CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-013979
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 E3 ubiquitin-protein ligase UBR4 
Protein Synonyms/Alias
 600 kDa retinoblastoma protein-associated factor; N-recognin-4; Retinoblastoma-associated factor of 600 kDa; RBAF600; p600; Zinc finger UBR1-type protein 1 
Gene Name
 UBR4 
Gene Synonyms/Alias
 KIAA0462; KIAA1307; RBAF600; ZUBR1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
127EACAVSQKHLILLIKubiquitination[1]
174LSDVEDQKELASPVSubiquitination[2, 3]
187VSPELRQKEVQMNFLubiquitination[3]
234TDQASAIKTKNVFIAubiquitination[2, 4]
236QASAIKTKNVFIAQNubiquitination[1, 3, 4]
255QELGGSEKLLRVCLNubiquitination[3]
366RTGSTSSKEDDYESDubiquitination[1, 2, 3, 4]
436LADKGKEKDPLAALRubiquitination[3]
605TISPSKEKAAPPPPPubiquitination[2]
634SKQAPGEKGNILASRubiquitination[1, 3]
920EVEENWSKHFSSDAVubiquitination[3]
1079LELASTTKCSSVKYDubiquitination[1, 3, 5]
1084TTKCSSVKYDVEIVEacetylation[6]
1150AAETDPHKSSEITKNubiquitination[1, 2, 3, 4, 7]
1156HKSSEITKNLLPATLubiquitination[2]
1189NEEGTTEKPSKEKLQubiquitination[2]
1194TEKPSKEKLQGFAAVubiquitination[3]
1477RMTTSPPKDSDQLDVubiquitination[2, 3]
1574CKKYLSQKNVVEKLNubiquitination[2, 3]
1579SQKNVVEKLNANVMHubiquitination[3]
1741SGMSSTMKESAFQSEubiquitination[2, 8]
2210KTLPAKAKIQDMVAIubiquitination[3]
2502IIEKERNKNAAQELAubiquitination[3]
2543RSAYHSHKDQALLSKubiquitination[3]
2560QCLNTSSKEGKDLDPubiquitination[3]
2563NTSSKEGKDLDPEVFubiquitination[3]
2608TEGMDEGKEPQKQLEubiquitination[2]
2698PAVSFSCKQALIRVLubiquitination[3]
3126VATSQLLKPHTTSSPubiquitination[3]
3173RLPYQIKKITDTNSRubiquitination[3]
3405QLNKFADKETLIQFLubiquitination[8]
3464ELPAYGRKAAQFVDLubiquitination[1, 3]
3606VQAIVELKNKPARWHubiquitination[3]
3608AIVELKNKPARWHKAubiquitination[3]
3745NINTLLDKADRVYHQubiquitination[3]
3816NSFDELSKIIQKVFAubiquitination[3]
3826QKVFASRKELLEYDLubiquitination[3]
4035APTSKKNKDVPVEALubiquitination[8]
4100RHLYLTEKYVWRWKQubiquitination[3]
4106EKYVWRWKQFLSRRGubiquitination[3]
4122RTSPLDLKLGHNNWLubiquitination[1, 3, 8]
4215YVGNLITKEIARLLAubiquitination[2, 3, 8]
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] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
 Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048]
 [8] 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
Functional Description
 E3 ubiquitin-protein ligase which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. Together with clathrin, forms meshwork structures involved in membrane morphogenesis and cytoskeletal organization. Regulates integrin-mediated signaling. May play a role in activation of FAK in response to cell-matrix interactions. 
Sequence Annotation
 ZN_FING 1656 1729 UBR-type.
 MOD_RES 178 178 Phosphoserine.
 MOD_RES 181 181 Phosphoserine.
 MOD_RES 365 365 Phosphoserine (By similarity).
 MOD_RES 1084 1084 N6-acetyllysine.
 MOD_RES 1402 1402 Phosphoserine (By similarity).
 MOD_RES 1763 1763 Phosphoserine.
 MOD_RES 2715 2715 Phosphothreonine.
 MOD_RES 2719 2719 Phosphoserine.
 MOD_RES 2722 2722 Phosphoserine (By similarity).
 MOD_RES 2724 2724 Phosphothreonine (By similarity).  
