STRUCTURE OF A UBIQUITIN-LOADED HECT LIGASE REVEALS THE MOLECULAR BASIS FOR CATALYTIC PRIMING SUPPLEMENTARY INFORMATION

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1 STRUCTURE OF A UBIQUITINLOADED ECT LIGASE REVEALS TE MOLECULAR BASIS FOR CATALYTIC PRIMING Elena Maspero 1, Eleonora Valentini 1, Sara Mari 1, Valentina Cecatiello 2, Paolo Soffientini 1, Sebastiano Pasqualato 2 and Simona Polo 1,3 1 Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy. 2 Crystallography Unit, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy 3 Dipartimento di Scienze della Salute, Universita degli Studi di Milano, Milan, Italy. SUPPLEMENTARY INFORMATION Short title: E3iquitin Thioester Intermediate Structure

2 a b R74 c P P 7 7N 7N ut ST T 707A627AC62 C62 C62 p In G W F C Δ Δ IΔ R74 G G G76 C867 C867 E3 Thioester Bond E3 IB: Disulfide Bond time (h): ECT~ECT C76 d A280nm ECT~ ECT %B ECT~ ECT coomassie Elution volume (ml) fractions: D3 D2 D1 E1 E2 E4 E6 E8 E10 E11E12F12 F11 C lobe C lobe Cys76 C Cys867 D Cys627 Ile626 Asn627 Asn Glu629 C lobe g f D C lobe N 200 ECT~ e 10 Leu626 Pro628 Ser777 Cys778

3 Supplementary Figure 1 Preparation of ECT Nedd4 ~ D : complex. (a) Schematic drawings of the disulfide bond present in the crystal structure and the naturally occurring thioester bond. NMR studies have shown that the disulfide bond nicely mimics the native thioester bond, most likely thanks to the flexibility of Gly76 in the thioester, able to compensate for the extra bond length distance present in the SS bridge 1. (b) To favor the catalytic Cys867 for disulfide bond formation with G76C the two other ECT cysteine residues (Cys627 and Cys778) were either deleted or mutated. Mutants were tested for their ability to bind by GST pulldown assay. The indicated GSTfusion proteins were incubated for 2 hr at 4 C in YY buffer ( mm NaEPES p 7.5, 1 mm NaCl, 1 mm EDTA, 1 mm EGTA, 10% glycerol, 1% triton X100) with synthetic K63poly chains and analyzed by IB as indicated. Cys627 mutation/deletion showed impairment in the binding ability. We thus decided to substitute the residues surrounding this cysteine with the ones of Nedd4 budding yeast counterpart, Rsp5, which naturally doesn t possess it (Supplementary Figure 3), generating the ECT I CNP mutant that behaves as wildtype ECT. Coomassie staining shows comparable loading of GST proteins. (c) Disulfide bond formation between ECT I CNP and G76C was monitored using nonreducing SDSPAGE. At 48h the reaction was stopped due to monomer depletion. (d) Chromatogram from anionic exchange, showing separation of ECT I CNP ~ from ECT I CNP dimer, monomer and dimer. Lower panel shows fractions from the peak containing ECT I CNP ~, loaded on nonreducing SDSPAGE. Fractions from E1 to E11 were collected and concentrated for crystallization studies. (e) Comparison between ECT Nedd4 ~ D : and ECT Nedd4 :. Cartoon representation of the superposition of ECT Nedd4 ~ D : with ECT Nedd4 : (pdb 2xbb). The structures have been superposed through their Nlobe domains. ECT Nedd4 ~ D : is represented in the same colors as in Figure 1. The N and Clobe of ECT Nedd4 : are in dark blue and light green, respectively, whilst is in brown. (f) Same as right panel of e, but the Clobes and D are not shown, to permit a clearer view of the Nlobes and superposition. The Nlobe adopts the same conformation in the presence or absence of D (rootmeansquare deviation of 0.8 Å over 8 C ) with free kept in the binding site crafted by the Nlobe subdomains. (g) Insets display in ballandstick representation the sequences that have been mutated to generate the ECT Nedd4 ~ D : complex. Top panel highlights the three residues stretch (IleGlnPro) introduced at the place of the wild type four residues sequence (LeuCysGlnGlu) around Cys627. Bottom panel shows the Cys778 to Ser mutation.

