CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-008206
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 E3 SUMO-protein ligase RanBP2 
Protein Synonyms/Alias
 358 kDa nucleoporin; Nuclear pore complex protein Nup358; Nucleoporin Nup358; Ran-binding protein 2; RanBP2; p270; Putative peptidyl-prolyl cis-trans isomerase; PPIase; Rotamase 
Gene Name
 RANBP2 
Gene Synonyms/Alias
 NUP358 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
34MKGFYFAKLYYEAKEubiquitination[1]
40AKLYYEAKEYDLAKKubiquitination[1]
94VELNPTQKDLVLKIAubiquitination[1, 2]
115DVTDGRAKYWLERAAacetylation[3]
115DVTDGRAKYWLERAAubiquitination[4, 5]
123YWLERAAKLFPGSPAubiquitination[6, 7]
365LLNLSRGKQDFLKEIubiquitination[4]
370RGKQDFLKEIVETFAubiquitination[4]
379IVETFANKSGQSALYubiquitination[1, 2, 4, 5, 8]
542VCTLIHRKAVPGNVAubiquitination[4]
614KKVLPLLKIIKKKNSubiquitination[6, 7]
733DSNLSVVKKLPVPLEubiquitination[2]
764SEGGPLYKNGSLRNAubiquitination[8]
776RNADSEIKHSTPSPTubiquitination[4, 5]
791RYSLSPSKSYKYSPKubiquitination[4]
822CQQVEAIKKEMQELKubiquitination[4]
823QQVEAIKKEMQELKLubiquitination[4]
997ASRSAESKTIEFGKTubiquitination[4]
1220ERGIGNVKILRHKTSacetylation[5]
1220ERGIGNVKILRHKTSubiquitination[4]
1842SQVGTGFKSNFSEKAubiquitination[2]
1963GEGFQFGKKDPNFKGubiquitination[4]
1964EGFQFGKKDPNFKGFubiquitination[4]
1977GFSGAGEKLFSSQYGubiquitination[9]
2061ERGLGNLKILKNEVNubiquitination[6, 7, 9, 10]
2125KLEQLAAKFKTPELAubiquitination[1, 4, 6, 7, 9]
2136PELAEEFKQKFEECQubiquitination[1]
2156IPLQTPHKLVDTGRAubiquitination[10]
2181KSGLKDFKTFLTNDQubiquitination[6, 7]
2190FLTNDQTKVTEEENKubiquitination[1]
2358ERGIGDIKILQNYDNubiquitination[6, 7, 9]
2396DMTLQNMKGTERVWLubiquitination[4, 5, 6, 7]
2424EHLAVRFKLQDVADSubiquitination[6, 7, 9]
2522VFGSESVKSIFSSEKubiquitination[6, 7]
2529KSIFSSEKSKPFAFGubiquitination[10]
2571AQSGSESKVEPKKCEsumoylation[11]
2571AQSGSESKVEPKKCEubiquitination[1]
2592IEQSSDSKVKNLFASsumoylation[11]
2594QSSDSKVKNLFASFPsumoylation[11]
2935EDEEILFKERAKLYRubiquitination[1, 2, 4, 5, 10, 12]
2959ERGVGDIKILWHTMKubiquitination[4, 5, 6, 7, 9]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [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] 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]
 [11] Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif.
 Matic I, Schimmel J, Hendriks IA, van Santen MA, van de Rijke F, van Dam H, Gnad F, Mann M, Vertegaal AC.
 Mol Cell. 2010 Aug 27;39(4):641-52. [PMID: 20797634]
 [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
Functional Description
 E3 SUMO-protein ligase which facilitates SUMO1 and SUMO2 conjugation by UBE2I. Involved in transport factor (Ran-GTP, karyopherin)-mediated protein import via the F-G repeat-containing domain which acts as a docking site for substrates. Could also have isomerase or chaperone activity and may bind RNA or DNA. Component of the nuclear export pathway. Specific docking site for the nuclear export factor exportin-1. Sumoylates PML at 'Lys-490' which is essential for the proper assembly of PML-NB. 
Sequence Annotation
 REPEAT 60 93 TPR.
 DOMAIN 1171 1307 RanBD1 1.
 DOMAIN 2012 2148 RanBD1 2.
 DOMAIN 2309 2445 RanBD1 3.
 REPEAT 2633 2685 1.
 REPEAT 2711 2761 2.
 DOMAIN 2911 3046 RanBD1 4.
 DOMAIN 3067 3223 PPIase cyclophilin-type.
 ZN_FING 1351 1381 RanBP2-type 1.
 ZN_FING 1415 1444 RanBP2-type 2.
