. Translation: AAB64691.1.
    BK006939 Genomic DNA. Translation: DAA07826.1.
    PIRiS30818.
    RefSeqiNP_011091.1. NM_001179054.1.

    Genome annotation databases

    EnsemblFungiiYER164W; YER164W; YER164W.
    GeneIDi856911.
    KEGGisce:YER164W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18917 Genomic DNA. Translation: AAB64691.1.
    BK006939 Genomic DNA. Translation: DAA07826.1.
    PIRiS30818.
    RefSeqiNP_011091.1. NM_001179054.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2DY7NMR-A172-252[»]
    2DY8NMR-A279-347[»]
    2H1EX-ray2.20A/B174-339[»]
    2XB0X-ray2.00X1009-1274[»]
    3MWYX-ray3.70W142-939[»]
    3TEDX-ray2.00A1006-1274[»]
    ProteinModelPortaliP32657.
    SMRiP32657.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi36917. 234 interactors.
    DIPiDIP-6362N.
    IntActiP32657. 39 interactors.
    MINTiMINT-618890.

    PTM databases

    iPTMnetiP32657.

    Proteomic databases

    MaxQBiP32657.
    PRIDEiP32657.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYER164W; YER164W; YER164W.
    GeneIDi856911.
    KEGGisce:YER164W.

    Organism-specific databases

    EuPathDBiFungiDB:YER164W.
    SGDiS000000966. CHD1.

    Phylogenomic databases

    GeneTreeiENSGT00760000119067.
    HOGENOMiHOG000207917.
    InParanoidiP32657.
    KOiK11367.
    OrthoDBiEOG092C1YH4.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30325-MONOMER.
    SABIO-RKP32657.

    Miscellaneous databases

    EvolutionaryTraceiP32657.
    PROiP32657.

    Family and domain databases

    Gene3Di1.10.10.60. 1 hit.
    3.40.50.300. 2 hits.
    InterProiIPR000953. Chromo/shadow_dom.
    IPR023780. Chromo_domain.
    IPR016197. Chromodomain-like.
    IPR023779. Chromodomain_CS.
    IPR025260. DUF4208.
    IPR014001. Helicase_ATP-bd.
    IPR001650. Helicase_C.
    IPR009057. Homeodomain-like.
    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]
    SUPFAMiSSF46689. SSF46689. 1 hit.
    SSF52540. 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_YEAST
    AccessioniPrimary (citable) accession number: P32657
    Secondary accession number(s): D3DM72
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1993
    Last sequence update: October 1, 1993
    Last modified: November 2, 2016
    This is version 169 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 1620 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome V
      Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

    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.