4 a b ECTNedd4: time (sec): 120 WT Y616D Y616A Clobe D coomassie ECTNedd4: time (sec): 120 Nlobe E3~ WT R832G R832A C76 T830 C867 L841 L779 R832 E774 K598 M M835 N615 P834 Y616 Y Y610 c coomassie ECTNedd4: Y616A Y616D WT R832A R832G e2d3: time (sec): Y842 E3~ IB: coomassie Supplementary Figure 2 The Tyrlocked conformation of ECTNedd4~D: complex. (a) Details of the interactions at the interface between the ECT Clobe (green) and Nlobe (blue). Residues buried or participating at the interface are drawn in ballandstick representation and labeled. ydrogen bonds are highlighted with red dashed lines. (b) E2toECTNedd4 transthiolation assay. Upper panel, streptavidin blot. Thioester ECT~ is indicated. Lower panel, Coomassie stainig showing comparable loading of the different ECT mutants tested. (c) chain formation assay. Upper panel, kinetics of free chains formation with wildtype ECT and the indicated mutants. Lower panel, Coomassie staining showing comparable loading of proteins. Point mutations of Tyr616 to Asp or of Arg832 to Glu impair chain formation as a consequence of compromised E2 to E3 transfer. Tyr616 to Ala mutant shows reduced transthiolation, but unaffected chain formation. Less drastic mutations of Arg832 in Ala or in Gly are capable of transthiolation at the same extent of the Y616A mutant, show significantly reduced kinetic of chain formation and processivity. Nature Structural & Molecular Biology: doi: /nsmb.66