 ZN_FING 1479 1508 RanBP2-type 3.
 ZN_FING 1543 1572 RanBP2-type 4.
 ZN_FING 1606 1635 RanBP2-type 5.
 ZN_FING 1665 1694 RanBP2-type 6.
 ZN_FING 1724 1753 RanBP2-type 7.
 ZN_FING 1781 1810 RanBP2-type 8.
 REGION 2631 2635 Interaction with sumoylated RANGAP1.
 REGION 2633 2761 2 X 50 AA approximate repeats.
 REGION 2633 2710 Required for E3 SUMO-ligase activity.
 REGION 2633 2685 Interaction with UBE2I.
 REGION 2686 2761 Interaction with SUMO1.
 MOD_RES 19 19 Phosphothreonine.
 MOD_RES 21 21 Phosphoserine.
 MOD_RES 781 781 Phosphoserine.
 MOD_RES 788 788 Phosphoserine (By similarity).
 MOD_RES 837 837 Phosphoserine.
 MOD_RES 948 948 Phosphoserine.
 MOD_RES 955 955 Phosphoserine.
 MOD_RES 1107 1107 Phosphoserine.
 MOD_RES 1110 1110 Phosphoserine.
 MOD_RES 1144 1144 Phosphothreonine.
 MOD_RES 1160 1160 Phosphoserine.
 MOD_RES 1396 1396 Phosphothreonine.
 MOD_RES 1412 1412 Phosphothreonine.
 MOD_RES 1443 1443 Phosphoserine.
 MOD_RES 1456 1456 Phosphoserine.
 MOD_RES 1509 1509 Phosphoserine.
 MOD_RES 1573 1573 Phosphoserine.
 MOD_RES 1835 1835 Phosphoserine.
 MOD_RES 1869 1869 Phosphoserine.
 MOD_RES 1871 1871 Phosphoserine.
 MOD_RES 2246 2246 Phosphoserine (By similarity).
 MOD_RES 2251 2251 Phosphoserine (By similarity).
 MOD_RES 2270 2270 Phosphoserine.
 MOD_RES 2276 2276 Phosphoserine (By similarity).
 MOD_RES 2280 2280 Phosphoserine (By similarity).
 MOD_RES 2293 2293 Phosphothreonine (By similarity).
 MOD_RES 2297 2297 Phosphoserine (By similarity).
 MOD_RES 2613 2613 Phosphothreonine.
 MOD_RES 2668 2668 Phosphoserine.
 MOD_RES 2741 2741 Phosphoserine.
 MOD_RES 2743 2743 Phosphothreonine.
 MOD_RES 2900 2900 Phosphoserine.
 MOD_RES 3207 3207 Phosphoserine.
 CROSSLNK 2592 2592 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; Complete proteome; Isomerase; Isopeptide bond; Ligase; Membrane; Metal-binding; mRNA transport; Nuclear pore complex; Nucleus; Phosphoprotein; Polymorphism; Protein transport; Reference proteome; Repeat; Rotamase; TPR repeat; Translocation; Transport; Ubl conjugation; Ubl conjugation pathway; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 3224 AA 
Protein Sequence
MRRSKADVER YIASVQGSTP SPRQKSMKGF YFAKLYYEAK EYDLAKKYIC TYINVQERDP 60
KAHRFLGLLY ELEENTDKAV ECYRRSVELN PTQKDLVLKI AELLCKNDVT DGRAKYWLER 120
AAKLFPGSPA IYKLKEQLLD CEGEDGWNKL FDLIQSELYV RPDDVHVNIR LVEVYRSTKR 180
LKDAVAHCHE AERNIALRSS LEWNSCVVQT LKEYLESLQC LESDKSDWRA TNTDLLLAYA 240
NLMLLTLSTR DVQESRELLQ SFDSALQSVK SLGGNDELSA TFLEMKGHFY MHAGSLLLKM 300
GQHSSNVQWR ALSELAALCY LIAFQVPRPK IKLIKGEAGQ NLLEMMACDR LSQSGHMLLN 360
