Streptococcus bovis ATCC 700338, alpha-L-rhamnosidase, ZP_07467393.1; R.obeumCel: Ruminococcus obeum A2-162, Cellobiose phosphorylase ...
Supplementary data for
Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations
Melanie Grandits, Herbert Michlmayr, Christoph Sygmund and Chris Oostenbrink Contents: 1. Multiple sequence alignment of bacterial GH78 rhamnosidases 2. Molecular topology building blocks of substrates according to the GROMOS force field parameter set 54a7 3. Atom-positional root-mean-square deviations (rmsd) from the initial structures 4. Shortest average distances (center of mass) between hydrophobic amino acids and ligands (rutinose, p-NPR)
Supplementary data 1. Multiple sequence alignment of bacterial GH78 rhamnosidases P.acidilacticiRam2: L.plantarumRhaB2 : L.fermentumRhaB2 : S.bovisRam2 : R.obeumCel : C.difficileRam : BacillusGl1RhamA : P.acidilacticiRam1: L.plantarumRhaB1 : E.faeciumRham : PbacillusJDR-2Rham: Bacteroides3_1Rham: P.saltansRham : B.vulgatusRham : BacillusGl1RhamB :
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAEIEVYGLSCNNRSNPMGIGDKAPRLGWKLRSERRGVVQEAYRIQVAEDASFEGGLAWDTERMAGGRSVAVPYEGEPLRSRTRYFYRVKVWGNRGQESEWS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAGRNWNASWIWGGQEESPRNEWRCFRGSFDAPASVEGPAMLHITADSRYVLFVNGEQVGRGPVRSWPKEQFYDSYDIGGQLRPGVRNTIAVLVLHFGVSNFYYLRGRGGLIAEIEADGRTLAATDAAWRTERLGGQRSNSPRMACQQGF
: : : : : : : 102 : : : : : : : : 150
P.acidilacticiRam2: L.plantarumRhaB2 : L.fermentumRhaB2 : S.bovisRam2 : R.obeumCel : C.difficileRam : BacillusGl1RhamA : P.acidilacticiRam1: L.plantarumRhaB1 : E.faeciumRham : PbacillusJDR-2Rham: Bacteroides3_1Rham: P.saltansRham : B.vulgatusRham : BacillusGl1RhamB :
------------------------------------------------------------------MAFTFQINDDVEFNHDKQLLKKADDNIPELAKRVVTPVQVVETVIDKNLLDNVGTKKVADATQLSQMKFGRD---DRLILDFGN ------------------------------------------------------------------MAFTFQINNDVQFRHNQALLDKSASYRPILKETQVKAASIVALELDTQYLEGWGVKQIAPIERLSSYELKRD---DQIIIDFGD ------------------------------------------------------------------MGFKFQINDDVKFNHNMDLLTKADNYKPELHITKVKAKSIVELNEDPTKLEGVGIKRIGGINDLSKMKLTRD---DQVIIDMGE ------------------------------------------------------------------MAFTFQMNHSIKFNHDEGLLKKAELLTPPLINKEKKLVRLGELTKDITKFEGWTIKTLD--MKIDDKEYKKD---DSLILDFGN ------------------------------------------------------------------MAEVSIDLNMVRVT-NDAFVEKAEACAPKLLETVVRPVSIVDIAKTENVYP--DVNKKDDIENLSSYHLAKG---DKICLDFGD ------------------------------------------------------------------MSNITNSIKDFRMEINQDFIDKAEKLKPILIEKLIKPKQIVNIKMGKNDWE--VIDTKS-IDEISNISLGKG---ESICIDFGN -----------------------AAAYFETALLSVEEWAGAEWISHTLPANEEGHEPIAYLRKSFRLDRPVASARIYATALGMYRLFVNGEAADDTHLNPGWTSYGHRVQYQTYDVTALLTEGANALGLMLGNGWYRGRLGWQQASKYGD ------------------------------------------------------MNQTY------WIWYPGDFAIHQGMLQNFSREERGMQWPAYWYLEDCYRNVKFLKTYQLKNATSFMVRSHQPGYVTVNEQ-KYS-LNEPINLTAGE ------------------------------------------------------MSKEA-----VWLWYPGDFEIHQGMLQNFKREERGMGWPAYWYIDDCNRNVNFKRHYDLKESTQFTVLAKGTGYVDVNGT-KYR-LNHAINCDAGA ------------------------------------------------------MTNEKSQN--RWLWYPGDFEIRHGLLQNFQREERGFDWPAYWYMDDCHRNVKFKRYYFLDHPSMFKVTIQGVGYVEINGQ-KHP-CGKWLTCPAGK ------------------------------------------------------MVSQDKKK-ATWIWYPGDFEIRLHEKMSAKRTARGVAYPAYWRLDRHYSNIKFRYAYELEHEEEITIAAEGVFSLYLDGKDNYRSNRSTITLPAGR -------------------------------------MKKKYMILLSALS----LASSTFAQ--TWIWYPGDYEIWLGNQMNNRRTERGAFFPPFWKTDSHYVVVEFSKQLNLSEPEEIFIAAEGKYNVKLDGKLQFG-MPETMLLPAGK --------------------------------MNILYPKNLCVALVIAITSLCSLTTKAQEQKSTWIWYPGDFEIWLSNDMQNRRTERGTFFPPFWRMDSHYVLVEFHKVFNLTEPEDIEIFAEGRYNVKINGKMVSG-YPKKLTIPAGQ -------------------------------------MKNKLATLVGALA----LSAAASAQ--TWIWYPGDYEIWLGNRMNNRRTERGAFFPPFWKTDSHYVVVEFSKKLDLAEPEEIFIAAEGKYNVKLDGKLQFG-MPSTLKLPAGK GEVIDARELAEDWALPAFDDGGWAQARSIGPAGTAPWTSLVPRDIPFLTEEKLYPASIQSLSRVKAPKYAAALDLRNQMVPESVNHANPVSYCGYVATILTLETSGVVTLGFPTGVRGSGVWVDGVLQTEWTGVQPER--YYSLNLAAGE