5 a snedd4_p46934 snedd4like_q69pu5 ScRsp5_P39940 sitch_q96j02 ssmurf1_q9ce7 ssmurf2_q9au4 swwp1_q90m0 swwp2_o00308 secw1_q76n89 secw2_q9p2p RDYKRKYEFFRRKLKKQNDIPNKFEMKLRRATVLEDSYRRIMGVKRADFLKARLWIEFDGEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQINPNSGLC REFKQKYDYFRKKLKKPADIPNRFEMKLRNNIFEESYRRIMSVKRPDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNSGLC RDFRRKVIYFRSQPALRILPGQCIKVRRKNIFEDAYQEIMRQTPEDLKKRLMIKFDGEEGLDYGGVSREFFFLLSEMFNPFYCLFEYSAYDNYTIQINPNSGI RDFKAKVQYFRFWCQQLAMPQIKITVTRKTLFEDSFQQIMSFSPQDLRRRLWVIFPGEEGLDYGGVAREWFFLLSEVLNPMYCLFEYAGKDNYCLQINPASYI RDLVQKLKVLRELSLQQPQAGCRIEVSREEIFEESYRQIMKMRPKDLKKRLMVKFRGEEGLDYGGVAREWLYLLCEMLNPYYGLFQYSTDNIYMLQINPDSSI RDLVQKLKILRQELSQQQPQAGCRIEVSREEIFEESYRQVMKMRPKDLWKRLMIKFRGEEGLDYGGVAREWLYLLSEMLNPYYGLFQYSRDDIYTLQINPDSAV RGFRWKLAFRYLCQSNALPSVKINVSRQTLFEDSFQQIMALKPYDLRRRLYVIFRGEEGLDYGGLAREWFFLLSEVLNPMYCLFEYAGKNNYCLQINPASTI RSFRWKYQFRFLCSNALPSVKISVSRQTLFEDSFQQIMNMKPYDLRRRLYIIMRGEEGLDYGGIAREWFFLLSEVLNPMYCLFEYAGKNNYCLQINPASSI RDFEAKLRNFYRKLEAKGFGQGPGKIKLIIRRDLLEGTFNQVMAYSRKELQRNKLYVTFVGEEGLDYSGPSREFFFLLSQELFNPYYGLFEYSANDTYTVQISPMSAF RDFEAKLRNFYRKLETKGYGQGPGKLKLIIRRDLLEDAFNQIMGYSRKDLQRNKLYVTFVGEEGLDYSGPSREFFFLVSRELFNPYYGLFEYSANDTYTVQISPMSAF snedd4_p46934 snedd4like_q69pu5 ScRsp5_P39940 sitch_q96j02 ssmurf1_q9ce7 ssmurf2_q9au4 swwp1_q90m0 swwp2_o00308 secw1_q76n89 secw2_q9p2p5 NEDLSYFKFIGRVAGMAVYGKLLDGFFIRPFYKMMLKPITLDMESVDSEYYNSLRWILENDPTELDLRFIIDEELFGQTQELKNGGSEIVVTNKNKKEYIYL NEDLSYFTFIGRVAGLAVFGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILENDPTELDLMFCIDEENFGQTYQVDLKPNGSEIMVTNENKREYIDL NPELNYFKFIGRVVGLGVFRRFLDAFFVGALYKMMLRKKVVLQDMEGVDAEVYNSLNWMLENSIDGVLDLTFSADDERFGEVVTVDLKPDGRNIEVTDGNKKEYVEL NPDLKYFRFIGRFIAMALFGKFIDTGFSLPFYKRILNKPVGLKDLESIDPEFYNSLIWVKENNIEECDLEMYFSVDKEILGEIKSDLKPNGGNILVTEENKEEYIRM NPDLSYFFVGRIMGLAVFGYINGGFTVPFYKQLLGKPIQLSDLESVDPELKSLVWILENDITPVLDTFCVENAFGRILQELKPNGRNVPVTEENKKEYVRL NPELSYFFVGRIMGMAVFGYIDGGFTLPFYKQLLGKSITLDDMELVDPDLNSLVWILENDITGVLDTFCVENAYGEIIQELKPNGKSIPVNEENKKEYVRL NPDLSYFCFIGRFIAMALFGKFIDTGFSLPFYKRMLSKKLTIKDLESIDTEFYNSLIWIRDNNIEECGLEMYFSVDMEILGKVTSDLKLGGSNILVTEENKDEYIGL NPDLTYFRFIGRFIAMALYGKFIDTGFTLPFYKRMLNKRPTLKDLESIDPEFYNSIVWIKENNLEECGLELYFIQDMEILGKVTTELKEGGESIRVTEENKEEYIML VENLEWFRFSGRILGLALIQYLLDAFFTRPFYKALLRLPCDLSDLEYLDEEFQSLQWMKDNNITDILDLTFTVNEEVFGQVTERELKSGGANTQVTEKNKKEYIER VDNEWFRFSGRILGLALIQYLLDAFFTRPFYKALLRILCDLSDLEYLDEEFQSLQWMKDNDIDILDLTFTVNEEVFGQITERELKPGGANIPVTEKNKKEYIER snedd4_p46934 snedd4like_q69pu5 ScRsp5_P39940 sitch_q96j02 ssmurf1_q9ce7 ssmurf2_q9au4 swwp1_q90m0 swwp2_o00308 secw1_q76n89 secw2_q9p2p VIQWRFVNRIQKQMAAFKEGFFELIPQDLIKIFDENELELLMCGLGDVDVNDWRETKYKNGYSANQVIQWFWKAVLMMDSEKRIRLLQFVTGTSRVPMNGFAELYGSN VIQWRFVNRVQKQMNAFLEGFTELLPIDLIKIFDENELELLMCGLGDVDVNDWRQSIYKNGYCPNPVIQWFWKAVLLMDAEKRIRLLQFVTGTSRVPMNGFAELYGSN YTQWRIVDRVQEQFKAFMDGFNELIPEDLVTVFDERELELLIGGIAEIDIEDWKKTDYRGYQESDEVIQWFWKCVSEWDNEQRARLLQFTTGTSRIPVNGFKDLQGSD VAEWRLSRGVEEQTQAFFEGFNEILPQQYLQYFDAKELEVLLCGMQEIDLNDWQRAIYRYARTSKQIMWFWQFVKEIDNEKRMRLLQFVTGTCRLPVGGFADLMGSN YVNWRFMRGIEAQFLALQKGFNELIPQLLKPFDQKELELIIGGLDKIDLNDWKSNTRLKCVADSNIVRWFWQAVETFDEERRARLLQFVTGSTRVPLQGFKALQGST YVNWRFLRGIEAQFLALQKGFNEVIPQLLKTFDEKELELIICGLGKIDVNDWKVNTRLKCTPDSNIVKWFWKAVEFFDEERRARLLQFVTGSSRVPLQGFKALQGAA MTEWRFSRGVQEQTKAFLDGFNEVVPLQWLQYFDEKELEVMLCGMQEVDLADWQRNTVYRYTRNSKQIIWFWQFVKETDNEVRMRLLQFVTGTCRLPLGGFAELMGSN LTDWRFTRGVEEQTKAFLDGFNEVAPLEWLRYFDEKELELMLCGMQEIDMSDWQKSTIYRYTKNSKQIQWFWQVVKEMDNEKRIRLLQFVTGTCRLPVGGFAELIGSN MVKWRVERGVVQQTEALVRGFYEVVDSRLVSVFDARELELVIAGTAEIDLNDWRNNTEYRGGYDGLVIRWFWAAVERFNNEQRLRLLQFVTGTSSVPYEGFAALRGSN MVKWRIERGVVQQTESLVRGFYEVVDARLVSVFDARELELVIAGTAEIDLSDWRNNTEYRGGYDNIVIRWFWAAVERFNNEQRLRLLQFVTGTSSIPYEGFASLRGSN snedd4_p46934 snedd4like_q69pu5 ScRsp5_P39940 sitch_q96j02 ssmurf1_q9ce7 ssmurf2_q9au4 swwp1_q90m0 swwp2_o00308 secw1_q76n89 secw2_q9p2p5 GPQSFTVEQWGTPEKLPRATCFNRLDLPPYESFEELWDKLQMAIENTQGFDGVD GPQLFTIEQWGSPEKLPRATCFNRLDLPPYETFEDLREKLLMAVENAQGFEGVD GPRRFTIEKAGEVQQLPKSTCFNRVDLPQYVDYDSMKQKLTLAVEETIGFGQE GPQKFCIEKVGKENWLPRSTCFNRLDLPPYKSYEQLKEKLLFAIEETEGFGQE GAAGPRLFTILIDANTDNLPKATCFNRIDIPPYESYEKLYEKLLTAVEETCGFAVE GPRLFTIQIDACTNNLPKATCFNRIDIPPYESYEKLYEKLLTAIEETCGFAVE GPQKFCIEKVGKDTWLPRSTCFNRLDLPPYKSYEQLKEKLLFAIEETEGFGQE GPQKFCIDKVGKETWLPRSTCFNRLDLPPYKSYEQLREKLLYAIEETEGFGQE GLRRFCIEKWGKITSLPRATCFNRLDLPPYPSYSMLYEKLLTAVEETSTFGLE GPRRFCVEKWGKITALPRATCFNRLDLPPYPSFSMLYEKLLTAVEETSTFGLE Nlobe Clobe % sequence identity catalytic cysteine Cterminal residues mutated in this study