LSRGKQDFLK EIVETFANKS GQSALYDALF SSQSPKDTSF LGSDDIGNID VREPELEDLT 420
RYDVGAIRAH NGSLQHLTWL GLQWNSLPAL PGIRKWLKQL FHHLPHETSR LETNAPESIC 480
ILDLEVFLLG VVYTSHLQLK EKCNSHHSSY QPLCLPLPVC KQLCTERQKS WWDAVCTLIH 540
RKAVPGNVAK LRLLVQHEIN TLRAQEKHGL QPALLVHWAE CLQKTGSGLN SFYDQREYIG 600
RSVHYWKKVL PLLKIIKKKN SIPEPIDPLF KHFHSVDIQA SEIVEYEEDA HITFAILDAV 660
NGNIEDAVTA FESIKSVVSY WNLALIFHRK AEDIENDALS PEEQEECKNY LRKTRDYLIK 720
IIDDSDSNLS VVKKLPVPLE SVKEMLNSVM QELEDYSEGG PLYKNGSLRN ADSEIKHSTP 780
SPTRYSLSPS KSYKYSPKTP PRWAEDQNSL LKMICQQVEA IKKEMQELKL NSSNSASPHR 840
WPTENYGPDS VPDGYQGSQT FHGAPLTVAT TGPSVYYSQS PAYNSQYLLR PAANVTPTKG 900
PVYGMNRLPP QQHIYAYPQQ MHTPPVQSSS ACMFSQEMYG PPALRFESPA TGILSPRGDD 960
YFNYNVQQTS TNPPLPEPGY FTKPPIAAHA SRSAESKTIE FGKTNFVQPM PGEGLRPSLP 1020
TQAHTTQPTP FKFNSNFKSN DGDFTFSSPQ VVTQPPPAAY SNSESLLGLL TSDKPLQGDG 1080
YSGAKPIPGG QTIGPRNTFN FGSKNVSGIS FTENMGSSQQ KNSGFRRSDD MFTFHGPGKS 1140
VFGTPTLETA NKNHETDGGS AHGDDDDDGP HFEPVVPLPD KIEVKTGEED EEEFFCNRAK 1200
LFRFDVESKE WKERGIGNVK ILRHKTSGKI RLLMRREQVL KICANHYISP DMKLTPNAGS 1260
DRSFVWHALD YADELPKPEQ LAIRFKTPEE AALFKCKFEE AQSILKAPGT NVAMASNQAV 1320
RIVKEPTSHD NKDICKSDAG NLNFEFQVAK KEGSWWHCNS CSLKNASTAK KCVSCQNLNP 1380
SNKELVGPPL AETVFTPKTS PENVQDRFAL VTPKKEGHWD CSICLVRNEP TVSRCIACQN 1440
TKSANKSGSS FVHQASFKFG QGDLPKPINS DFRSVFSTKE GQWDCSACLV QNEGSSTKCA 1500
ACQNPRKQSL PATSIPTPAS FKFGTSETSK TLKSGFEDMF AKKEGQWDCS SCLVRNEANA 1560
TRCVACQNPD KPSPSTSVPA PASFKFGTSE TSKAPKSGFE GMFTKKEGQW DCSVCLVRNE 1620
ASATKCIACQ NPGKQNQTTS AVSTPASSET SKAPKSGFEG MFTKKEGQWD CSVCLVRNEA 1680
SATKCIACQN PGKQNQTTSA VSTPASSETS KAPKSGFEGM FTKKEGQWDC SVCLVRNEAS 1740
ATKCIACQCP SKQNQTTAIS TPASSEISKA PKSGFEGMFI RKGQWDCSVC CVQNESSSLK 1800
CVACDASKPT HKPIAEAPSA FTLGSEMKLH DSSGSQVGTG FKSNFSEKAS KFGNTEQGFK 1860
FGHVDQENSP SFMFQGSSNT EFKSTKEGFS IPVSADGFKF GISEPGNQEK KSEKPLENGT 1920
GFQAQDISGQ KNGRGVIFGQ TSSTFTFADL AKSTSGEGFQ FGKKDPNFKG FSGAGEKLFS 1980
SQYGKMANKA NTSGDFEKDD DAYKTEDSDD IHFEPVVQMP EKVELVTGEE DEKVLYSQRV 2040
KLFRFDAEVS QWKERGLGNL KILKNEVNGK LRMLMRREQV LKVCANHWIT TTMNLKPLSG 2100
SDRAWMWLAS DFSDGDAKLE QLAAKFKTPE LAEEFKQKFE ECQRLLLDIP LQTPHKLVDT 2160
GRAAKLIQRA EEMKSGLKDF KTFLTNDQTK VTEEENKGSG TGAAGASDTT IKPNPENTGP 2220
TLEWDNYDLR EDALDDSVSS SSVHASPLAS SPVRKNLFRF GESTTGFNFS FKSALSPSKS 2280
PAKLNQSGTS VGTDEESDVT QEEERDGQYF EPVVPLPDLV EVSSGEENEQ VVFSHRAKLY 2340
RYDKDVGQWK ERGIGDIKIL QNYDNKQVRI VMRRDQVLKL CANHRITPDM TLQNMKGTER 2400
VWLWTACDFA DGERKVEHLA VRFKLQDVAD SFKKIFDEAK TAQEKDSLIT PHVSRSSTPR 2460
ESPCGKIAVA VLEETTRERT DVIQGDDVAD ATSEVEVSST SETTPKAVVS PPKFVFGSES 2520
VKSIFSSEKS KPFAFGNSSA TGSLFGFSFN APLKSNNSET SSVAQSGSES KVEPKKCELS 2580