: : : : : : : : : : : : : : :
81 81 81 79 78 78 229 88 89 92 95 106 117 106 298
P.acidilacticiRam2: L.fermentumRhaB2 : L.plantarumRhaB2 : S.bovisRam2 : R.obeumCel : C.difficileRam : BacillusGl1RhamA : P.acidilacticiRam1: L.plantarumRhaB1 : E.faeciumRham : PbacillusJDR-2Rham: Bacteroides3_1Rham: P.saltansRham : B.vulgatusRham : BacillusGl1RhamB :
HYVGHFTIRIKSVGS----------------------------PMDAPLTLK--------------------------------------------------------------------LKFAELPTELNQDSQDYQGWLSRSWMQEET HQVGQFSININAVGS----------------------------PMDAPLCFK--------------------------------------------------------------------IKFAEMPAELARKSEDYDGWLSKSWIQEET HCVGKFNLHLSHIGS----------------------------PMDSPLALK--------------------------------------------------------------------IKFAEMPNELTYKSEDYDGWLSKAWIQEEV HYVGRFAIDINSVGS----------------------------PMDAPLYIR--------------------------------------------------------------------LRFAEVAAELSHESEEYDGWLARGWIQEEF HQVGYVTMKLNSVGS----------------------------PQDAPAFFR--------------------------------------------------------------------LKFAEIAKEITEDSKDYDGWISRGWIQEEF HQVGYVNFKIKPIGS----------------------------PPDAPTHLR--------------------------------------------------------------------IKLGETLCEIGEDSSTYKGSISSSWIQEET TRAALVWLHVRYADG------------------------TESVVGSDGSWLGSDGALRWSELYDGEHYDARLARKDWSLPAFDDSEWGNVSPYAHP--------------KTALVAQESEPVRIVDTIVSVSVWTTPSGETLLDMGQNMV QQIVIYVFSAKDLPC----------------------------VYVAGAEIYSDASWVASNYIQERPVG---------------WSAMFT----------------------SNTDDPNQIPYRCRETFPKQIVERAGG-KLIDFGREIN TDIQVFVGNVQGLPT----------------------------IYIVGEIIKSDSGWLASNFVTTLPAG---------------HDILYT----------------------DRNQDPNVIEYRTEKVVAKAQQAVDGG-VLYDFGRAVN VKIRIFVGHTSGLPA----------------------------MFIEGDEIKSDIGWTASNFIEEYPAG---------------WSPLYV----------------------DIAKDPNQIYYQKECVHPVTETEVNGG-VLFDFGRAVN HEISVSVFNDKEMPA----------------------------LYVAGDSIQSDSSWEVTSYQNDWLP---------------AGLWNFD----------------------APENRPSAFRLAVTPQEPVS-VIDQEGYPLLDFCKETF HNLNIKVWNQATPPT----------------------------IYVKGKTVNSDSSWRVTYEDKEWIDESGKASDTSATIYMDAGCWNFD----------------------GATQRPSQFSLMREPQQPVTKSEQSEGGILYDFGKETF QKINIKIHNQGHVPA----------------------------LYIKGKTIKTDNTWLVTFEDKEWIDETGKASDQSGTTYVKAGTWNFN----------------------TPDNKPSAFKLATRPQEAIN-TEKKGNQQVIDFGKNTF HSLNIKVWNQSTPPT----------------------------IYVKGKTVNTDKTWKVTYEDKEWIDESGKASDTSATVYMDAGCWNFD----------------------GATQLPSKFSLARKPMKAVSSTPRKEG-VLYDFGKETF HLVLVDITSSDHGGSSHFAIDSEAAFTLRSPAGDNGVPLATIGTFDQSEYIDHRPGRRMQTDHPDYRALPEAAPTAAALEAFASWVKPFEPSLYTEENVFGSNVWRTLAERRAVPRSVLNAILPVPEPGVLPVFEDGDCELVIDLGAERS
: : : : : : : : : : : : : : :
135 135 135 133 132 132 341 172 173 176 179 206 216 205 448
*+,-+$./$+01$2,+,34+52$6.7,58$ P.acidilacticiRam2: L.plantarumRhaB2 : L.fermentumRhaB2 : S.bovisRam2 : R.obeumCel : C.difficileRam : BacillusGl1RhamA : P.acidilacticiRam1: L.plantarumRhaB1 : E.faeciumRham : PbacillusJDR-2Rham: Bacteroides3_1Rham: P.saltansRham : B.vulgatusRham : BacillusGl1RhamB :
