CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-006197
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Chromo domain-containing protein 1 
Protein Synonyms/Alias
 ATP-dependent helicase CHD1 
Gene Name
 CHD1 
Gene Synonyms/Alias
 YER164W; SYGP-ORF4 
Created Date
 July 27, 2013 
Organism
 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 
NCBI Taxa ID
 559292 
Lysine Modification
Position
Peptide
Type
References
4****MAAKDISTEVLacetylation[1]
1144VEDLKYLKNLINSNYubiquitination[2, 3, 4]
1280PSADIGSKKLPTGPSacetylation[1]
Reference
 [1] Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae.
 Henriksen P, Wagner SA, Weinert BT, Sharma S, Bacinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C.
 Mol Cell Proteomics. 2012 Nov;11(11):1510-22. [PMID: 22865919]
 [2] A proteomics approach to understanding protein ubiquitination.
 Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP.
 Nat Biotechnol. 2003 Aug;21(8):921-6. [PMID: 12872131]
 [3] Computational identification of ubiquitylation sites from protein sequences.
 Tung CW, Ho SY.
 BMC Bioinformatics. 2008 Jul 15;9:310. [PMID: 18625080]
 [4] Identification, analysis, and prediction of protein ubiquitination sites.
 Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM.
 Proteins. 2010 Feb 1;78(2):365-80. [PMID: 19722269] 
Functional Description
 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. 
Sequence Annotation
 DOMAIN 195 257 Chromo 1.
 DOMAIN 285 350 Chromo 2.
 DOMAIN 388 562 Helicase ATP-binding.
 DOMAIN 699 860 Helicase C-terminal.
 NP_BIND 401 408 ATP (Potential).
 MOTIF 513 516 DEAH box.
 MOD_RES 36 36 Phosphoserine.
 MOD_RES 72 72 Phosphoserine.
 MOD_RES 987 987 Phosphoserine.
 MOD_RES 989 989 Phosphoserine.
 MOD_RES 1336 1336 Phosphoserine.
 MOD_RES 1372 1372 Phosphoserine.
 CROSSLNK 1144 1144 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; ATP-binding; Chromatin regulator; Complete proteome; DNA-binding; Helicase; Hydrolase; Isopeptide bond; Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome; Repeat; Transcription; Transcription regulation; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1468 AA 
Protein Sequence
MAAKDISTEV LQNPELYGLR RSHRAAAHQQ NYFNDSDDED DEDNIKQSRR KRMTTIEDDE 60
DEFEDEEGEE DSGEDEDEED FEEDDDYYGS PIKQNRSKPK SRTKSKSKSK PKSQSEKQST 120
VKIPTRFSNR QNKTVNYNID YSDDDLLESE DDYGSEEALS EENVHEASAN PQPEDFHGID 180
IVINHRLKTS LEEGKVLEKT VPDLNNCKEN YEFLIKWTDE SHLHNTWETY ESIGQVRGLK 240
RLDNYCKQFI IEDQQVRLDP YVTAEDIEIM DMERERRLDE FEEFHVPERI IDSQRASLED 300
GTSQLQYLVK WRRLNYDEAT WENATDIVKL APEQVKHFQN RENSKILPQY SSNYTSQRPR 360
FEKLSVQPPF IKGGELRDFQ LTGINWMAFL WSKGDNGILA DEMGLGKTVQ TVAFISWLIF 420
ARRQNGPHII VVPLSTMPAW LDTFEKWAPD LNCICYMGNQ KSRDTIREYE FYTNPRAKGK 480
KTMKFNVLLT TYEYILKDRA ELGSIKWQFM AVDEAHRLKN AESSLYESLN SFKVANRMLI 540
TGTPLQNNIK ELAALVNFLM PGRFTIDQEI DFENQDEEQE EYIHDLHRRI QPFILRRLKK 600
