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1 Supporting Information Naganuma et al /pnas SI Text The Recognition of Ala-SA. Ala-SA is a nonhydrolyzable analog of alanyl-adenylate and is a potent inhibitor of AlaRS (1). The recognition manners of the amino acid and adenosine moieties are similar to those observed in the A. aeolicus AlaRS-N ATP and AlaRS-N alanine structures (2). In A. fulgidus AlaRS- C, the side-chain methyl group of the alanyl moiety is docked in a pocket formed by Met-147, Thr-212, Val-214, and Asp-242. The -amino group interacts with the strictly conserved Asp-242, whereas the -carbonyl oxygen interacts with Arg-128 in motif 2 (residues ). The adenine ring of Ala-SA is sandwiched between Phe-145 and Arg-249 and hydrogen-bonds with Asp- 131 and Leu-142 in motif 2. The ribose moiety adopts a C3 -endo conformation and hydrogen-bonds with Glu-209, Val-210, and Gly-246. The phosphate group interacts with Arg-128 and Thr The adenine N3 interacts with a water molecule, which is fixed by the Glu-248 side chain and the Arg-249 main-chain amide NH. Protein Preparation. Selenomethionine (SeMet)-containing AlaRS- C was prepared as described (3). One modification of the previous method is that a purification step with Resource ISO (GE Healthcare Life Sciences) was added after the UnoQ (Bio-Rad) purification step. The protein fractions were dialyzed against 50 mm Hepes NaOH buffer (ph 8.0), containing 500 mm NaCl and 5 mm 2-mercaptoethanol. Lys residues were methylated as described (4). The protein sample was dialyzed against 10 mm Tris HCl buffer (ph 8.0), containing 5 mm MgCl 2, 0.2 mm zinc acetate, and 5 mm 2-mercaptoethanol, and was concentrated to 10 mg ml 1 by using Amicon Ultra centrifugal filter devices (Millipore). Crystallization and Data Collection. Crystals of AlaRS- C were obtained by the sitting-drop vapor-diffusion method, by mixing 1 L of protein solution with 1 L of precipitant solution containing 0.1 M Bis Tris HCl (ph 7.2), 18% (wt/vol) polyethylene glycol (PEG) 2,000-MME, 5 mm MgCl 2, and 0.25 mm Ala-SA (Integrated DNA Technologies) and equilibrating the drop against the precipitant solution at 293 K. They belong to the space group C2, with unit cell dimensions of a Å, b 49.1 Å, c 98.0 Å, and 108.1, which differ from those of the previous P4 3 crystals (3). Before cryo-cooling, the crystals were transferred to the precipitant solution, containing 25% PEG2000-MME and 7.5% MPD. The crystals were then picked up with a nylon loop (Hampton Research) and flash-cooled with liquid nitrogen. Diffraction data sets were collected at 95 K at the beamlines BL17A and NW12A of the Photon Factory. The data were indexed, integrated, and scaled with the HKL2000 program suite (5). 