KNSDIEQSSD SKVKNLFASF PTEESSINYT FKTPEKAKEK KKPEDSPSDD DVLIVYELTP 2640
TAEQKALATK LKLPPTFFCY KNRPDYVSEE EEDDEDFETA VKKLNGKLYL DGSEKCRPLE 2700
ENTADNEKEC IIVWEKKPTV EEKAKADTLK LPPTFFCGVC SDTDEDNGNG EDFQSELQKV 2760
QEAQKSQTEE ITSTTDSVYT GGTEVMVPSF CKSEEPDSIT KSISSPSVSS ETMDKPVDLS 2820
TRKEIDTDST SQGESKIVSF GFGSSTGLSF ADLASSNSGD FAFGSKDKNF QWANTGAAVF 2880
GTQSVGTQSA GKVGEDEDGS DEEVVHNEDI HFEPIVSLPE VEVKSGEEDE EILFKERAKL 2940
YRWDRDVSQW KERGVGDIKI LWHTMKNYYR ILMRRDQVFK VCANHVITKT MELKPLNVSN 3000
NALVWTASDY ADGEAKVEQL AVRFKTKEVA DCFKKTFEEC QQNLMKLQKG HVSLAAELSK 3060
ETNPVVFFDV CADGEPLGRI TMELFSNIVP RTAENFRALC TGEKGFGFKN SIFHRVIPDF 3120
VCQGGDITKH DGTGGQSIYG DKFEDENFDV KHTGPGLLSM ANQGQNTNNS QFVITLKKAE 3180
HLDFKHVVFG FVKDGMDTVK KIESFGSPKG SVCRRITITE CGQI 3224 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0042405; C:nuclear inclusion body; IDA:UniProtKB.
 GO:0031965; C:nuclear membrane; IDA:UniProtKB.
 GO:0044615; C:nuclear pore nuclear basket; IDA:UniProtKB.
 GO:0016874; F:ligase activity; IEA:UniProtKB-KW.
 GO:0003755; F:peptidyl-prolyl cis-trans isomerase activity; IEA:UniProtKB-KW.
 GO:0008536; F:Ran GTPase binding; TAS:ProtInc.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0005975; P:carbohydrate metabolic process; TAS:Reactome.
 GO:0019221; P:cytokine-mediated signaling pathway; TAS:Reactome.
 GO:0015758; P:glucose transport; TAS:Reactome.
 GO:0000278; P:mitotic cell cycle; TAS:Reactome.
 GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
 GO:0006457; P:protein folding; IEA:UniProtKB-KW.
 GO:0006606; P:protein import into nucleus; TAS:ProtInc.
 GO:0000413; P:protein peptidyl-prolyl isomerization; IEA:GOC.
 GO:0016925; P:protein sumoylation; IDA:UniProtKB.
 GO:0010827; P:regulation of glucose transport; TAS:Reactome.
 GO:0044281; P:small molecule metabolic process; TAS:Reactome.
 GO:0055085; P:transmembrane transport; TAS:Reactome.
 GO:0022415; P:viral reproductive process; TAS:Reactome. 
Interpro
 IPR002130; Cyclophilin-like_PPIase_dom.
 IPR020892; Cyclophilin-type_PPIase_CS.
 IPR022011; IR1-M.
 IPR011993; PH_like_dom.
 IPR000156; Ran_bind_dom.
 IPR001440; TPR-1.
 IPR013026; TPR-contain_dom.
 IPR011990; TPR-like_helical.
 IPR019734; TPR_repeat.
 IPR001876; Znf_RanBP2. 
Pfam
 PF12185; IR1-M
 PF00160; Pro_isomerase
 PF00638; Ran_BP1
 PF00515; TPR_1
 PF00641; zf-RanBP 
SMART
 SM00160; RanBD
 SM00547; ZnF_RBZ 
PROSITE
 PS00170; CSA_PPIASE_1
 PS50072; CSA_PPIASE_2
 PS50196; RANBD1
 PS50005; TPR
 PS50293; TPR_REGION
 PS01358; ZF_RANBP2_1
 PS50199; ZF_RANBP2_2 
PRINTS
 PR00153; CSAPPISMRASE.