CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-012400
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Chromodomain-helicase-DNA-binding protein 4 
Protein Synonyms/Alias
 CHD-4; ATP-dependent helicase CHD4; Mi-2 autoantigen 218 kDa protein; Mi2-beta 
Gene Name
 CHD4 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
179YRTLTNYKAFSQFVRubiquitination[1]
403CLDPDMEKAPEGKWSubiquitination[2]
499RCTCPALKGKVQKILubiquitination[2]
501TCPALKGKVQKILIWubiquitination[2]
504ALKGKVQKILIWKWGubiquitination[2]
577MFRNYQRKNDMDEPPubiquitination[2]
594DFGGDEEKSRKRKNKubiquitination[2]
604KRKNKDPKFAEMEERubiquitination[2]
635LNHSVDKKGHVHYLIubiquitination[2]
984ELSPMQKKYYKYILTubiquitination[2]
987PMQKKYYKYILTRNFubiquitination[2]
1017NVVMDLKKCCNHPYLubiquitination[2]
1057GKLLLLQKMLKNLKEubiquitination[2]
1092FLEHEGYKYERIDGGubiquitination[2, 3]
1316VDPDYWEKLLRHHYEubiquitination[2]
1426GLRNDKDKPLPPLLAubiquitination[1]
1450GFNARQRKAFLNAIMubiquitination[1]
1752RAATVTKKTYEIWHRubiquitination[2]
1794AILNEPFKGEMNRGNubiquitination[1, 2]
1865ESHQHLSKESMAGNKubiquitination[2]
1872KESMAGNKPANAVLHubiquitination[2]
1880PANAVLHKVLKQLEEubiquitination[2]
1883AVLHKVLKQLEELLSubiquitination[2, 3]
1893EELLSDMKADVTRLPubiquitination[2, 4]
Reference
 [1] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [2] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [3] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [4] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724] 
Functional Description
 Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. 
Sequence Annotation
 DOMAIN 494 594 Chromo 1.
 DOMAIN 622 697 Chromo 2.
 DOMAIN 738 922 Helicase ATP-binding.
 DOMAIN 1054 1203 Helicase C-terminal.
 ZN_FING 370 417 PHD-type 1.
 ZN_FING 449 496 PHD-type 2.
 NP_BIND 751 758 ATP (Potential).
 REGION 1577 1912 Required for interaction with PCNT.
 MOTIF 873 876 DEAH box.
 MOD_RES 44 44 Phosphoserine.
 MOD_RES 303 303 Phosphoserine.
 MOD_RES 308 308 Phosphoserine.
 MOD_RES 309 309 Phosphoserine.
 MOD_RES 310 310 Phosphoserine.
 MOD_RES 319 319 Phosphoserine.
 MOD_RES 428 428 Phosphoserine.
 MOD_RES 515 515 Phosphoserine.
 MOD_RES 517 517 Phosphothreonine.
 MOD_RES 529 529 Phosphothreonine.
 MOD_RES 531 531 Phosphoserine.
 MOD_RES 1308 1308 Phosphoserine (By similarity).
 MOD_RES 1349 1349 Phosphoserine.
 MOD_RES 1531 1531 Phosphoserine.
 MOD_RES 1535 1535 Phosphoserine.
 MOD_RES 1537 1537 Phosphoserine.
 MOD_RES 1540 1540 Phosphothreonine (By similarity).
 MOD_RES 1545 1545 Phosphothreonine (By similarity).
 MOD_RES 1549 1549 Phosphothreonine (By similarity).
 MOD_RES 1553 1553 Phosphothreonine.
 MOD_RES 1602 1602 Phosphoserine.
 MOD_RES 1643 1643 N6-acetyllysine.
 MOD_RES 1653 1653 Phosphothreonine.
 MOD_RES 1679 1679 Phosphothreonine.  