VHLDELPANLY---LPRRYSFRYVEIKVVDTSPKWQVSFFEP--------------------------------------------ALIAESAAQGAPTPF-HTDDKLLQKIDQVGLKTLADCMQDVFEDGPKRD-RRLWIGDLRLQALA VHLDVLPTTLT---LPRRYSFRYAEITVVDTSPKWRAVFSNP--------------------------------------------VVTATSAVDTATVHQPELADAQLQRIYEVGLKTLADCMQDVFEDGPKRD-RRLWIGDLRLQALA IHLDQLPADLN---LTRRYAFRYVQISVIDTSPKWQVMLSEP--------------------------------------------YATITSSVTSLEGKWPDFHDDELNEIYKVGVKTLHDCMQDVFEDGPKRD-RRLWLGDLRLQALA IHLDELPTLLS---LPRRYAFRYVEIKVLDTSPKWSVVFSNP--------------------------------------------RLITESCVDSDNLPFPKIEDMELAAIYQVGLKTLEDCMTDVFEDGPKRD-RRLWLGDLRLQALA IHVDVLPAELK---LPRRYAFRYMEIEAIDTSLKWQLVVEDV--------------------------------------------SCTSVSAVRIEDVEPVKSDDEMIRRLDRVSLRTLQNCMQSVFEDGPKRD-RRLWLGDLRLQALA MHIDILPDKIN---MKRRYAFRYLEIKVLDTSPKYKVIVEDV--------------------------------------------SCNFVSSVDMSEINYLSNIDDDLIKIDKIALKTMQDCMQTVFEDGPKRD-RRLWIGDLRLQAIT GWVRFTVRAEAGTVVTVRHAEVLDKHGNFYTGNLRSAKQTVAYVCSGEGEETFEP--------TFSFQGFRYVKIEGIPPEQVPGRFVGCVLTSDLQTAGRFRCSDPMINKLADNIVWGQIGNFVDVPTDCPQRDERLGWTGDAQAFVRA ATVRFTKLS---HPIQVCYGESVAEALDTVNCYYQQRDVREN---------------------EELPKRAFRYLFIPDYP-DGQLEAVATQIDLPMQNHGIFKSDDPLLNQIWQVSLRTFKLCSDLFFIDGIKRD-RWIWGGDAYQDNFI GTVTVKTNG----PVTLCYGESETEARDVEMCYYKQSDVTAT---------------------TKVRKRAFRYVFVPHCQ-LGDIELTAMHEYIPKNNPSSFTSDNKLINQIWNVATETLNLCSDLFFIDGIKRD-RWIWAGDAYQANFI GCVELISLDNPIESITLCYGESDVEAMDIEYCYYKQIGMTRK---------------------MKARKRAFRYLFIPEVS-TGMVQLQVFHEFLSLSKQATFSSDSSLLNQIWSVSEETFKLCSDLFFIDGIKRD-RWIWSGDAYQSFMI GYLRFHNLRGN-GFVNVYFGESIAEALSPEECVTLDAFEAEEAR---VLEEDG--------VFTLEEPKAFRYAWIHADPDVTWERVSMLYEYVPVQYRSTFECSDSRLNDIYKMSLYTLHLNTREFFLDGIKRD-RWVWSGDAYQAFLM GFITLKNLSGK-GKIEIYYGESPEEAKDKAYCETLDKLLLEPGQVTDLAIRSTSPLSNSENEYTLENSKAFRYVYVTHEPGVQIGEVSMQYEYLPEEYRGSFRCNDEELNRIWEVGAYTMHLTTREFFIDGIKRD-RWVWSGDAIQSYLM GFVKLHQLKGK-GKIQIYYGESKEEALGTKTCETFDIFDIN-----NVSAKDS----------VLELSKAFRYVNIVTDPEVSIAKVSMLYEYLPMKDRGRFTSSDAELNKIWDVSKYTMELTTREFFIDGIKRD-RWIWSGDAYQSYLM GYITLKEVKGK-GTIHIYYGESPEEALDTEYCETLDKLLAEPGQITDLAIRNTRKLYD---EYTLDNSKAFRYVYVTCDPGVTIQDVSMQYEYLPEEYRGSFKCNDEELNRIWEVGAYTMHLTTREFFIDGIKRD-RWVWSGDAIQSYLM GFIGFELEAPAG-TIIDAYGVEYMREGYTQHTYGLDNTFRYICREGRQSYVSP----------VRRGFRYLFLTVRGNSAPVKLHEIYIRQSTYPVAEQGSFRCSDALLNATWEISRHTTRLCMEDTFVDCPSYE-QVFWVGDSRNEALV
%'&$ P.acidilacticiRam2: L.plantarumRhaB2 : L.fermentumRhaB2 : S.bovisRam2 : R.obeumCel : C.difficileRam : BacillusGl1RhamA : P.acidilacticiRam1: L.plantarumRhaB1 : E.faeciumRham : PbacillusJDR-2Rham: Bacteroides3_1Rham: P.saltansRham : B.vulgatusRham : BacillusGl1RhamB :
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%"9$!!%%"$ %%%!!!!%%:!%%)$$%("! 236 237 237 235 234 234 483 296 296 303 316 354 349 350 586
: : : : : : : : : : : : : : :
377 377 377 376 375 375 622 425 423 436 445 485 479 481 724
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DYQTYDNQTLIKRCLYLFGALAAKDGRIPANVFVKPTYTPDDTFLLDYSLFFVSILDDYFQHTDDYTVLEDLYPVAKKQIDYVMKNMVQSNGKIVFDEDYPVFVDWSN----EFNKDTAGVAIIIYALKQFIHLSRLQRLD-TIDY---NYATFKDTDLVKRCLYLFGAMPTTAGRIPANVFTKPTAVPDDTFLFDYSLFFISILADYEAFSSDKTVLNDLYRVAKNQMD-LALAQVTSEGKLKLTEENPVFIDWSN----DFDKETAGQAIIIYTLKQFITLAELVNDT-SLET---NYSTFDNQALVKRCLYLFGAMTATDGRISANVFTNQEYVPDDTFMYDYSLFFITTLADFEDQHNDMELLSDLYLVAKKQWE-VMEGFISEEGMVKPPKEYTVFVDWST----KFDKSTATQAITIYAIKKLIKLTTQMDDP-VVNH---NYESFKQNDLVKRCLYLFGAMTTEDGRISANVFTKPYPIPDDTFLFEYSLFFISVLHDYLAQEDDEELLGDLYPIAKKQIN-TSLTYIQEDGKVCADESYPVFVDWST----EFDKTTCLQAIMIYVLRQFIELAQKAGDFGITEY---NYETFHNMDLVKRCLYLFAAQTKDNGQVSACLFTEPKFIVDDTFLLDYSMFFGATLYDYYEASGDKKTLKDLSACAYRQME-IAEEWFDEKNLLKNGEGFWGFIDWTD----GLNKQSAMQGVYIYCARKAQKIAEALGDTEKAAY---NYETFKNNDLVKRCLYLFAGLTQNRGQVGACLFIEPKLLVDDTALFDYSLFFISCLHDYYEATKDMEILNELWKVAYIQAK-LALERVGINGVVYDSDDWWCFLDWKE----GLNKQAGAQGVLIYALKQAHKLAIILGDNEKKEE---STYNRNVQSFFAKWLRDLAADQQPDGGVPHVVPDVS---IAGANSSAWGDAAAIVPWVLYERYGDDRVLREQYASMKGWVEYIRAQGESE----YLWDTGFHFGDWLGLDAKENSYIGATPRELIATAFYAHSTDLLAKSADVLGY---NQYSFFNEEVDRRTILALRGHDEVRQHINT--------------IVDYSLLWIISIYNHYEMSGDRDFLQMIMPRMEKMMD-YLLAQTNSLGFIIGRPQDWIFVDWSP--IDKEGPVAAEQMFLLQALKAMTVTKKVLGKTADAQH---NQYSFFNEDIDKRTLLALRGQDDIKQHMNT--------------IVDYSMLWVIGVLNHYQMTGDREFLKIIYPKLESMVQ-YFIQQTNEHGFIYGRKNDWIFVDWSE--MDKQGTVAAEQILLLEDYKTIMTCGEVLGKDVAG-----NQYLFFDEEINKRTIFALRGQNEIKQHMNT--------------IVDYSILWLIGIENHYMMTKDCEFLRIVYPKMQSLIG-YLMEQTNELGFIYGRAKDWIFIDWSE--MDKEGTLAAEQVLLLKAYHSMITCRNILAETYGEAEIYPT