6 b RDYKRKYEFFRRKLKKQNDIPNKFEMKLRRATVLEDSYRRIMGVKRADFLKARLWIEFDGEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQ α1 β1 α1 α2 β2 α3 α3 β3 β INPNSGINPDLSYFKFIGRVAGMAVYGKLLDGFFIRPFYKMMLKPITLDMESVDSEYYNSLRWILENDPTELDLRFIIDEELFGQTQELKNGG β4 α4 α4 α5 α6 α7 β5 β SEIVVTNKNKKEYIYLVIQWRFVNRIQKQMAAFKEGFFELIPQDLIKIFDENELELLMSGLGDVDVNDWRETKYKNGYSANQVIQWFWKAVLMMDSEK α8 α9 α10 α10 α11 β7 α12 α RIRLLQFVTGTSRVPMNGFAELYGSNGPQSFTVEQWGTPEKLPRATCFNRLDLPPYESFEELWDKLQMAIENTQGFDGVD S α13 α13 β8 S β9 β10 α14 Nlobe residues interacting with Clobe Clobe residues interacting with Nlobe ECT residues interacting thiolester ECT residues interacting with noncovalently bound Nlobe Buried Surface Area %33% engaged in an bond 33%66% S engaged in a salt bridge 66%100% % sequence identity Clobe Supplementary Figure 3 Sequence alignment of the ECT domains. (a) Sequence alignment of ECT domains of human Nedd4 family members and yeast Rsp5, performed with Muscle 2. Uniprot accession codes are provided with the protein names. (b) Sequence of Nedd4 ECT domain, colorcoded according to sequence conservation. Secondary structure elements are depicted, together with colored circles indicating residues involved in the interaction with ubiquitin or other lobe s residues. The radius of the circles is proportional to the buried area percentage, as calculated by PISA 3. Mutations introduced to produce a stable disulfide bridge between ECT and D are indicated in red. The catalytic cysteine is highlighted by a red triangle.

