Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2

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1 Structural evidence for consecutive -like modules in the spliceosomal ATPase Brr2 Lingdi Zhang, Tao Xu, Corina Maeder, Laura-Oana Bud, James Shanks, Jay Nix, Christine Guthrie, Jeffrey A. Pleiss, Rui Zhao

2 -S S S S S S S S S S α1 α2 α3 α4 LIASHYGVSF FTIQSFVSSL SNTSTLK-NM LYVLSTAVEF ESVPLRKGDR ALLVKLS-KR NIASSFYINH ASMDVYNREL DEHTTQI-DL FRIFSMSEEF KYVSVRYEEK RELKQLL-EK HHH HHHHHHHHHH HH HH HHHHHHHHHH HHH HHHHHHH HH SRLYIDP LTGFIFHDVL SRMELSDIGA LHLICRTPDM ERLTVRKTD- SWVEEEAFRL α1 α2 α3 α5 α6 LPLRFPEHT- ---SSGS--V SFKVFLLLQA YFSRL---EL PV--DFQN-D LKDILEKVVP APIPIR--E- ---DIDD--P LAKVNVLLQS YFSQL--KFE GF--ALNS-D IVFIHQNAGR HHHHHHHH HHHHH H HH H HHHHHHHHHH RKELSYYPSD FSVEYDWFLS EVKTALCLKD WIEEKDEDEI CAKYGIAPGD LRRIVETAEW α4 α5 α6 α6 α7 α8 α9 LINVVVDILS ANGYLN-ATT ATT AMDLAQMLIQ GVWDVDNPLR QIPHF----N NKILEKCKEI LLRAMFEICL KRGWGHPTRM LLNLCKSATT KMWPTNCPLR QFKTC----P VEVIKRLEA- HHHHHHHHHH HH HHHHH HHHHHHHHHH HHH HHHHHHHH LSNAMNRIAE E--VGN-T-S VSGLTERIKH GVKEELLELV RIRHIGRVRA RKLYNAG--- α6 α7 α8 α9 α10 α11 α12 β1 β2 NVETVYDIMA LE-DEERDEI LTLTDSQLAQ VAAFVNNYPN VELTYSLNNS DSLISGVKQK STVPWGDYLQ LETPAEVGRA IRSE-KYGKQ VYDLLKRFPK MSVTCNAQPI TRSVMRFNIE HHHHHh H EEE EE HHHH HHHHH EEEEEEE EEEEEEEEE -IRNAEDIVR H--REKVASL I-----GRGI AERVVEGISV KS 686 α10 α11 α12 β2 β3 β4 β5 ITIQLTRDVE PENLQVTSEK YPFDKLESWW LVLGEVSKKE LYAIKKVTLN KET--QQYEL IIADWIWDMN VHGS LEPFL LMLEDTPGDS ILYYDVLFIT PDIVGHEFTL EEEEEEE EEE EEEE EEEEEEEEEE EEEE -S S β6 β7 EFDTPTSG - KHNLTIWCVC DSYLDADKEL SFEINVK SFTYELKQHL PPNFFLTLIS ENWWHSEFEI PVSFN EEE EEEEEEEE E E Supplementary Fig. 1

3 Supplementary Figure 1. Sequence alignment of S2, S1, and domains 4 & 5. The alignment between S2 and is structure-based 1 and that between S1 and S2 is taken from Ponting 2. Secondary structures of S2 and derived from the crystal structures are labeled. Predicted secondary structures for S2 and S1 2 are also labeled as H (helix) and E (beta strands). Blue, green, and purple residues designate the N-terminal helical domain, the middle helical domain, and the C-terminal Fn3 domain in S2.

4 ys2 ys2 ys2 ys2 ys2 ys LIASHYGVSFFTIQSFVSSLSNTSTLKNMLYVLSTAVEFESVPLRKGDRALLVK APLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPIRHHEDNLLRQ LSKRLPLRFPEHTSSGSVSFKVFLLLQAYFSRLELPVDFQNDLKDILEKV---VPLINVV LAQKVPHKL-NNPKFNDPHVKTNLLLQAHLSRMQLSAELQSDTEEILSKAIMDVRLIQAC VDILSANGYLN-ATTAMDLAQMLIQGVWDVDNPLRQIPHFNNKILEKCKEINVETVYDIM VDVLSSNGWLSPALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGVESVFDIM ALEDEERDEILTLTDSQLAQVAAFVNNYPNVELTYSLNNSDSLISGVKQKITIQLTRDVE EMEDEERNALLQLTDSQIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEE PENLQVTSEKYPFDKLESWWLVLGEVSKKELYAIKKVTLNKETQQYELEFDTPTSGKHNL VTG-PVIAPLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAK-VKLDFVAPATGAHNY TIWCVCDSYLDADKELSFEINVK TLYFMSDAYMGCDQEYKFSVDVKEAETDSDSD Supplementary Figure 2. Sequence alignment between yeast S2 (ys2, residues ) and human S2 (, residues ) domains performed using program MULTALIN 3. Red and blue colors represent identical and similar residues, respectively.