NYYSFFDLDVTRRTLVALRGKDPLTMHLNT--------------IVDYSLYWFISLYDYYLYTGDFSFIRQNYDRAVTLME-FCLHQRNEEGFIEGRPQDWVFVDWAD--LNNTGAVSTLQILLARSLEAMRAFSGQIGEIEASSN---NYYLFFDNESVKRTIWLLRGKDPVTSHSNT--------------IMDYTFYWFLSVYDYYMYSGDRHFVNQLYPRMQTMMD-YVLGRTNKNGMVEGMTGDWVFVDWADGYLDKKGELSFEQILFCRSLETMALCAELVGDANGKQK---NYYLGFDSESVKRTTLALRGKEPTMSHINT--------------IMDYTFYWFLGIYDYYLYTGDKEFIELAYPKMQSLME-FCLQRRNKDGLMQGLSGDWIFIDWADG-LSKKGEVSFEQLLLCRSLETMALCADILKDQKAKDF---NYYLFFDNETVKRTIWLLRGKDPVTSHSNT--------------IMDYTFYWFLSIYDYYMYSGDKDFVTQLYPRMQSMMD-YVLGRTNANGMVEGMTGDWVFVDWADGYLDKKGELSFEQVLFCKSLETMALCAGLAGNTADKTK---NYYVFGETEIVERCLNLVPGSADETPLYLDQVPS-----AWSSVIPNWTFFWILACREYAAHTGNEAFAARIWPAVKHTLT-HYLEHIDDSGLLNMAG--WNLLDWAPIDQPNEGIVTHQNLFLVKALRDSRALAAAAGATEEADA----
&''$ P.acidilacticiRam2: L.plantarumRhaB2 : L.fermentumRhaB2 : S.bovisRam2 : R.obeumCel : C.difficileRam : BacillusGl1RhamA : P.acidilacticiRam1: L.plantarumRhaB1 : E.faeciumRham : PbacillusJDR-2Rham: Bacteroides3_1Rham: P.saltansRham : B.vulgatusRham : BacillusGl1RhamB :
: : : : : : : : : : : : : : :
!"#$$!"%$
--YQKELAQITNYAKQNLYNEERGLFISG------PDHEINIASQVWMVLAQVMTPEENHQLMSNAVKKLFPIKG--IATPYMYHHVTQALFEAGLTDAGIQLLKDYWGKMIELGADTFWEAFDPN---DPSYSPYGSAMVNSYCHAWSC --YTAILRKLNQYAKTQLFDSQSGLFVSG------DQREVNVASQVWMTLAHVLDPEQTTALMQTTVTKLFPITG--IATPYMYHHITEALFEAGLKQEAVQLMKDYWGKMITLGADTYWEAFDPN---QPDYSPYGSPILNSYCHAWSC --YQELCNKLVSYAKSELFDEDQGLFISG------DQREVNIASQVWMVLADVLDMQESKEVMKKALATLFPVKG--IATPYMYHHIDEALFKSGLSDEAIKLMKGYWGKMIDLGADTYWEAFEPE---KPNYSPYGSPIVNSYCHAWSC --YESVLDKLVNYSKNNLFDSEKNLFKT-------EKVEYNIASQVWMVLAGVFPKEMNRKIMMTTIEKLFPIKN--IATPYMYHHVTEALFVAGLKEEATELMKNYWGQMIRLGADTFWEAFDPD---KPDYSPYGSPIISSYCHAWSC --FAKEAKEKTESARKYLLDPENGLFVSG------EEKQLNYASQVWMILAGAVSAEEGAEILDKVIA-LNPEKG--MVSPYMNHHFVEALLKCGKKEQAMDYMKYYWGGMLSHGADTFWELYNPE---NPAESPYGGSIVNSYCHAWSC --LEYEIDRVVQGAKNHLWDEKQGFFVSG------SEKQVSWISQIWCVLADVFDKETNTKILDNLLD-NPPDMD--IVTPYAYHHLVECLILNNRKEKALECIRGYWGEMVKDGADCFWELYNPN---DKYVSPYGSRIINSYCHAWSC ----ADEAVKYAELRDNVARAFRAEYVTPSGRLASPTQTAYAVALMFDLLEEGTRQQAADRLAKLIEESGTQLTTGFVGTPYLCHVLTRFGRADLAYKLLERREYPSWLYPVVKGATTIWEHWDGIK----PDGSFWSDDMNSYNHAYGA --YQQRFDQLKQNVWKYFWDEASGAFIDSYES-KRRH--VTRHANILAVLFAVADRRQQQLILERVLL-NDRVTA--LTTPYFKFFEQDALCKLGQYDQVYQTIKEYWGAMVEKGATTVWEEYDPQVSGDAQYAMYGDPFGKSLCHAWGA --YQAKYDQLFKNLMKYFWDDEQGAFIDSYES-GKRH--VTRHANIFAILFDVVDENKQQLILKNVLL-NNAITQ--ITTPYFKFFEQDALCKLGEQHRVYQVLLDYWGGMLDRGAVTFWEEFDPSQHGKDMYAMYGDPYGKSLCHAWGA DLYQEKYQVLKQNLFDYFWDEELGAFIDCYES-GRRN--VTRHANIFAVLFDFANKEQQQSILKNVLL-NDSITQ--ITTPYFKFYEQDALCKLGQTEIVYQTILDYWGGMLSHDAVTFWEEYDPTQTGNEKYSMYGDPYGKSLCHAWGA --YGRLAAELKEKTLALFWDNERGGLLHHRVD-GETKPVLTKHANMFAMTYGYLSEEQRSSVIRQVML-NPEVPQ--IRTPYMRFHELAVLCDSGEHDVVRKEMLSYWGGMMDLGATSFWEEYDPSLADDQHYGMYGMPFGKSLCHAWGA --YEKLAAALKAKLEPAFWNNEKQAFVHNCVN-GQQSDAVTRYANMFSVFFQYLNEDKQQAIKQSVLL-NDSILK--ITTPYMRFYELEALCALGEQDAVMKEMKAYWGGMLKEGATSFWEKYNPEETGTQHLAMYGRPYGKSLCHAWGA --YSAEAKSLKSKIFNYYWNESKQAFAHSRID-GKQTDNVTRYTNMFAIFFDYLNAQQKQGVKQNVLL-NDNIQK--IMTPYMRFYELEALCAMGEQNYVMKEMKDYWGGMLKLGATTFWEEYNPAKSGAEHYTMYGREFGKSLCHSWGA --YEKLASALRSKLEPAFWNEQKQAMVHNRVQ-GKQSESVTRYANMFSVFFNYLNADKQQTIKHTVLQ-NDSILK--ITTPYMRFYELEALCALGEQESVMKEMKAYWGGMLKEGATSFWEKYNPEETGIRHLAMYGRPYGKSLCHAWGA --FAARADLLAETINAVLWDEEKRAYIDCIHADGRRSDVYSMQTQVVAYLCGVAQGEREAVIEGYLSSPPPAFVQ--IGSPFMSFFYYEALEKAGRQTLMLDDIRRNYGQMLRYDATTCWEMYPNF----AENRSNPDMLTRSHCHAWSA