7 a b Clobe8896 Clobe snedd4 snedd4like swwp1 swwp2 secw2 secw1 sitch ssmurf2 ssmurf1 ScRsp5 suwe1 sace1 se6ap serc3 serc4 serc5 serc6 8 catalytic Cys FAELYGSNGPQSFTVEQWGTPEKLPRATCFNRLDLPPYESFEELWDKLQMAIENTQGFDGVDFAELYGSNGPQLFTIEQWGSPEKLPRATCFNRLDLPPYETFEDLREKLLMAVENAQGFEGVDFAELMGSNGPQKFCIEKVGKDTWLPRSTCFNRLDLPPYKSYEQLKEKLLFAIEETEGFGQEFAELIGSNGPQKFCIDKVGKETWLPRSTCFNRL DLPPYKSYEQLREKLLYAIEETEGFGQEFASLRGSNGPRRFCVEKWGKITALPRATCFNRLDLPPYPSFSMLYEKLLTAVEETSTFGLEFAALRGSNGLRRFCIEKWGKITSLPRATCFNRLDLPPYPSYSMLYEKLLTAVEETSTFGLEFADLMGSNGPQKFCIEKVGKENWLPRSTCFNRLDLPPYKSYEQLKEKLLFAIEETEGFGQEFKALQGAAGPRLFTIQIDACTNNLPKATCFNRI DIPPYESYEKLYEKLLTAIEETCGFAVEFKALQGSTGAAGPRLFTILIDANTDNLPKATCFNRI DIPPYESYEKLYEKLLTAVEETCGFAVEFKDLQGSDGPRRFTIEKAGEVQQLPKSTCFNRVDLPQYVDYDSMKQKLTLAVEETIGFGQEFAALEGMNGIQKFQIRDDRSTDRLPSATCFNQL DLPAYESFEKLRMLLLAIQECSEGFGLAFANIMGGSGLQNFTIAAVPYTPNLLPTSSTCINMLKLPEYPSK EILKDRLLVALCGSYGYTMALGKLKMIIAKNGPDTERLPTSTCFNVLLLPEYSSK EKLKERLLKAITYAKGFGMLMASLQIVIQSTASGEEYLPVATCYNLL DLPKYSSKEILSARLTQALDNYEGFSLAMKSLKLVIQSTGGGEEYLPVSTCFNLL DLPKYTEKETLRSKLIQAIDNEGFSLILNNMKITFCCPESWNERDPIRALTCFSVLFLPKYSTM ETVEEALQEAINNNRGFGIQKMEIVFRCPETFSERDPTSITCNILSLPKYSTM ERMEEALQVAINNNRGFVSPMLTQS D Nlobe Supplementary Figure 4 Structural location of the last sixty amino acids responsible for chain specificity. (a) Multiple sequence alignment of the last sixty residues of ECT domains, colored according to Clustal X color scheme. (b) Surface/cartoon representation of ECTNedd4~D:. Colors are as in Figure 1, except for the last sixty residues of the Clobe, which have been depicted in pink. The catalytic Cys is shown in yellow. Data obtained in this paper together with previously published data strongly indicate that these sixty amino acids of the Clobe are capable of binding both D and A to achieve chain specificity.

8 a b C lobe A889F C lobe WWP1 (1nd7) A889F WWP1 (1nd7) Cys867 Cys890 C Phe889 Phe 826 N 14 C lobe A889F Supplementary Figure 5 Structure of ECTNedd4 A889F. (a) Cartoon representation of ECTNedd4 A889F structure superposed to ECTWWP1 (pdb 1nd7). The orientation and colors of ECTNedd4 are the same of Figure 1, with the Nlobe of WWP1 ECT domain depicted in dark blue and the Clobe in light green. The catalytic cysteines are highlighted in ballandstick representation. The overall superposition of the two ECT domains, performed via secondary b) Cartoon representation of the ECTNedd4 A889F Clobe contoured by the final 2FoFc map of the representation.

9 SUPPLEMENTARY REFERENCES 1. Serniwka, S.A. & Shaw, G.S. The structure of the c8ubiquitin complex shows a unique ubiquitin interaction site. Biochemistry 48, (2009). 2. Edgar, R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004). 3. Krissinel, E. & enrick, K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 2, (2007).