CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-012328
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Helicase-like transcription factor 
Protein Synonyms/Alias
 DNA-binding protein/plasminogen activator inhibitor 1 regulator; HIP116; RING finger protein 80; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3; Sucrose nonfermenting protein 2-like 3 
Gene Name
 HLTF 
Gene Synonyms/Alias
 HIP116A; RNF80; SMARCA3; SNF2L3; ZBU1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
6**MSWMFKRDPVWKYubiquitination[1]
12FKRDPVWKYLQTVQYubiquitination[2, 3]
95DPNNPYDKNAIKVNNubiquitination[1, 4, 5, 6]
112GNQVGHLKKELAGALubiquitination[1, 6]
113NQVGHLKKELAGALAubiquitination[1, 6]
158WGKEENRKAVSDQLKubiquitination[1]
165KAVSDQLKKHGFKLGubiquitination[1, 6]
166AVSDQLKKHGFKLGPubiquitination[1]
176FKLGPAPKTLGFNLEubiquitination[1, 2, 3, 4, 5, 6, 7]
216QLKTEFDKLFEDLKEubiquitination[2, 3]
258MVSRENSKELPPFWEubiquitination[1, 2, 3]
281TITNFSEKDRPENVHubiquitination[1]
329RVKKNLLKKEYNVNDubiquitination[1]
330VKKNLLKKEYNVNDDubiquitination[1]
340NVNDDSMKLGGNNTSubiquitination[1, 2, 3, 4]
349GGNNTSEKADGLSKDubiquitination[1, 2, 3, 4, 6]
355EKADGLSKDASRCSEubiquitination[1]
370QPSISDIKEKSKFRMubiquitination[1, 6]
428SETKGRAKAGSSKVIubiquitination[8]
433RAKAGSSKVIEDVAFubiquitination[8]
523REPALLSKQDIVLTTubiquitination[2, 3]
541LTHDYGTKGDSPLHSubiquitination[1]
571NPNAQQTKAVLDLESubiquitination[2, 3, 4]
638RRLQSLIKNITLRRTubiquitination[1, 4]
653KTSKIKGKPVLELPEubiquitination[4]
662VLELPERKVFIQHITubiquitination[2, 3]
676TLSDEERKIYQSVKNubiquitination[4]
682RKIYQSVKNEGRATIubiquitination[1, 4, 5, 9]
823ELARDSEKKSDMEWTubiquitination[1]
824LARDSEKKSDMEWTSubiquitination[1]
889DGSMAQKKRVESIQCubiquitination[1]
952RCHRLGQKQEVIITKubiquitination[1, 4, 5, 6, 8]
959KQEVIITKFIVKDSVubiquitination[1, 2, 3, 6]
972SVEENMLKIQNKKREubiquitination[1]
988AAGAFGTKKPNADEMacetylation[10]
988AAGAFGTKKPNADEMubiquitination[1]
989AGAFGTKKPNADEMKubiquitination[1]
999ADEMKQAKINEIRTLubiquitination[1]
Reference
 [1] 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]
 [2] 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]
 [3] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [4] 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]
 [5] 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]
 [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]
 [7] A data set of human endogenous protein ubiquitination sites.
 Shi Y, Chan DW, Jung SY, Malovannaya A, Wang Y, Qin J.
 Mol Cell Proteomics. 2011 May;10(5):M110.002089. [PMID: 20972266]
 [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] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [10] 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] 
Functional Description
 Has both helicase and E3 ubiquitin ligase activities. Possesses intrinsic ATP-dependent nucleosome-remodeling activity; This activity may be required for transcriptional activation or repression of specific target promoters (By similarity). These may include the SERPINE1 and HIV-1 promoters and the SV40 enhancer, to which this protein can bind directly. Plays a role in error-free postreplication repair (PRR) of damaged DNA and maintains genomic stability through acting as a ubiquitin ligase for 'Lys-63'-linked polyubiquitination of chromatin-bound PCNA. 
Sequence Annotation
 DOMAIN 435 606 Helicase ATP-binding.
 DOMAIN 837 996 Helicase C-terminal.
 DNA_BIND 38 287
 NP_BIND 294 301 ATP (By similarity).
 ZN_FING 760 801 RING-type.
 REGION 925 1009 Interaction with SP1 and SP3.
 MOTIF 557 560 DEGH box.
 MOD_RES 195 195 Phosphotyrosine; by JAK2.