: : : : : : : : : : : : : : :
514 514 514 512 511 511 765 567 565 580 589 629 623 625 866
!"#$$$$$!%&$ P.acidilacticiRam2: L.plantarumRhaB2 : L.fermentumRhaB2 : S.bovisRam2 : R.obeumCel : C.difficileRam : BacillusGl1RhamA : P.acidilacticiRam1: L.plantarumRhaB1 : E.faeciumRham : PbacillusJDR-2Rham: Bacteroides3_1Rham: P.saltansRham : B.vulgatusRham : BacillusGl1RhamB :
TPVYLMRKYL-S------------------------------------------------------------------------------------------------------------TPVYLINKYL-V------------------------------------------------------------------------------------------------------------TPVYLLKKYF-NLK----------------------------------------------------------------------------------------------------------TPVYLISKYL-HREE---------------------------------------------------------------------------------------------------------TPTYLLRKYF-I------------------------------------------------------------------------------------------------------------TPSYFIRKYF-GRDSKEVTSKYK-------------------------------------------------------------------------------------------------IGDWLFGSVAGIDTEASAPGYKRIRVRPVPGGSLKFAEATLESPYGEIRSAWRRRPDGGIDYEFEVPANAAANVLLPDASKANAMESQQPIDAAEGISVVTETAEGLAFVVGSGTYRFTVK SPVYLLGRYF-FGLRPTQAGYATFEIQPHLAY--------FQKLHGQLPIKDGLVHFKVNRGQLTITCDRNGGTVISQGK------------------RIPLLANQPVVIPIA-------SPIYLLGRHF-VGLRPTAPGYQTFEIKPELSE--------FHHLHTVLPIKGGTVTVVKDQHQLSVTASRAGGTLIVDGQ------------------RQSLEPNRTAVVPV--------SPIYLLGRYF-IGLYPTKPGYEEFMIQPNLDS--------FETLNCTLPIKDGMISLEKTEDKIVITSDRTGGTVKMNGKSYP------------LLAKQPLALTSHSKINA--------GPIYLIGKYY-LGITPASPGYETYRIQPNLGG--------LQHMQGTIPIGEGQITVKMDLSSIQVESTSGSGVLTFVSYRIPECSDAEVKAIGNNTYEVTVEAGKPYRIIYQA------SPIYLLGKYY-LGVKPVKEGYKEFAIAPVLGG--------LKWMEGTVPTPNGNIHVYMNSKTMKVKATEGKGYLTIKSRRPPKANIGTPEKVSEGVWRLWIDSPEERIVTYHL------SPIYLLGKYY-LGVRPTAPGYENYTIEPHLGG--------LKWMQGSIPTPKGEIELYVSTSEIKVKSPVGTGTLKINNKKKPVCKDATIKTVGKNQYELQVEKGREYLVKL--------SPIYLLGKYY-LGVKPTKPGYEEYSVTPCLGG--------LKWMEGTVPTPYGNIHIYMDKKEIRIKSDGGKGVLNIPTRKGMKAMT--------------IEPGEEQVFKY--------APGYFLGSSI-LGVKRGADGWRTVDIAPQPCD--------LTWAEGVVPLPQG--------GHIAVSWEFVSAGKLKLRIEAPEDIEVNVTLPEGIEGEVTQVKYMS--------------
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525 525 527 526 522 533 886 653 650 671 694 734 726 714 956
Sequence alignment of bacterial GH78 rhamnosidases (P.acidilacticiRam2: Pediococcus acidilactici DSM 20284, alpha-Lrhamnosidase, ZP_07366943.1; L.plantarumRhaB2: Lactobacillus plantarum, alpha-L-rhamnosidase ACR19005.1; L.fermentumRhaB2: Lactobacillus fermentum 28-3-CHN, alpha-L-rhamnosidase, ZP_05863092.1; S.bovisRam2: Streptococcus bovis ATCC 700338, alpha-L-rhamnosidase, ZP_07467393.1; R.obeumCel: Ruminococcus obeum A2-162, Cellobiose phosphorylase, CBL22278.1; C.difficileRam: Clostridium difficile NAP08, alpha-L-rhamnosidase, ZP_06892452.1; BacillusGl1RhamA: Bacillus sp. (strain GL1), alpha-L-rhamnosidase, Q93RE8; P.acidilacticiRam1: Pediococcus acidilactici DSM 20284, alpha-L-rhamnosidase, ZP_07367044.1; L.plantarumRhaB1: Lactobacillus plantarum, alpha-L-rhamnosidase, ACR19007.1; E.faeciumRham: Enterococcus faecium E980, alpha-L-rhamnosidase, ZP_06681507.1; PbacillusJDR-2Rham: Paenibacillus sp. JDR-2, alpha-L-rhamnosidase, YP_003012390.1; Bacteroides3_1Rham: Bacteroides sp. 3_1_23, alpha-L-rhamnosidase (putative), ZP_07038591.1, P.saltansRham: Pedobacter saltans DSM 12145, alpha-L-rhamnosidase, YP_004272872.1; B.vulgatusRham: Bacteroides vulgatus PC510, bacterial alpha-L-rhamnosidase, ZP_06743233.1, BacillusGl1RhamB: Bacillus Sp. Gl1, alpha-Lrhamnosidase, 2OKX). Conserved amino acids are highlighted in green.