Keyword
 3D-structure; Acetylation; Alternative splicing; ATP-binding; Chromatin regulator; Complete proteome; Cytoplasm; Cytoskeleton; DNA-binding; Helicase; Hydrolase; Metal-binding; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; Transcription; Transcription regulation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1912 AA 
Protein Sequence
MASGLGSPSP CSAGSEEEDM DALLNNSLPP PHPENEEDPE EDLSETETPK LKKKKKPKKP 60
RDPKIPKSKR QKKERMLLCR QLGDSSGEGP EFVEEEEEVA LRSDSEGSDY TPGKKKKKKL 120
GPKKEKKSKS KRKEEEEEED DDDDSKEPKS SAQLLEDWGM EDIDHVFSEE DYRTLTNYKA 180
FSQFVRPLIA AKNPKIAVSK MMMVLGAKWR EFSTNNPFKG SSGASVAAAA AAAVAVVESM 240
VTATEVAPPP PPVEVPIRKA KTKEGKGPNA RRKPKGSPRV PDAKKPKPKK VAPLKIKLGG 300
FGSKRKRSSS EDDDLDVESD FDDASINSYS VSDGSTSRSS RSRKKLRTTK KKKKGEEEVT 360
AVDGYETDHQ DYCEVCQQGG EIILCDTCPR AYHMVCLDPD MEKAPEGKWS CPHCEKEGIQ 420
WEAKEDNSEG EEILEEVGGD LEEEDDHHME FCRVCKDGGE LLCCDTCPSS YHIHCLNPPL 480
PEIPNGEWLC PRCTCPALKG KVQKILIWKW GQPPSPTPVP RPPDADPNTP SPKPLEGRPE 540
RQFFVKWQGM SYWHCSWVSE LQLELHCQVM FRNYQRKNDM DEPPSGDFGG DEEKSRKRKN 600
KDPKFAEMEE RFYRYGIKPE WMMIHRILNH SVDKKGHVHY LIKWRDLPYD QASWESEDVE 660
IQDYDLFKQS YWNHRELMRG EEGRPGKKLK KVKLRKLERP PETPTVDPTV KYERQPEYLD 720
ATGGTLHPYQ MEGLNWLRFS WAQGTDTILA DEMGLGKTVQ TAVFLYSLYK EGHSKGPFLV 780
SAPLSTIINW EREFEMWAPD MYVVTYVGDK DSRAIIRENE FSFEDNAIRG GKKASRMKKE 840
ASVKFHVLLT SYELITIDMA ILGSIDWACL IVDEAHRLKN NQSKFFRVLN GYSLQHKLLL 900
TGTPLQNNLE ELFHLLNFLT PERFHNLEGF LEEFADIAKE DQIKKLHDML GPHMLRRLKA 960
DVFKNMPSKT ELIVRVELSP MQKKYYKYIL TRNFEALNAR GGGNQVSLLN VVMDLKKCCN 1020
HPYLFPVAAM EAPKMPNGMY DGSALIRASG KLLLLQKMLK NLKEGGHRVL IFSQMTKMLD 1080
LLEDFLEHEG YKYERIDGGI TGNMRQEAID RFNAPGAQQF CFLLSTRAGG LGINLATADT 1140
VIIYDSDWNP HNDIQAFSRA HRIGQNKKVM IYRFVTRASV EERITQVAKK KMMLTHLVVR 1200
PGLGSKTGSM SKQELDDILK FGTEELFKDE ATDGGGDNKE GEDSSVIHYD DKAIERLLDR 1260
NQDETEDTEL QGMNEYLSSF KVAQYVVREE EMGEEEEVER EIIKQEESVD PDYWEKLLRH 1320
HYEQQQEDLA RNLGKGKRIR KQVNYNDGSQ EDRGVCGRPR PPPMGRSTRA VGPAHLPSLP 1380
PDWQDDQSDN QSDYSVASEE GDEDFDERSE APRRPSRKGL RNDKDKPLPP LLARVGGNIE 1440
VLGFNARQRK AFLNAIMRYG MPPQDAFTTQ WLVRDLRGKS EKEFKAYVSL FMRHLCEPGA 1500
DGAETFADGV PREGLSRQHV LTRIGVMSLI RKKVQEFEHV NGRWSMPELA EVEENKKMSQ 1560
PGSPSPKTPT PSTPGDTQPN TPAPVPPAED GIKIEENSLK EEESIEGEKE VKSTAPETAI 1620
ECTQAPAPAS EDEKVVVEPP EGEEKVEKAE VKERTEEPME TEPKGAADVE KVEEKSAIDL 1680
TPIVVEDKEE KKEEEEKKEV MLQNGETPKD LNDEKQKKNI KQRFMFNIAD GGFTELHSLW 1740
QNEERAATVT KKTYEIWHRR HDYWLLAGII NHGYARWQDI QNDPRYAILN EPFKGEMNRG 1800
NFLEIKNKFL ARRFKLLEQA LVIEEQLRRA AYLNMSEDPS HPSMALNTRF AEVECLAESH 1860
QHLSKESMAG NKPANAVLHK VLKQLEELLS DMKADVTRLP ATIARIPPVA VRLQMSERNI 1920
LSRLANRAPE PTPQQVAQQQ 1940 
Gene Ontology
 GO:0005813; C:centrosome; IDA:UniProtKB.
 GO:0005737; C:cytoplasm; IDA:UniProtKB.
 GO:0016581; C:NuRD complex; IDA:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0004003; F:ATP-dependent DNA helicase activity; TAS:ProtInc.
 GO:0003677; F:DNA binding; TAS:ProtInc.
 GO:0008270; F:zinc ion binding; TAS:ProtInc.
 GO:0016568; P:chromatin modification; IEA:UniProtKB-KW.
 GO:0006357; P:regulation of transcription from RNA polymerase II promoter; TAS:ProtInc.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
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.
 IPR027417; P-loop_NTPase.
 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. 
Pfam
 PF08074; CHDCT2
 PF08073; CHDNT
 PF00385; Chromo
 PF06461; DUF1086
 PF06465; DUF1087
 PF00271; Helicase_C
 PF00628; PHD
 PF00176; SNF2_N 
SMART
 SM00298; CHROMO
 SM00487; DEXDc
 SM00490; HELICc
 SM00249; PHD
 SM00184; RING 
PROSITE
 PS00598; CHROMO_1
 PS50013; CHROMO_2
 PS00690; DEAH_ATP_HELICASE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER
 PS01359; ZF_PHD_1
 PS50016; ZF_PHD_2 
PRINTS