Keyword
 Acetylation; Alternative splicing; Calmodulin-binding; Complete proteome; Cytoplasm; Cytoskeleton; Direct protein sequencing; Host-virus interaction; Ligase; Membrane; Metal-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Transmembrane; Transmembrane helix; Ubl conjugation pathway; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 5183 AA 
Protein Sequence
MATSGGEEAA AAAPAPGTPA TGADTTPGWE VAVRPLLSAS YSAFEMKELP QLVASVIESE 60
SEILHHEKQY EPFYSSFVAL STHYITTVCS LIPRNQLQSV AAACKVLIEF SLLRLENPDE 120
ACAVSQKHLI LLIKGLCTGC SRLDRTEIIT FTAMMKSAKL PQTVKTLSDV EDQKELASPV 180
SPELRQKEVQ MNFLNQLTSV FNPRTVASQP ISTQTLVEGE NDEQSSTDQA SAIKTKNVFI 240
AQNVASLQEL GGSEKLLRVC LNLPYFLRYI NRFQDAVLAN SFFIMPATVA DATAVRNGFH 300
SLVIDVTMAL DTLSLPVLEP LNPSRLQDVT VLSLSCLYAG VSVATCMAIL HVGSAQQVRT 360
GSTSSKEDDY ESDAATIVQK CLEIYDMIGQ AISSSRRAGG EHYQNFQLLG AWCLLNSLFL 420
ILNLSPTALA DKGKEKDPLA ALRVRDILSR TKEGVGSPKL GPGKGHQGFG VLSVILANHA 480
IKLLTSLFQD LQVEALHKGW ETDGPPAALS IMAQSTSIQR IQRLIDSVPL MNLLLTLLST 540
SYRKACVLQR QRKGSMSSDA SASTDSNTYY EDDFSSTEED SSQDDDSEPI LGQWFEETIS 600
PSKEKAAPPP PPPPPPLESS PRVKSPSKQA PGEKGNILAS RKDPELFLGL ASNILNFITS 660
SMLNSRNNFI RNYLSVSLSE HHMATLASII KEVDKDGLKG SSDEEFAAAL YHFNHSLVTS 720
DLQSPNLQNT LLQQLGVAPF SEGPWPLYIH PQSLSVLSRL LLIWQHKASA QGDPDVPECL 780
KVWDRFLSTM KQNALQGVVP SETEDLNVEH LQMLLLIFHN FTETGRRAIL SLFVQIIQEL 840
SVNMDAQMRF VPLILARLLL IFDYLLHQYS KAPVYLFEQV QHNLLSPPFG WASGSQDSNS 900
RRATTPLYHG FKEVEENWSK HFSSDAVPHP RFYCVLSPEA SEDDLNRLDS VACDVLFSKL 960
VKYDELYAAL TALLAAGSQL DTVRRKENKN VTALEACALQ YYFLILWRIL GILPPSKTYI 1020
NQLSMNSPEM SECDILHTLR WSSRLRISSY VNWIKDHLIK QGMKAEHASS LLELASTTKC 1080
SSVKYDVEIV EEYFARQISS FCSIDCTTIL QLHEIPSLQS IYTLDAAISK VQVSLDEHFS 1140
KMAAETDPHK SSEITKNLLP ATLQLIDTYA SFTRAYLLQN FNEEGTTEKP SKEKLQGFAA 1200
VLAIGSSRCK ANTLGPTLVQ NLPSSVQTVC ESWNNINTNE FPNIGSWRNA FANDTIPSES 1260
YISAVQAAHL GTLCSQSLPL AASLKHTLLS LVRLTGDLIV WSDEMNPPQV IRTLLPLLLE 1320
SSTESVAEIS SNSLERILGP AESDEFLARV YEKLITGCYN ILANHADPNS GLDESILEEC 1380
LQYLEKQLES SQARKAMEEF FSDSGELVQI MMATANENLS AKFCNRVLKF FTKLFQLTEK 1440
SPNPSLLHLC GSLAQLACVE PVRLQAWLTR MTTSPPKDSD QLDVIQENRQ LLQLLTTYIV 1500
RENSQVGEGV CAVLLGTLTP MATEMLANGD GTGFPELMVV MATLASAGQG AGHLQLHNAA 1560
VDWLSRCKKY LSQKNVVEKL NANVMHGKHV MILECTCHIM SYLADVTNAL SQSNGQGPSH 1620
LSVDGEERAI EVDSDWVEEL AVEEEDSQAE DSDEDSLCNK LCTFTITQKE FMNQHWYHCH 1680