Supplementary data 2. Molecular topology building blocks of substrates according to the GROMOS force field parameter set 54a7 rutinose # SOLUTEATOM # NRP: number of solute atoms 29 # ATNM: atom number
# MRES: residue number # PANM: atom name of solute atom # IAC: integer (van der Waals) atom type code # MASS: mass of solute atom # CG: charge of solute atom # CGC: charge group code (0 or 1) # INE: number of excluded atoms # INE14: number of 1-4 interactions # # ATNM MRES PANM IAC MASS CG CGC INE # INE14 1 1 C6 16 15.03500 0.00000 1 3 3 2 1 C3 14 13.01900 0.23200 0 8 3
1
O3
3 15.99940 -0.64200
4
1
HO3
5
1
C2
6
1
O2
7
1
HO2
8
1
C4
9
1
O4
10
1
HO4
11
1
C5
12
1
O5
13
1
C1
14
1
O1
15
2
C6
15 14.02700
0.23200
1
16
2
C3
14 13.01900
0.23200
0
17
2
O3
3 15.99940 -0.64200
0
18
2
HO3
19
2
C2
20
2
O2
21
0
1.00800
0.41000
1
14 13.01900
0.23200
0
3 15.99940 -0.64200
0
21
1.00800
0.41000
1
14 13.01900
0.23200
0
3 15.99940 -0.64200
0
21
1.00800
0.41000
1
14 13.01900
0.37600
0
3 15.99940 -0.48000
0
14 13.01900
0.23200
0
3 15.99940 -0.36000
0
21
1.00800
0.41000
1
14 13.01900
0.23200
0
3 15.99940 -0.64200
0
4 3 4 0 2 6 3 2 3 0 1 4 1 2 1 0 1 2 1 2 1 2 1 2 2 3 3 8 4 3 4 0 2 6 3 2
8 2 3 11 7 4 6
11 9 4 13 10 5 9
5 6 9 7 8
8 7 11 13 12
13 9 13 10 12 11 12 14 13 15 14 25 15 22 22 16 17 25 21 18 20 19 20 23 21
10
12 13 5
6
12 8 11
14
8 15
12
8
9
13
14
22
23
27
28
13
14 11
12
26 27 19
20
11
13 14 15 25 26 25 23 18 27 24 19 23 22 21 25 27
26 22 25
28
22 29
26
27
21
2
HO2
22
2
C4
23
2
O4
24
2
HO4
25
2
C5
26
2
O5
27
2
C1
28
2
O1
29
2
HO1
21
1.00800
0.41000
1
14 13.01900
0.23200
0
3 15.99940 -0.64200
0
21
1.00800
0.41000
1
14 13.01900
0.37600
0
3 15.99940 -0.48000
0
14 13.01900
0.23200
0
3 15.99940 -0.53800
0
21
1.00800
0.41000
1
3 0 1 4 1 2 1 0 1 2 1 3 0 2 0 1 0 0 0
22 27 23 27 24 26 25 26 28 27 28
26
28
24
25
25
27 28 29
29
END # BONDH # NBONH: number of bonds involving H atoms in solute 7 # IBH, JBH: atom sequence numbers of atoms forming a bond # ICBH: bond type code # # IBH JBH ICBH 3 4 1 6 7 1 9 10 1 17 18 1 20 21 1 23 24 1 28 29 1 END # BOND # NBON: number of bonds NOT involving H atoms in solute 23 # IB, JB: atom sequence numbers of atoms forming a bond # ICB: bond type code # # IB JB ICB 1 11 26 2 3 20 2 5 26 2 8 26 5 6 20 5 13 26 8 9 20 8 11 26
29
26
11 12 13 14 15 16 16 16 19 19 22 22 25 26 27
12 13 14 15 25 17 19 22 20 27 23 25 26 27 28
20 20 20 20 26 20 26 26 20 26 20 26 20 20 20
END # BONDANGLEH # NTHEH: number of bond angles involving H atoms in solute 7 # ITH, JTH, KTH: atom sequence numbers of atoms forming a bond angle in solute # ICTH: bond angle type code # # ITH JTH KTH ICTH 2 3 4 12 5 6 7 12 8 9 10 12 16 17 18 12 19 20 21 12 22 23 24 12 27 28 29 12 END # BONDANGLE # NTHE: number of bond angles NOT involving H atoms in solute 34 # IT, JT, KT: atom sequence numbers of atoms forming a bond angle # ICT: bond angle type code # # IT JT KT ICT 3 2 5 9 3 2 8 9 5 2 8 8 2 5 6 9 2 5 13 8 6 5 13 9 2 8 9 9 2 8 11 8 9 8 11 9 1 11 8 8 1 11 12 9 8 11 12 9
11 5 5 12 13 14 17 17 19 16 16 20 16 16 23 15 15 22 25 19 19 26
12 13 13 13 14 15 16 16 16 19 19 19 22 22 22 25 25 25 26 27 27 27
13 12 14 14 15 25 19 22 22 20 27 27 23 25 25 22 26 26 27 26 28 28
10 9 9 9 10 9 9 9 8 9 8 9 9 8 9 8 9 9 10 9 9 9
END # IMPDIHEDRALH # NQHIH: number of improper dihedrals involving H atoms in the solute 0 # IQH,JQH,KQH,LQH: atom sequence numbers of atoms forming an improper dihedral # ICQH: improper dihedral type code # IQH JQH KQH LQH ICQH END # IMPDIHEDRAL # NQHI: number of improper dihedrals NOT involving H atoms in solute 10 # IQ,JQ,KQ,LQ: atom sequence numbers of atoms forming an improper dihedral # ICQ: improper dihedral type code # # IQ JQ KQ LQ ICQ 5 12 14 13 2 8 3 5 2 2 11 1 12 8 2 11 2 9 8 2 13 2 6 5 2 16 17 19 22 2 19 26 28 27 2 22 15 26 25 2 22 16 23 25 2 27 16 20 19 2 END # DIHEDRALH