DVEKSLPSKT ERILRVELSD VQTEYYKNIL TKNYSALTAG AKGGHFSLLN IMNELKKASN 660
HPYLFDNAEE RVLQKFGDGK MTRENVLRGL IMSSGKMVLL DQLLTRLKKD GHRVLIFSQM 720
VRMLDILGDY LSIKGINFQR LDGTVPSAQR RISIDHFNSP DSNDFVFLLS TRAGGLGINL 780
MTADTVVIFD SDWNPQADLQ AMARAHRIGQ KNHVMVYRLV SKDTVEEEVL ERARKKMILE 840
YAIISLGVTD GNKYTKKNEP NAGELSAILK FGAGNMFTAT DNQKKLEDLN LDDVLNHAED 900
HVTTPDLGES HLGGEEFLKQ FEVTDYKADI DWDDIIPEEE LKKLQDEEQK RKDEEYVKEQ 960
LEMMNRRDNA LKKIKNSVNG DGTAANSDSD DDSTSRSSRR RARANDMDSI GESEVRALYK 1020
AILKFGNLKE ILDELIADGT LPVKSFEKYG ETYDEMMEAA KDCVHEEEKN RKEILEKLEK 1080
HATAYRAKLK SGEIKAENQP KDNPLTRLSL KKREKKAVLF NFKGVKSLNA ESLLSRVEDL 1140
KYLKNLINSN YKDDPLKFSL GNNTPKPVQN WSSNWTKEED EKLLIGVFKY GYGSWTQIRD 1200
DPFLGITDKI FLNEVHNPVA KKSASSSDTT PTPSKKGKGI TGSSKKVPGA IHLGRRVDYL 1260
LSFLRGGLNT KSPSADIGSK KLPTGPSKKR QRKPANHSKS MTPEITSSEP ANGPPSKRMK 1320
ALPKGPAALI NNTRLSPNSP TPPLKSKVSR DNGTRQSSNP SSGSAHEKEY DSMDEEDCRH 1380
TMSAIRTSLK RLRRGGKSLD RKEWAKILKT ELTTIGNHIE SQKGSSRKAS PEKYRKHLWS 1440
YSANFWPADV KSTKLMAMYD KITESQKK 1468 
Gene Ontology
 GO:0005739; C:mitochondrion; IDA:SGD.
 GO:0030874; C:nucleolar chromatin; IDA:SGD.
 GO:0000124; C:SAGA complex; IDA:SGD.
 GO:0046695; C:SLIK (SAGA-like) complex; IDA:SGD.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0031490; F:chromatin DNA binding; IDA:SGD.
 GO:0008094; F:DNA-dependent ATPase activity; IDA:SGD.
 GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
 GO:0035064; F:methylated histone residue binding; IDA:SGD.
 GO:0000182; F:rDNA binding; IDA:SGD.
 GO:0043044; P:ATP-dependent chromatin remodeling; IDA:SGD.
 GO:0071894; P:histone H2B conserved C-terminal lysine ubiquitination; IMP:SGD.
 GO:2000104; P:negative regulation of DNA-dependent DNA replication; IGI:SGD.
 GO:0071441; P:negative regulation of histone H3-K14 acetylation; IMP:SGD.
 GO:2000616; P:negative regulation of histone H3-K9 acetylation; IMP:SGD.
 GO:0042766; P:nucleosome mobilization; IDA:SGD.
 GO:0016584; P:nucleosome positioning; IDA:SGD.
 GO:0034401; P:regulation of transcription by chromatin organization; IMP:SGD.
 GO:0001178; P:regulation of transcriptional start site selection at RNA polymerase II promoter; IGI:SGD.
 GO:0006363; P:termination of RNA polymerase I transcription; IGI:SGD.
 GO:0006369; P:termination of RNA polymerase II transcription; IMP:SGD.
 GO:0006368; P:transcription elongation from RNA polymerase II promoter; IGI:SGD. 
Interpro
 IPR023780; Chromo_domain.
 IPR000953; Chromo_domain/shadow.
 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. 
Pfam
 PF00385; Chromo
 PF13907; DUF4208
 PF00271; Helicase_C
 PF00176; SNF2_N 
SMART
 SM00298; CHROMO
 SM00487; DEXDc
 SM00490; HELICc 
PROSITE
 PS00598; CHROMO_1
 PS50013; CHROMO_2
 PS00690; DEAH_ATP_HELICASE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER 
PRINTS