CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-039582
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
  
Protein Name
 Chromodomain-helicase-DNA-binding protein 4 
Protein Synonyms/Alias
  
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
297KLGGFGSKRKRSSSEacetylation[1]
396CLDPDMEKAPEGKWSubiquitination[2]
492RCTCPALKGKVQKILubiquitination[1, 2]
494TCPALKGKVQKILIWubiquitination[2]
497ALKGKVQKILIWKWGubiquitination[2, 3]
570MFRNYQRKNDMDEPPubiquitination[2]
587DFGGDEEKSRKRKNKubiquitination[2]
597KRKNKDPKFAEMEERubiquitination[2]
628LNHSVDKKGHVHYLIubiquitination[2]
977ELSPMQKKYYKYILTubiquitination[2]
980PMQKKYYKYILTRNFacetylation[4]
980PMQKKYYKYILTRNFubiquitination[2, 3]
1009LNVVMDLKKCCNHPYubiquitination[5, 6]
1010NVVMDLKKCCNHPYLubiquitination[2]
1050GKLLLLQKMLKNLKEubiquitination[2, 3]
1085FLEHEGYKYERIDGGubiquitination[2, 3, 5, 6, 7, 8]
1205SKTGSMSKQELDDILubiquitination[1]
1245SVIHYDDKAIERLLDubiquitination[5]
1274NEYLSSFKVAQYVVRubiquitination[6]
1297EVEREIIKQEESVDPubiquitination[5]
1309VDPDYWEKLLRHHYEubiquitination[2]
1391GLRNDKDKPLPPLLAubiquitination[1]
1415GFNARQRKAFLNAIMubiquitination[2]
1565KIEENSLKEEESIEGubiquitination[5]
1577IEGEKEVKSTAPETAubiquitination[5]
1636KGAADVEKVEEKSAIubiquitination[1]
1640DVEKVEEKSAIDLTPubiquitination[5]
1674LQNGETPKDLNDEKQacetylation[9]
1717RAATVTKKTYEIWHRubiquitination[2]
1759AILNEPFKGEMNRGNubiquitination[1, 2]
1830ESHQHLSKESMAGNKubiquitination[1, 2]
1837KESMAGNKPANAVLHubiquitination[1, 2]
1845PANAVLHKVLKQLEEubiquitination[2, 3]
1848AVLHKVLKQLEELLSubiquitination[1, 2, 5, 6, 8]
1858EELLSDMKADVTRLPubiquitination[1, 2, 5, 6, 10]
Reference
 [1] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [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] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [4] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [5] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [6] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [7] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
 Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
 J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931]
 [8] 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]
 [9] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [10] 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
  