# 8 # # # #
NPHIH: number of dihedrals involving H atoms in solute IPH, JPH, KPH, LPH: atom sequence numbers of atoms forming a dihedral ICPH: dihedral type code IPH 5 13 2 19 27 16 26 26
JPH 2 5 8 16 19 22 27 27
KPH 3 6 9 17 20 23 28 28
LPH ICPH 4 30 7 30 10 30 18 30 21 30 24 30 29 2 29 32
END # DIHEDRAL # NPHI: number of dihedrals NOT involving H atoms in solute 39 # IP, JP, KP, LP: atom sequence numbers of atoms forming a dihedral # ICP: dihedral type code #
IP 3 3 8 8 3 3 5 5 2 2 2 6 2 2 9 8 11 12 12 13 14 14 17 17 22 22 17 17
JP 2 2 2 2 2 2 2 2 5 5 5 5 8 8 8 11 12 13 13 14 15 15 16 16 16 16 16 16
KP 5 5 5 5 8 8 8 8 13 13 13 13 11 11 11 12 13 14 14 15 25 25 19 19 19 19 22 22
LP 6 13 6 13 9 11 9 11 12 12 14 14 12 12 1 13 5 15 15 25 26 26 20 27 20 27 23 25
ICP 18 17 17 34 18 17 17 34 17 34 17 18 17 34 17 29 29 6 28 30 5 37 18 17 17 34 18 17
19 19 16 16 16 20 16 16 23 22 25
16 16 19 19 19 19 22 22 22 25 26
22 22 27 27 27 27 25 25 25 26 27
23 25 26 26 28 28 26 26 15 27 19
17 34 17 34 17 18 17 34 17 29 29
END # CROSSDIHEDRALH # NPHIH: number of cross dihedrals involving H atoms in solute 0 # APH, BPH, CPH, DPH, EPH, FPH, GPH, HPH: atom sequence numbers of atoms forming a dihedral # ICCH: dihedral type code # APH BPH CPH DPH EPH FPH GPH HPH ICCH END # CROSSDIHEDRAL # NPPC: number of cross dihedrals NOT involving H atoms in solute 0 # AP, BP, CP, DP, EP, FP, GP, HP: atom sequence numbers of atoms forming a dihedral # ICC: dihedral type code # AP BP CP DP EP FP GP HP ICC END LJEXCEPTIONS # This block defines special LJ-interactions based on atom numbers # This overrules the normal LJ-parameters (including 1-4 interactions) # NEX: number of exceptions 0 # AT1 AT2 C12 C6 END
p-NPR # SOLUTEATOM # NRP: number of solute atoms 27 # ATNM: atom number # MRES: residue number # PANM: atom name of solute atom # IAC: integer (van der Waals) atom type code # MASS: mass of solute atom # CG: charge of solute atom # CGC: charge group code (0 or 1) # INE: number of excluded atoms # INE14: number of 1-4 interactions
# # ATNM MRES PANM IAC MASS # 1 1 C6 16 15.03500 2
1
C3
14 13.01900
3
1
O3
4
1
HO3
5
1
C2
6
1
O2
7
1
HO2
8
1
C4
9
1
O4
10
1
HO4
11
1
C5
12
1
O5
13
1
C1
14
1
O1
15
1
CA1
12 12.01100
16
1
17
CG 0.00000 0.23200
CGC INE INE14 1 3 3 0 8
0.23200
0
3 15.99940 -0.36000
0
4 3 4 0 2 6 3 2 3 0 1 4 1 2 1 0 1 2 1 3 0 2 2 7
0.23200
1
0 9
CA2
12 12.01100 -0.14000
0
0 8
1
HA2
20
0.14000
1
18
1
CA3
12 12.01100 -0.14000
0
19
1
HA3
20
0.14000
1
20
1
CA4
12 12.01100 -0.10000
0
21
1
N9
9 14.00670
0.86000
0
22
1
O1
1 15.99940 -0.38000
0
3 15.99940 -0.64200 21
0
1.00800
0.41000
1
14 13.01900
0.23200
0
3 15.99940 -0.64200
0
21
1.00800
0.41000
1
14 13.01900
0.23200
0
3 15.99940 -0.64200
0
21
1.00800
0.41000
1
14 13.01900
0.37600
0
3 15.99940 -0.48000
0
14 13.01900
1.00800
1.00800
0 4 0 6 2 3 0 7 0 5 0 1
8 2 3 11 7 4 6
11 9 4 13 10 5 9
5 6 9 7 8
8 7 11 13 12
13 9 13 10 12 11 12 14 13
10
12 13 5
6
12 8 11
14
8 15
12
8
9
13
14
13
14 11
12
11
13 14
15
14 16 15 27
15 26 16
17
18
24
26
16 25
17 26
18 27
19
20
24
17 26
18 27
19
20
21
24
18
19
20
26
19 22 20
20 23 21
21
24
25
26
24
21 27
22
23
24
25
26
22
23
24
25
26
23
23
1
O2
1 15.99940 -0.38000
1
24
1
CA5
12 12.01100 -0.14000
0
25
1
HA5
20
0.14000
1
26
1
CA6
12 12.01100 -0.14000
0
27
1
HA6
20
1
1.00800
1.00800
0.14000
1 0 1 3 0 2 0 1 0 0 0
24 24 25
26
26
27
27
END # BONDH # NBONH: number of bonds involving H atoms in solute 7 # IBH, JBH: atom sequence numbers of atoms forming a bond # ICBH: bond type code # # IBH JBH ICBH 3 4 1 6 7 1 9 10 1 16 17 3 18 19 3 24 25 3 26 27 3 END # BOND # NBON: number of bonds NOT involving H atoms in solute 21 # IB, JB: atom sequence numbers of atoms forming a bond # ICB: bond type code # IB JB ICB 1 11 26 2 3 20 2 5 26 2 8 26 5 6 20 5 13 26 8 9 20 8 11 26 11 12 20 12 13 20 13 14 20 14 15 13 15 16 16 15 26 16 16 18 16 18 20 16 20 21 11
27
20 21 21 24
24 22 23 26
16 6 6 16
