CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-019623
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 ATPase WRNIP1 
Protein Synonyms/Alias
 Werner helicase-interacting protein 1 
Gene Name
 WRNIP1 
Gene Synonyms/Alias
 WHIP 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
62HRAGERAKGPSPPGAubiquitination[1, 2]
70GPSPPGAKRRRLSESubiquitination[3, 4]
81LSESSALKQPATPTAsumoylation[5]
81LSESSALKQPATPTAubiquitination[6]
141PGRKGSGKRPAAAAAubiquitination[6]
225IRQMLQGKPLADTMRubiquitination[1, 2, 3, 4, 6, 7, 8, 9, 10]
244QDYFGQSKAVGQDTLubiquitination[4, 8, 10]
286HIIASNSKKHSIRFVubiquitination[1, 2, 3, 4, 6, 7, 8, 10]
287IIASNSKKHSIRFVTubiquitination[1, 2]
301TLSATNAKTNDVRDVubiquitination[1, 2, 3, 4, 6, 7, 8, 9, 10, 11]
310NDVRDVIKQAQNEKSubiquitination[1, 2, 3, 4, 6, 7, 10, 11]
316IKQAQNEKSFFKRKTubiquitination[1, 2, 6, 7]
322EKSFFKRKTILFIDEubiquitination[1, 6]
335DEIHRFNKSQQDTFLubiquitination[6]
464SRKMFCKKSGQSYSPubiquitination[4]
482LITENDVKEGLQRSHubiquitination[1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12]
508NCISALHKSMRGSDQubiquitination[1, 2, 4, 6, 7, 8, 9]
601YSAYNNVKACLRNHQubiquitination[1, 2, 4, 6, 7, 8, 9, 11]
627NAPTRLMKDLGYGKGubiquitination[1, 2, 3, 6, 7, 8, 9, 10]
633MKDLGYGKGYKYNPMacetylation[13, 14]
633MKDLGYGKGYKYNPMubiquitination[1, 2, 3, 4, 6, 7, 8, 9, 10, 11]
636LGYGKGYKYNPMYSEubiquitination[1, 2, 3, 6, 7, 8, 10, 11]
661LRGVDFFKQRRC***ubiquitination[1, 2, 3, 4, 6, 7, 8, 9, 10, 11]
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] 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]
 [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] Werner helicase-interacting protein 1 binds polyubiquitin via its zinc finger domain.
 Bish RA, Myers MP.
 J Biol Chem. 2007 Aug 10;282(32):23184-93. [PMID: 17550899]
 [6] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [10] 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]
 [11] 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]
 [12] 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]
 [13] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
 [14] 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
Functional Description
 Functions as a modulator for initiation or reinitiation events during DNA polymerase delta-mediated DNA synthesis. Has an intrinsic ATPase activity that functions as a sensor of DNA damage or of arrested replication forks and regulates the extent of DNA synthesis. 
Sequence Annotation
 ZN_FING 17 40 UBZ-type.
 NP_BIND 268 275 ATP (Potential).
 MOD_RES 75 75 Phosphoserine.
 MOD_RES 85 85 Phosphothreonine.
 MOD_RES 91 91 Phosphoserine.
 MOD_RES 92 92 Phosphoserine.
 MOD_RES 116 116 Phosphothreonine.
 MOD_RES 153 153 Phosphoserine.
 MOD_RES 534 534 Phosphotyrosine.
 MOD_RES 562 562 Phosphotyrosine.
 MOD_RES 633 633 N6-acetyllysine; alternate.
 CROSSLNK 81 81 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 141 141 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 225 225 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 301 301 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 310 310 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 316 316 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 322 322 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 335 335 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 482 482 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 627 627 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 633 633 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 636 636 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; Acetylation; Alternative splicing; ATP-binding; Complete proteome; DNA damage; DNA replication; Hydrolase; Isopeptide bond; Metal-binding; Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome; Ubl conjugation; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 665 AA 
Protein Sequence
MEVSGPEDDP FLSQLHQVQC PVCQQMMPAA HINSHLDRCL LLHPAGHAEP AAGSHRAGER 60
AKGPSPPGAK RRRLSESSAL KQPATPTAAE SSEGEGEEGD DGGETESRES YDAPPTPSGA 120
RLIPDFPVAR SSSPGRKGSG KRPAAAAAAG SASPRSWDEA EAQEEEEAVG DGDGDGDADA 180
DGEDDPGHWD ADAAEAATAF GASGGGRPHP RALAAEEIRQ MLQGKPLADT MRPDTLQDYF 240
GQSKAVGQDT LLRSLLETNE IPSLILWGPP GCGKTTLAHI IASNSKKHSI RFVTLSATNA 300
KTNDVRDVIK QAQNEKSFFK RKTILFIDEI HRFNKSQQDT FLPHVECGTI TLIGATTENP 360
SFQVNAALLS RCRVIVLEKL PVEAMVTILM RAINSLGIHV LDSSRPTDPL SHSSNSSSEP 420
AMFIEDKAVD TLAYLSDGDA RAGLNGLQLA VLARLSSRKM FCKKSGQSYS PSRVLITEND 480
VKEGLQRSHI LYDRAGEEHY NCISALHKSM RGSDQNASLY WLARMLEGGE DPLYVARRLV 540
RFASEDIGLA DPSALTQAVA AYQGCHFIGM PECEVLLAQC VVYFARAPKS IEVYSAYNNV 600
KACLRNHQGP LPPVPLHLRN APTRLMKDLG YGKGYKYNPM YSEPVDQEYL PEELRGVDFF 660
KQRRC 665 
Gene Ontology
 GO:0005739; C:mitochondrion; IDA:HPA.
 GO:0005634; C:nucleus; IDA:UniProtKB.
 GO:0048471; C:perinuclear region of cytoplasm; IDA:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0016887; F:ATPase activity; IMP:UniProtKB.
 GO:0003677; F:DNA binding; IEA:InterPro.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
 GO:0000731; P:DNA synthesis involved in DNA repair; IDA:UniProtKB.
 GO:0030174; P:regulation of DNA-dependent DNA replication initiation; IDA:UniProtKB. 
Interpro
 IPR003593; AAA+_ATPase.
 IPR003959; ATPase_AAA_core.
 IPR021886; MgsA_C.
 IPR027417; P-loop_NTPase.
 IPR006642; Znf_Rad18_put. 
Pfam
 PF00004; AAA
 PF12002; MgsA_C 
SMART
 SM00382; AAA
 SM00734; ZnF_Rad18 
PROSITE
 PS00674; AAA 
PRINTS