Sequence Annotation
  
Keyword
 Complete proteome; Metal-binding; Nucleus; Reference proteome; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1905 AA 
Protein Sequence
MASGLGSPSP CSAGSEEEDM DALLNNSLPP PHPENEEDPE EDLSETETPK LKKKKKPKKP 60
RDPKIPKSKR QKKELGDSSG EGPEFVEEEE EVALRSDSEG SDYTPGKKKK KKLGPKKEKK 120
SKSKRKEEEE EEDDDDDSKE PKSSAQLLED WGMEDIDHVF SEEDYRTLTN YKAFSQFVRP 180
LIAAKNPKIA VSKMMMVLGA KWREFSTNNP FKGSSGASVA AAAAAAVAVV ESMVTATEVA 240
PPPPPVEVPI RKAKTKEGKG PNARRKPKGS PRVPDAKKPK PKKVAPLKIK LGGFGSKRKR 300
SSSEDDDLDV ESDFDDASIN SYSVSDGSTS RSSRSRKKLR TTKKKKKGEE EVTAVDGYET 360
DHQDYCEVCQ QGGEIILCDT CPRAYHMVCL DPDMEKAPEG KWSCPHCEKE GIQWEAKEDN 420
SEGEEILEEV GGDLEEEDDH HMEFCRVCKD GGELLCCDTC PSSYHIHCLN PPLPEIPNGE 480
WLCPRCTCPA LKGKVQKILI WKWGQPPSPT PVPRPPDADP NTPSPKPLEG RPERQFFVKW 540
QGMSYWHCSW VSELQLELHC QVMFRNYQRK NDMDEPPSGD FGGDEEKSRK RKNKDPKFAE 600
MEERFYRYGI KPEWMMIHRI LNHSVDKKGH VHYLIKWRDL PYDQASWESE DVEIQDYDLF 660
KQSYWNHREL MRGEEGRPGK KLKKVKLRKL ERPPETPTVD PTVKYERQPE YLDATGGTLH 720
PYQMEGLNWL RFSWAQGTDT ILADEMGLGK TVQTAVFLYS LYKEGHSKGP FLVSAPLSTI 780
INWEREFEMW APDMYVVTYV GDKDSRAIIR ENEFSFEDNA IRGGKKASRM KKEASVKFHV 840
LLTSYELITI DMAILGSIDW ACLIVDEAHR LKNNQSKFFR VLNGYSLQHK LLLTGTPLQN 900
NLEELFHLLN FLTPERFHNL EGFLEEFADI AKEDQIKKLH DMLGPHMLRR LKADVFKNMP 960
SKTELIVRVE LSPMQKKYYK YILTRNFEAL NARGGGNQVS LLNVVMDLKK CCNHPYLFPV 1020
AAMEAPKMPN GMYDGSALIR ASGKLLLLQK MLKNLKEGGH RVLIFSQMTK MLDLLEDFLE 1080
HEGYKYERID GGITGNMRQE AIDRFNAPGA QQFCFLLSTR AGGLGINLAT ADTVIIYDSD 1140
WNPHNDIQAF SRAHRIGQNK KVMIYRFVTR ASVEERITQV AKKKMMLTHL VVRPGLGSKT 1200
GSMSKQELDD ILKFGTEELF KDEATDGGGD NKEGEDSSVI HYDDKAIERL LDRNQDETED 1260
TELQGMNEYL SSFKVAQYVV REEEMGEEEE VEREIIKQEE SVDPDYWEKL LRHHYEQQQE 1320
DLARNLGKGK RIRKQVNYND GSQEDRDWQD DQSDNQSDYS VASEEGDEDF DERSEAPRRP 1380
SRKGLRNDKD KPLPPLLARV GGNIEVLGFN ARQRKAFLNA IMRYGMPPQD AFTTQWLVRD 1440
LRGKSEKEFK AYVSLFMRHL CEPGADGAET FADGVPREGL SRQHVLTRIG VMSLIRKKVQ 1500
EFEHVNGRWS MPELAEVEEN KKMSQPGSPS PKTPTPSTPG DTQPNTPAPV PPAEDGIKIE 1560
ENSLKEEESI EGEKEVKSTA PETAIECTQA PAPASEDEKV VVEPPEGEEK VEKAEVKERT 1620
EEPMETEPKG AADVEKVEEK SAIDLTPIVV EDKEEKKEEE EKKEVMLQNG ETPKDLNDEK 1680
QKKNIKQRFM FNIADGGFTE LHSLWQNEER AATVTKKTYE IWHRRHDYWL LAGIINHGYA 1740
RWQDIQNDPR YAILNEPFKG EMNRGNFLEI KNKFLARRFK LLEQALVIEE QLRRAAYLNM 1800
SEDPSHPSMA LNTRFAEVEC LAESHQHLSK ESMAGNKPAN AVLHKVLKQL EELLSDMKAD 1860
VTRLPATIAR IPPVAVRLQM SERNILSRLA NRAPEPTPQQ VAQQQ 1905 
Gene Ontology
 GO:0005634; C:nucleus; IDA:HPA.
 GO:0005524; F:ATP binding; IEA:InterPro.
 GO:0008026; F:ATP-dependent helicase activity; IEA:InterPro.
 GO:0003677; F:DNA binding; IEA:InterPro.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0006355; P:regulation of transcription, DNA-dependent; IEA:InterPro. 
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
 PS50013; CHROMO_2
 PS00690; DEAH_ATP_HELICASE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER
 PS01359; ZF_PHD_1
 PS50016; ZF_PHD_2 
PRINTS