5 a dsdna Supplementary Fig. 3 β-hairpin Domain 2 ssdna 2P6R Motif V β hairpin in Motif VI b 335-GVNLPARRVIVRSLYRFD---GYSKRIKVSEYKQMAGRAGR-372 Brr2 837-GVNLPAHTVIIKGTDVYSPEKGSWEQLSPQDVLQMLGRAGR-877 G GS S Q Q G G 877 eif4a LISTDLLARGID.... YIHRIGRGGRFG c WT brr2-3gs WT brr2-3gs 30 o C 18 o C MW (kda) Brr2 Snu114 Prp8 d WT brr2-3gs 37 o C serial dilution

6 Supplementary Figure 3. (a) A prominent β-hairpin (red) between motifs V and VI in domain 2 of (PDB ID 2P6R 23 ) inserts into the dsdna and disrupts base-pairing i of the DNA duplex. Domains 1-4 are colored in dark blue, light blue, green, and purple, respectively. (b) Sequence alignment between and Brr2 in the putative β-hairpin region. Motifs V, VI, and the β-hairpin of are labeled, and identical residues between the two proteins are colored red. Motifs V and VI in DEAD-box protein eif4a (red designates residues conserved in many DEAD-box proteins) are also shown. Residues that have been changed to GSGSGS in Brr2 are underlined. (c) brr2-3gs mutant has impaired growth in all temperatures. In the right panel, Brr2 proteins in yeast cell extracts were pulled down using IgG resin and probed on a Western blot using anti-brr2, anti-prp8, and anti-snu114 antibodies. Note that Brr2 appears larger because it contains the Protein A tag. (d) SDS PAGE of purified Brr2 WT and Brr2-3GS mutant.

7 MTEHETKDKAKKIREIYRYDEMSNKVLKVDKRFMNTSQNPQRDAEISQPKSMSGRISAKD MGQGLCNNINKGLKENDVAVEKTGKSASLKKIQQHNTILNSSSDFRLHYYPKDPSNVETY EQILQWVTEVLGNDIPHDLIIGTADIFIRQLKENEENEDGNIEERKEKIQHELGINIDSL KFNELVKLMKNITDYETHPDNSNKQAVAILADDEKSDEEEVTEMSNNANVLGGEINDNED DDEEYDYNDVEVNSKKKNKRALPNIENDIIKLSDSKTSNIESVPIYSIDEFFLQRKLRSE LGYKDTSVIQDLSEKILNDIETLEHNPVALEQKLVDLLKFENISLAEFILKNRSTIFWGI RLAKSTENEIPNLIEKMVAKGLNDLVEQYKFRETTHSKRELDSGDDQPQSSEAKRTKFSN PAIPPVIDLEKIKFDESSKLMTVTKVSLPEGSFKRVKPQYDEIHIPAPSKPVIDYELKEI MKVEEL T-SLPDWCQEAFPSSETTSLNPIQSKVFHAAFEGDSNMLICAPTGSGKTNIALLTVLKAL AESISSYAVGILKEEGIEELFPPQAEAVEKVFSG-KNLLLAMPTAAGKTLLAEMAMVREA motif I SHHYNPKTKKLNLSAFKIVYIAPLKALVQEQVREFQRRLAFLGIKVAELTGDSRLSRKQI IKGGKSLYVVPLRALAGEKYESF-KKWEKIGLRIGISTGDYESRDEHL DETQVLVSTPEKWDITTRNSNNLAIVELVRLLIIDEIHLLHDD-RGPVLESIVARTFWAS GDCDIIVTTSEKADSLIRN--RASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMN II KYGQEYPRIIGLSATLPNYEDVGRFLRVPKEGLFYFDSSFRPCPLSQQFC--GIKERNSL KA----LRVIGLSATAPNVTEIAEWLDAD-----YYVSDWRPVPLVEGVLCEGTLELFDG III KKLKAMNDACYEKVLESINEGNQIIVFVHSRKETSRTATWLKNKFAEENITHKLTKNDAG AFSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSA------ITAKYVENEGL IV

