CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-021384
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 
Protein Synonyms/Alias
 ATP-dependent helicase 1; hHEL1 
Gene Name
 SMARCAD1 
Gene Synonyms/Alias
 KIAA1122 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
261SIVLKLQKEFPNFDKubiquitination[1]
268KEFPNFDKQELREVLmethylation[2]
310QSEVPNGKEVSSRSQubiquitination[3]
410LIPQCSQKKAQKITEubiquitination[4, 5]
430SWEALFTKMSKTNGLubiquitination[5]
446EDLIWHCKTLIQERDubiquitination[5]
468KCEDISNKLTKQVTMubiquitination[5]
695RMFSSKTKSADEQSIubiquitination[5]
705DEQSIYEKERIAHAKubiquitination[3, 5, 6]
780NVMMQLRKMANHPLLubiquitination[5]
903RYLRLDGKTQISERIubiquitination[3, 5, 6]
994MLKINQQKLKLEQDMacetylation[6]
Reference
 [1] 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]
 [2] Large-scale global identification of protein lysine methylation in vivo.
 Cao XJ, Arnaudo AM, Garcia BA.
 Epigenetics. 2013 May 1;8(5):477-85. [PMID: 23644510]
 [3] 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]
 [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]
 [5] 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]
 [6] 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] 
Functional Description
 DNA helicase that possesses intrinsic ATP-dependent nucleosome-remodeling activity and is both required for DNA repair and heterochromatin organization. Promotes DNA end resection of double-strand breaks (DSBs) following DNA damage: probably acts by weakening histone DNA interactions in nucleosomes flanking DSBs. Required for the restoration of heterochromatin organization after replication. Acts at replication sites to facilitate the maintenance of heterochromatin by directing H3 and H4 histones deacetylation, H3 'Lys-9' trimethylation (H3K9me3) and restoration of silencing. 
Sequence Annotation
 DOMAIN 157 199 CUE 1.
 DOMAIN 251 294 CUE 2.
 DOMAIN 509 677 Helicase ATP-binding.
 DOMAIN 858 1010 Helicase C-terminal.
 NP_BIND 521 529 ATP (By similarity).
 NP_BIND 897 904 ATP (By similarity).
 MOTIF 628 631 DEGH box.
 MOTIF 721 738 Nuclear localization signal (Potential).
 MOTIF 1005 1008 DEGD box.
 MOD_RES 54 54 Phosphothreonine.
 MOD_RES 57 57 Phosphoserine.
 MOD_RES 79 79 Phosphoserine.
 MOD_RES 124 124 Phosphoserine.
 MOD_RES 127 127 Phosphoserine.
 MOD_RES 132 132 Phosphoserine.
 MOD_RES 146 146 Phosphoserine.
 MOD_RES 152 152 Phosphoserine.
 MOD_RES 211 211 Phosphoserine.
 MOD_RES 212 212 Phosphoserine (By similarity).
 MOD_RES 213 213 Phosphoserine (By similarity).
 MOD_RES 214 214 Phosphoserine.
 MOD_RES 239 239 Phosphoserine.
 MOD_RES 242 242 Phosphoserine.
 MOD_RES 302 302 Phosphoserine.
 MOD_RES 408 408 Phosphoserine (By similarity).  
Keyword
 Alternative splicing; ATP-binding; Chromatin regulator; Chromosome; Complete proteome; DNA damage; DNA repair; DNA-binding; Helicase; Hydrolase; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1026 AA 
Protein Sequence
MNLFNLDRFR FEKRNKIEEA PEATPQPSQP GPSSPISLSA EEENAEGEVS RANTPDSDIT 60
EKTEDSSVPE TPDNERKASI SYFKNQRGIQ YIDLSSDSED VVSPNCSNTV QEKTFNKDTV 120
IIVSEPSEDE ESQGLPTMAR RNDDISELED LSELEDLKDA KLQTLKELFP QRSDNDLLKL 180
IESTSTMDGA IAAALLMFGD AGGGPRKRKL SSSSEPYEED EFNDDQSIKK TRLDHGEESN 240
ESAESSSNWE KQESIVLKLQ KEFPNFDKQE LREVLKEHEW MYTEALESLK VFAEDQDMQY 300
VSQSEVPNGK EVSSRSQNYP KNATKTKLKQ KFSMKAQNGF NKKRKKNVFN PKRVVEDSEY 360
DSGSDVGSSL DEDYSSGEEV MEDGYKGKIL HFLQDASIGE LTLIPQCSQK KAQKITELRP 420
FNSWEALFTK MSKTNGLSED LIWHCKTLIQ ERDVVIRLMN KCEDISNKLT KQVTMLTGNG 480
GGWNIEQPSI LNQSLSLKPY QKVGLNWLAL VHKHGLNGIL ADEMGLGKTI QAIAFLAYLY 540
QEGNNGPHLI VVPASTIDNW LREVNLWCPT LKVLCYYGSQ EERKQIRFNI HSRYEDYNVI 600
VTTYNCAISS SDDRSLFRRL KLNYAIFDEG HMLKNMGSIR YQHLMTINAN NRLLLTGTPV 660
QNNLLELMSL LNFVMPHMFS SSTSEIRRMF SSKTKSADEQ SIYEKERIAH AKQIIKPFIL 720
RRVKEEVLKQ LPPKKDRIEL CAMSEKQEQL YLGLFNRLKK SINNLEKNTE MCNVMMQLRK 780
MANHPLLHRQ YYTAEKLKEM SQLMLKEPTH CEANPDLIFE DMEVMTDFEL HVLCKQYRHI 840
NNFQLDMDLI LDSGKFRVLG CILSELKQKG DRVVLFSQFT MMLDILEVLL KHHQHRYLRL 900
DGKTQISERI HLIDEFNTDM DIFVFLLSTK AGGLGINLTS ANVVILHDID CNPYNDKQAE 960
DRCHRVGQTK EVLVIKLISQ GTIEESMLKI NQQKLKLEQD MTTVDEGDEG SMPADIATLL 1020
KTSMGL 1026 
Gene Ontology
 GO:0000792; C:heterochromatin; ISS:UniProtKB.
 GO:0016363; C:nuclear matrix; NAS:UniProtKB.
 GO:0043596; C:nuclear replication fork; IDA:UniProtKB.
 GO:0035861; C:site of double-strand break; IDA:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0003677; F:DNA binding; IDA:UniProtKB.
 GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
 GO:0043044; P:ATP-dependent chromatin remodeling; IMP:UniProtKB.
 GO:0051304; P:chromosome separation; IMP:UniProtKB.
 GO:0000729; P:DNA double-strand break processing; IMP:UniProtKB.
 GO:0070932; P:histone H3 deacetylation; IMP:UniProtKB.
 GO:0070933; P:histone H4 deacetylation; IMP:UniProtKB.
 GO:0009117; P:nucleotide metabolic process; NAS:UniProtKB.
 GO:0045893; P:positive regulation of transcription, DNA-dependent; NAS:UniProtKB.
 GO:0051260; P:protein homooligomerization; NAS:UniProtKB.
 GO:0000018; P:regulation of DNA recombination; IEP:UniProtKB. 
Interpro
 IPR003892; CUE.
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR027417; P-loop_NTPase.
 IPR000330; SNF2_N.
 IPR009060; UBA-like. 
Pfam
 PF00271; Helicase_C
 PF00176; SNF2_N 
SMART
 SM00487; DEXDc
 SM00490; HELICc 
PROSITE
 PS51140; CUE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER 
PRINTS