END # BONDANGLEH # NTHEH: number of bond angles involving H atoms in solute 11 # ITH, JTH, KTH: atom sequence numbers of atoms forming a bond angle in solute # ICTH: bond angle type code # # ITH JTH KTH ICTH 2 3 4 12 5 6 7 12 8 9 10 12 15 16 17 25 17 16 18 25 16 18 19 25 19 18 20 25 20 24 25 25 25 24 26 25 15 26 27 25 24 26 27 25 END # BONDANGLE # NTHE: number of bond angles NOT involving H atoms in solute 30 # IT, JT, KT: atom sequence numbers of atoms forming a bond angle # ICT: bond angle type code # # IT JT KT ICT 3 2 5 9 3 2 8 9 5 2 8 8 2 5 6 9 2 5 13 8 6 5 13 9 2 8 9 9 2 8 11 8 9 8 11 9 1 11 8 8 1 11 12 9 8 11 12 9 11 12 13 10 5 13 12 9 5 13 14 9 12 13 14 9 13 14 15 10 14 15 16 27 14 15 26 27
16 15 16 18 18 21 20 20 22 20 15
15 16 18 20 20 20 21 21 21 24 26
26 18 20 21 24 24 22 23 23 26 24
27 27 27 27 27 27 27 27 27 27 27
END # IMPDIHEDRALH # NQHIH: number of improper dihedrals involving H atoms in the solute 4 # IQH,JQH,KQH,LQH: atom sequence numbers of atoms forming an improper dihedral # ICQH: improper dihedral type code # # IQH JQH KQH LQH ICQH 16 15 17 18 1 18 16 19 20 1 24 20 25 26 1 26 15 24 27 1 END # IMPDIHEDRAL # NQHI: number of improper dihedrals NOT involving H atoms in solute 14 # IQ,JQ,KQ,LQ: atom sequence numbers of atoms forming an improper dihedral # ICQ: improper dihedral type code # # IQ JQ KQ LQ ICQ 5 12 14 13 2 8 3 5 2 2 11 1 12 8 2 11 2 9 8 2 13 2 6 5 2 15 16 18 20 1 15 16 26 14 1 16 15 26 24 1 16 18 20 24 1 18 20 24 26 1 20 18 21 24 1 20 24 26 15 1 21 20 22 23 1 26 15 16 18 1 END # DIHEDRALH # NPHIH: number of dihedrals involving H atoms in solute 3
# # # #
IPH, JPH, KPH, LPH: atom sequence numbers of atoms forming a dihedral ICPH: dihedral type code IPH 5 13 2
JPH 2 5 8
KPH 3 6 9
LPH ICPH 4 30 7 30 10 30
END # DIHEDRAL # NPHI: number of dihedrals NOT involving H atoms in solute 21 # IP, JP, KP, LP: atom sequence numbers of atoms forming a dihedral # ICP: dihedral type code # IP JP KP LP ICP 3 2 5 6 18 3 2 5 13 17 8 2 5 6 17 8 2 5 13 34 3 2 8 9 18 3 2 8 11 17 5 2 8 9 17 5 2 8 11 34 2 5 13 12 17 2 5 13 12 34 2 5 13 14 17 6 5 13 14 18 2 8 11 12 17 2 8 11 12 34 9 8 11 1 17 8 11 12 13 29 11 12 13 5 29 12 13 14 15 6 12 13 14 15 28 13 14 15 16 11 18 20 21 22 14 END # CROSSDIHEDRALH # NPHIH: number of cross dihedrals involving H atoms in solute 0 # APH, BPH, CPH, DPH, EPH, FPH, GPH, HPH: atom sequence numbers of atoms forming a dihedral # ICCH: dihedral type code # APH BPH CPH DPH EPH FPH GPH HPH ICCH END # CROSSDIHEDRAL # NPPC: number of cross dihedrals NOT involving H atoms in solute 0 # AP, BP, CP, DP, EP, FP, GP, HP: atom sequence numbers of atoms forming a dihedral # ICC: dihedral type code # AP BP CP DP EP FP GP HP ICC
END # LJEXCEPTIONS # This block defines special LJ-interactions based on atom numbers # This overrules the normal LJ-parameters (including 1-4 interactions) # NEX: number of exceptions 0 # AT1 AT2 C12 C6 END
Supplementary data 3. Atom-positional root-mean-square deviations (rmsd) from the initial structures
Supplementary data 4. Shortest average distances (center of mass) between hydrophobic amino acids and ligands (rutinose, p-NPR). * shows that the nitrophenol ring was closest, ° stands for the rhamnose moiety and ^ for the glucose moiety. !!
"#$%&'()!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!*+,-.! Pose
1
Pose
2
Pose
1
Pose
!!
2
Sim1 Sim2 Sim3 Sim4 Sim1 Sim2 Sim3 Sim4 Sim1 Sim2 Sim3 Sim4 Sim1 Sim2 Sim3 Sim4
!!
Trp226 0.57^ 0.50^ 0.49^ 0.46^ 0.46^ 0.76^ 0.89° 0.55^ 0.53* 0.54* 0.53* 0.61* 0.58° 0.83* 0.57° 0.54°
!!
Tyr284 0.84^ 0.78^ 0.70° 0.71^ 0.71^ 0.84^ 0.68^ 0.58^ 0.66* 0.93* 0.75* 0.63* 0.79° 0.56* 0.93° 0.47*
!!
Phe339 0.81° 0.62° 0.78° 0.61° 0.68^ 0.83^ 0.58^ 0.56^ 0.47° 0.91° 0.60° 0.60° 0.47* 0.85* 0.78* 0.47*
!!
Tyr449 0.76° 0.64^ 1.0^ 0.94^ 1.0^
1.1°
!!
Trp512 0.53^ 0.56^ 0.71^ 0.63^ 0.60° 0.96° 0.47° 0.62° 0.50* 0.51* 0.5* 0.53* 0.60° 0.62° 0.65° 0.68°
!!
1.1° 0.54^ 0.84^ 0.85* 0.88* 0.86* 0.81* 0.81° 0.68* 1.0*