8 SKQILKTEAANVLDPSLRKLIESGIGTHHAGLTRSDRSLSEDLFADGLLQVLVCTATLAW EKAILE-ENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAA GVNLPAHTVIIKGTDVYSPEKGSWEQLSPQDVLQMLGRAGRPRYDTFGEGIIITDQSNVQ GVNLPARRVIVRSLYRFD---GYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDRE V VI YYLSVLNQQLPIESQFVSKLVDNLNAEVVAGNIKCRNDAVNWLAYTYLYVRMLASPMLYK --IAVKRYIFGEPERITSKLGVETHLRFHSLSIICDGYAKTLEELEDFF----ADTFFFK VPDISSDGQLKKFRESLVHSALCILKEQELVLYDAENDVIEATDLGNIASSFYINHASMD QNEISLSYELERVVRQLENWGMVV EAAHLAPTKLGSLVSRLYIDPLTGF VYNRELDEHTTQIDLFRIFSMSEEFKYVSVRYEEKRELKQLLEKAPIPIREDIDDPLAKV IFHDVL----SRMELSDIGALHLICRTPDMERLTVRKTDSWVEEEAFRLRKELSYYPSDF NVLLQSYFSQLKFEGFALNSDIVFIHQNAGRLLRAMFEICLKRGWGHPTRMLLNLCKSAT SVEYDWFLSEVK-TALCLKDWIEEKDED EICAK--YGIAPGDLRRIVETAE TKMWPTNCPLRQFKTCPVEVIKRLEASTVPWGDYLQLETPAEVGRAIRSEKYGKQVYDLL WLSNAMNRIAEEVGNTSVSGLTERIKHGVK-EELLELVRIRHIGRVRARKLYNAGIRNA KRFPKMSVTCNAQPITRSVMRFNIEIIADWIWDMNVHGSLEPFLLMLEDTDGDSILYYDV -----EDIVRHREKVASLIGRGIAERVVEGISVKSLNPES LFITPDIVGHEFTLSFTYELKQHNQNNLPPNFFLTLISENWWHSEFEIPVSFNGFKLPKK FPPPTPLLENISISTSELGNDDFSEVFEFKTFNKIQSQVFESLYNSNDSVFVGSGKGTGK MKVEELAESISSYAVGILKEEGIEELFPP-QAEAVEKVF-SGKNLLLAMPTAAGK I TAMAELALLNHWRQNKGRAVYINPSGEKIDFLLSDWNKRFSHLAGGKIINKLGNDPSLNL TLLAEMAMVREAIKG-GKSLYVVPLRALAGEKYESFKKW--EKIGLRIGISTGDYESRD KLLAKSHVLLATPVQFELLSRRWRQRKNIQSLELMIYDDAHEISQGVYGAVYETLISRMI EHLGDCDIIVTTSEKADSLIRN--RASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKM- II

9 FIATQLEKKIRFVCLSNCLANARDFGEWAGMTKSNIYNFSPSERIEPL--EINIQSFKDV ---RRMNKALRVIGLSATAPNVTEIAEWLD-ADYYVSDWRPVPLVEGVLCEGTLELFDGA III EHISFNFSMLQMAFEASAAAAGNRNSSSVFLPSRKDCMEVASAFMKFSKAIEWDMLNVEE FSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKY---VENEGL---E IV EQIVPYIEKLTDGHLRAPLKHGVGILYKGMASNDERIVKRLYEYGAVSVLLISKDCSAFA KAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGV CKTDEVIILGTNLYDGAEHKYMPYTINELLEMVGLASGNDSMAGKVLILTSHNMKAYYK NLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAG-RPGMDERGEAIIIVGKRDREIAVK V VI KFLI-EPLPTESYLQYIIHDTLNNE--IANSIIQSKQDCVDWFTYSYFYRRIHVNPSYY- RYIFGEPERITSKLGVETHLRFHSLSIICDGYAKTLEELEDFFADTFFFKQNEISLSYEL GVRDTSPHGISVFLSNLVETCLNDLVESSFIEIDDTEAEVTAEVNGGDDEATEIISTL ERVVRQLENWGMVVEAAHLAPTKLGSLV--SRLYIDPLTGFIFHDVLSRM-ELSDIGALH SNGLIASHYGVSFFTIQSFVSSLSNTSTLKNMLYVLSTAVEFESVPLRKGDRALLVKLSK LICRTPDMERLTVRKTDSWVEEEAFRLRKELSYYPSDFSVEYDWF-LSEVKTALCLK RLPLRFPEHTSSGSVSFKVFLLLQAYFSRLELPVDFQNDLKDILEKVVPLINVVVDILSA ----DWIEEKDEDEICAKYGIA PGDLRRIVETAEWLSNAMNRIAEE NGYLNATTAMDLAQMLIQGVWDVDNPLRQIPHFNNKILEKCKEINVETVYDIMALEDEER VGN---TSVSGLTERIKHGVKEELLELVRIRHIGRVRARKLYNAGIRNAEDIVRHREKVA DEILTLTDSQLAQVAAFVNNYPNVELTYSLNNSDSLISGVKQKITIQLTRDVEPENLQVT SLIGRGIAERVVEGISVKSLNPES SEKYPFDKLESWWLVLGEVSKKELYAIKKVTLNKETQQYELEFDTPTSGKHNLTIWCVCD SYLDADKELSFEINVK

10 Supplementary Figure 4. Sequence alignment between and Archaeoglobus fulgidus performed using program MULTALIN 3. Red and blue indicate identical and similar residues, respectively. Major helicase motifs of are underlined. Notice that the second putative helicase domain of Brr2 is much more deviated from the canonical helicase motifs. Also notice that there is very low sequence similarity in regions outside of the helicase domain (i.e., the S1 and S2 regions) and the sequence alignment in these regions is not very accurate. A much more accurate alignment based on the structure of S2 and is presented in Supplementary Fig. 1. References: 1. Holm, L. & Sander, C. Dali: a network tool for protein structure comparison. Trends Biochem Sci 20, (1995). 2. Ponting, C.P. Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction. Biochem J 351 Pt 2, (2000). 3. Corpet, F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16, (1988).