TCKMVDGVGV CTVCAKVCHK DHEISYAKYG SFFCDCGAKE DGSCLALVKR TPSSGMSSTM 1740
KESAFQSEPR ISESLVRHAS TSSPADKAKV TISDGKVADE EKPKKSSLCR TVEGCREELQ 1800
NQANFSFAPL VLDMLNFLMD AIQTNFQQAS AVGSSSRAQQ ALSELHTVEK AVEMTDQLMV 1860
PTLGSQEGAF ENVRMNYSGD QGQTIRQLIS AHVLRRVAMC VLSSPHGRRQ HLAVSHEKGK 1920
ITVLQLSALL KQADSSKRKL TLTRLASAPV PFTVLSLTGN PCKEDYLAVC GLKDCHVLTF 1980
SSSGSVSDHL VLHPQLATGN FIIKAVWLPG SQTELAIVTA DFVKIYDLCV DALSPTFYFL 2040
LPSSKIRDVT FLFNEEGKNI IVIMSSAGYI YTQLMEEASS AQQGPFYVTN VLEINHEDLK 2100
DSNSQVAGGG VSVYYSHVLQ MLFFSYCQGK SFAATISRTT LEVLQLFPIN IKSSNGGSKT 2160
SPALCQWSEV MNHPGLVCCV QQTTGVPLVV MVKPDTFLIQ EIKTLPAKAK IQDMVAIRHT 2220
ACNEQQRTTM ILLCEDGSLR IYMANVENTS YWLQPSLQPS SVISIMKPVR KRKTATITTR 2280
TSSQVTFPID FFEHNQQLTD VEFGGNDLLQ VYNAQQIKHR LNSTGMYVAN TKPGGFTIEI 2340
SNNNSTMVMT GMRIQIGTQA IERAPSYIEI FGRTMQLNLS RSRWFDFPFT REEALQADKK 2400
LNLFIGASVD PAGVTMIDAV KIYGKTKEQF GWPDEPPEEF PSASVSNICP SNLNQSNGTG 2460
DSDSAAPTTT SGTVLERLVV SSLEALESCF AVGPIIEKER NKNAAQELAT LLLSLPAPAS 2520
VQQQSKSLLA SLHTSRSAYH SHKDQALLSK AVQCLNTSSK EGKDLDPEVF QRLVITARSI 2580
AIMRPNNLVH FTESKLPQME TEGMDEGKEP QKQLEGDCCS FITQLVNHFW KLHASKPKNA 2640
FLAPACLPGL THIEATVNAL VDIIHGYCTC ELDCINTASK IYMQMLLCPD PAVSFSCKQA 2700
LIRVLRPRNK RRHVTLPSSP RSNTPMGDKD DDDDDDADEK MQSSGIPNGG HIRQESQEQS 2760
EVDHGDFEMV SESMVLETAE NVNNGNPSPL EALLAGAEGF PPMLDIPPDA DDETMVELAI 2820
ALSLQQDQQG SSSSALGLQS LGLSGQAPSS SSLDAGTLSD TTASAPASDD EGSTAATDGS 2880
TLRTSPADHG GSVGSESGGS AVDSVAGEHS VSGRSSAYGD ATAEGHPAGP GSVSSSTGAI 2940
STTTGHQEGD GSEGEGEGET EGDVHTSNRL HMVRLMLLER LLQTLPQLRN VGGVRAIPYM 3000
QVILMLTTDL DGEDEKDKGA LDNLLSQLIA ELGMDKKDVS KKNERSALNE VHLVVMRLLS 3060
VFMSRTKSGS KSSICESSSL ISSATAAALL SSGAVDYCLH VLKSLLEYWK SQQNDEEPVA 3120
TSQLLKPHTT SSPPDMSPFF LRQYVKGHAA DVFEAYTQLL TEMVLRLPYQ IKKITDTNSR 3180
IPPPVFDHSW FYFLSEYLMI QQTPFVRRQV RKLLLFICGS KEKYRQLRDL HTLDSHVRGI 3240
KKLLEEQGIF LRASVVTASS GSALQYDTLI SLMEHLKACA EIAAQRTINW QKFCIKDDSV 3300
LYFLLQVSFL VDEGVSPVLL QLLSCALCGS KVLAALAASS GSSSASSSSA PVAASSGQAT 3360
TQSKSSTKKS KKEEKEKEKD GETSGSQEDQ LCTALVNQLN KFADKETLIQ FLRCFLLESN 3420
SSSVRWQAHC LTLHIYRNSS KSQQELLLDL MWSIWPELPA YGRKAAQFVD LLGYFSLKTP 3480
QTEKKLKEYS QKAVEILRTQ NHILTNHPNS NIYNTLSGLV EFDGYYLESD PCLVCNNPEV 3540
PFCYIKLSSI KVDTRYTTTQ QVVKLIGSHT ISKVTVKIGD LKRTKMVRTI NLYYNNRTVQ 3600
AIVELKNKPA RWHKAKKVQL TPGQTEVKID LPLPIVASNL MIEFADFYEN YQASTETLQC 3660