 MOD_RES 397 397 Phosphoserine.
 MOD_RES 398 398 Phosphoserine.
 MOD_RES 400 400 Phosphoserine.
 MOD_RES 635 635 Phosphoserine (By similarity).
 MOD_RES 736 736 Phosphothreonine.  
Keyword
 3D-structure; Activator; Alternative initiation; ATP-binding; Chromatin regulator; Complete proteome; Cytoplasm; DNA-binding; Helicase; Hydrolase; Ligase; Metal-binding; Multifunctional enzyme; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Transcription; Ubl conjugation pathway; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1009 AA 
Protein Sequence
MSWMFKRDPV WKYLQTVQYG VHGNFPRLSY PTFFPRFEFQ DVIPPDDFLT SDEEVDSVLF 60
GSLRGHVVGL RYYTGVVNNN EMVALQRDPN NPYDKNAIKV NNVNGNQVGH LKKELAGALA 120
YIMDNKLAQI EGVVPFGANN AFTMPLHMTF WGKEENRKAV SDQLKKHGFK LGPAPKTLGF 180
NLESGWGSGR AGPSYSMPVH AAVQMTTEQL KTEFDKLFED LKEDDKTHEM EPAEAIETPL 240
LPHQKQALAW MVSRENSKEL PPFWEQRNDL YYNTITNFSE KDRPENVHGG ILADDMGLGK 300
TLTAIAVILT NFHDGRPLPI ERVKKNLLKK EYNVNDDSMK LGGNNTSEKA DGLSKDASRC 360
SEQPSISDIK EKSKFRMSEL SSSRPKRRKT AVQYIESSDS EEIETSELPQ KMKGKLKNVQ 420
SETKGRAKAG SSKVIEDVAF ACALTSSVPT TKKKMLKKGA CAVEGSKKTD VEERPRTTLI 480
ICPLSVLSNW IDQFGQHIKS DVHLNFYVYY GPDRIREPAL LSKQDIVLTT YNILTHDYGT 540
KGDSPLHSIR WLRVILDEGH AIRNPNAQQT KAVLDLESER RWVLTGTPIQ NSLKDLWSLL 600
SFLKLKPFID REWWHRTIQR PVTMGDEGGL RRLQSLIKNI TLRRTKTSKI KGKPVLELPE 660
RKVFIQHITL SDEERKIYQS VKNEGRATIG RYFNEGTVLA HYADVLGLLL RLRQICCHTY 720
LLTNAVSSNG PSGNDTPEEL RKKLIRKMKL ILSSGSDEEC AICLDSLTVP VITHCAHVFC 780
KPCICQVIQN EQPHAKCPLC RNDIHEDNLL ECPPEELARD SEKKSDMEWT SSSKINALMH 840
ALTDLRKKNP NIKSLVVSQF TTFLSLIEIP LKASGFVFTR LDGSMAQKKR VESIQCFQNT 900
EAGSPTIMLL SLKAGGVGLN LSAASRVFLM DPAWNPAAED QCFDRCHRLG QKQEVIITKF 960
IVKDSVEENM LKIQNKKREL AAGAFGTKKP NADEMKQAKI NEIRTLIDL 1009 
Gene Ontology
 GO:0005634; C:nucleus; IDA:HPA.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0016887; F:ATPase activity; IEA:Compara.
 GO:0003677; F:DNA binding; TAS:ProtInc.
 GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
 GO:0016874; F:ligase activity; IEA:UniProtKB-KW.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0016568; P:chromatin modification; IEA:UniProtKB-KW.
 GO:0016567; P:protein ubiquitination; IEA:UniProtKB-UniPathway.
 GO:0006357; P:regulation of transcription from RNA polymerase II promoter; IEA:Compara.
 GO:0006355; P:regulation of transcription, DNA-dependent; TAS:ProtInc.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR014905; HIP116_Rad5p_N.
 IPR027417; P-loop_NTPase.
 IPR000330; SNF2_N.
 IPR001841; Znf_RING.
 IPR013083; Znf_RING/FYVE/PHD.
 IPR017907; Znf_RING_CS. 
Pfam
 PF00271; Helicase_C
 PF08797; HIRAN
 PF00176; SNF2_N 
SMART
 SM00487; DEXDc
 SM00490; HELICc
 SM00910; HIRAN
 SM00184; RING 
PROSITE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER
 PS00518; ZF_RING_1
 PS50089; ZF_RING_2 
PRINTS