PRCSASVPAN PGVCGNCGEN VYQCHKCRSI NYDEKDPFLC NACGFCKYAR FDFMLYAKPC 3720
CAVDPIENEE DRKKAVSNIN TLLDKADRVY HQLMGHRPQL ENLLCKVNEA APEKPQDDSG 3780
TAGGISSTSA SVNRYILQLA QEYCGDCKNS FDELSKIIQK VFASRKELLE YDLQQREAAT 3840
KSSRTSVQPT FTASQYRALS VLGCGHTSST KCYGCASAVT EHCITLLRAL ATNPALRHIL 3900
VSQGLIRELF DYNLRRGAAA MREEVRQLMC LLTRDNPEAT QQMNDLIIGK VSTALKGHWA 3960
NPDLASSLQY EMLLLTDSIS KEDSCWELRL RCALSLFLMA VNIKTPVVVE NITLMCLRIL 4020
QKLIKPPAPT SKKNKDVPVE ALTTVKPYCN EIHAQAQLWL KRDPKASYDA WKKCLPIRGI 4080
DGNGKAPSKS ELRHLYLTEK YVWRWKQFLS RRGKRTSPLD LKLGHNNWLR QVLFTPATQA 4140
ARQAACTIVE ALATIPSRKQ QVLDLLTSYL DELSIAGECA AEYLALYQKL ITSAHWKVYL 4200
AARGVLPYVG NLITKEIARL LALEEATLST DLQQGYALKS LTGLLSSFVE VESIKRHFKS 4260
RLVGTVLNGY LCLRKLVVQR TKLIDETQDM LLEMLEDMTT GTESETKAFM AVCIETAKRY 4320
NLDDYRTPVF IFERLCSIIY PEENEVTEFF VTLEKDPQQE DFLQGRMPGN PYSSNEPGIG 4380
PLMRDIKNKI CQDCDLVALL EDDSGMELLV NNKIISLDLP VAEVYKKVWC TTNEGEPMRI 4440
VYRMRGLLGD ATEEFIESLD STTDEEEDEE EVYKMAGVMA QCGGLECMLN RLAGIRDFKQ 4500
GRHLLTVLLK LFSYCVKVKV NRQQLVKLEM NTLNVMLGTL NLALVAEQES KDSGGAAVAE 4560
QVLSIMEIIL DESNAEPLSE DKGNLLLTGD KDQLVMLLDQ INSTFVRSNP SVLQGLLRII 4620
PYLSFGEVEK MQILVERFKP YCNFDKYDED HSGDDKVFLD CFCKIAAGIK NNSNGHQLKD 4680
LILQKGITQN ALDYMKKHIP SAKNLDADIW KKFLSRPALP FILRLLRGLA IQHPGTQVLI 4740
GTDSIPNLHK LEQVSSDEGI GTLAENLLEA LREHPDVNKK IDAARRETRA EKKRMAMAMR 4800
QKALGTLGMT TNEKGQVVTK TALLKQMEEL IEEPGLTCCI CREGYKFQPT KVLGIYTFTK 4860
RVALEEMENK PRKQQGYSTV SHFNIVHYDC HLAAVRLARG REEWESAALQ NANTKCNGLL 4920
PVWGPHVPES AFATCLARHN TYLQECTGQR EPTYQLNIHD IKLLFLRFAM EQSFSADTGG 4980
GGRESNIHLI PYIIHTVLYV LNTTRATSRE EKNLQGFLEQ PKEKWVESAF EVDGPYYFTV 5040
LALHILPPEQ WRATRVEILR RLLVTSQARA VAPGGATRLT DKAVKDYSAY RSSLLFWALV 5100
DLIYNMFKKV PTSNTEGGWS CSLAEYIRHN DMPIYEAADK ALKTFQEEFM PVETFSEFLD 5160
VAGLLSEITD PESFLKDLLN SVP 5183 
Gene Ontology
 GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
 GO:0005856; C:cytoskeleton; IEA:UniProtKB-SubCell.
 GO:0016021; C:integral to membrane; IEA:UniProtKB-KW.
 GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
 GO:0004842; F:ubiquitin-protein ligase activity; IEA:InterPro.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0019048; P:virus-host interaction; IEA:UniProtKB-KW. 
Interpro
 IPR025704; E3_Ub_ligase_UBR4.
 IPR003126; Znf_N-recognin. 
Pfam
 PF13764; E3_UbLigase_R4
 PF02207; zf-UBR 
SMART
  
PROSITE
 PS51157; ZF_UBR 
PRINTS