1. Ueda H, et al. (1991) X-ray crystallographic conformational study of 5 -O-[N-(L-alanyl)- sulfamoyl]adenosine, a substrate analogue for alanyl-trna synthetase. Biochim Biophys Acta 1080: Swairjo MA, Schimmel PR (2005) Breaking sieve for steric exclusion of a noncognate amino acid from active site of a trna synthetase. Proc Natl Acad Sci USA 102: Fukunaga R, Yokoyama S (2007) Crystallization and preliminary X-ray crystallographic study of alanyl-trna synthetase from the archaeon Archaeoglobus fulgidus. Acta Crystallogr F 63: Walter TS, et al. (2006) Lysine methylation as a routine rescue strategy for protein crystallization. Structure (London) 14: Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: Beebe K, Mock M, Merriman E, Schimmel P (2008) Distinct domains of trna synthetase recognize the same base pair. Nature 451: Davis MW, Buechter DD, Schimmel P (1994) Functional dissection of a predicted class-defining motif in a class II trna synthetase of unknown structure. Biochemistry 33: Hill K, Schimmel P (1989) Evidence that the 3 end of a trna binds to a site in the adenylate synthesis domain of an aminoacyl-trna synthetase. Biochemistry 28: Ho C, Jasin M, Schimmel P (1985) Amino acid replacements that compensate for a large polypeptide deletion in an enzyme. Science 229: Ribas de Pouplana L, Buechter D, Sardesai NY, Schimmel P (1998) Functional analysis of peptide motif for RNA microhelix binding suggests new family of RNA-binding domains. EMBO J 17: Shi JP, Musier-Forsyth K, Schimmel P (1994) Region of a conserved sequence motif in a class II trna synthetase needed for transfer of an activated amino acid to an RNA substrate. Biochemistry 33: of9

2 A 1-87 P.horikoshii α 1 α 2 β 1 β 2 AddA1 α 3 MTLDEEYLDITFLTENGFVRKRCPKCGKHFWTADPEREICGDPPCESYSFIGNPVFKKPFELDEMREYYLNFFERRG---HGRIERYPVV ---MEFIMKTRMFEEEGWIRKKCKVCGKPFWTLDPDRETCGDPPCDEYQFIGKPGIPRKYTLDEMREKFLRFFEKHEIYPHGRVKRYPVL MDSTLTASEIRQRFIDFFKRN---EHTYVHSSATI SKSTAEIRQAFLDFFHSKG---HQVVASSSLV SLSAHEIRELFLSFFEKKG---HTRVKSAPLV β 3 α 1 β P.horikoshii η 1 β 4 η 2 β 5 ARWRTDIYLTIASIADFQPFVTSGVAPPPANP----LTISQPCIRLD----DLDSVGRTGRHLTLFEMMAHHAFNYPGKEIYWKNETVAY PRWRDDVLLVGASIMDFQPWVISGEADPPANP----LVISQPSIRFT----DIDNVGITGRHFTIFEMMAHHAFNYPGKPIYWMDETVEL PLDDPTLLFANAGMNQFKPIFLNTIDPSHPMAKLSRAANTQKCIRAGGKHNDLDDVGKDVYHHTFFEMLGSWSFG----D-YFKELACKM PHNDPTLLFTNAGMNQFKDVFL-GLDKRNYS----RATTSQRCVRAGGKHNDLENVGYTARHHTFFEMLGNFSFG----D-YFKHDAIQF PENDPTLLFVNAGMVPFKNVFL-GLEKRPYK----RATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFG----D-YFKKEAIEY η 1 α 2 β 2 β 3 β 4 β 5 α 3 α 4 η 3 β 6 β CTELLN---ELGVKKEDIVYKEE PWAGGG--NAGPCLEAIV--G P.horikoshii AFEFFTK--ELKMKPEDITFKEN PWAGGG--NAGPAFEVLY-RG ALELLT--QEFGIPIERLYVTYFGGDEAAGLEADLECKQIWQNLGLDDTKILPGNMKDNFWEMGDTGPCGPCSEIHYDR----IGGRDAA AWELLTSEKWFALPKERLWVTVYESDDEAYEIWEKEVGIPRERIIRIGDNKGAPYASDNFWQMGDTGPCGPCTEIFYDHGDHIWGGPPG AWEFVT--EVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSERIWRLGEE DNFWQMGDVGPCGPSSEIYVDRG η 2 β 6 α 4 η 3 β 7 α5 β 8 β 9 InsB/E1 InsB/E2 InsA1 β 8 β 9 β 10 α 5 α 6 α GLEVATLVFMNLEEHPEGD-----IEIKGARYRKMDNYIVDTGYGLERFVWASKGTPTVYDAIFPEVVDTIIDNSN--VSF P.horikoshii LEVATLVFMQYKKAPENAPQDQVVVIKGEKYIPMETKVVDTGYGLERLVWMSQGTPTAYDAVLGYVVEPLKKMAG--IEK HLVNQDDPNVLEIWNLVFIQYNR--EADG ILKPLPKKSIDTGMGLERLVSVLQNKMSNYDTDLFVPYFEAIQKGTG-ARP -SPEEDGDRYIEIWNIVFMQFNR--QAD GTMEPLPKPSVDTGMGLERIAAVLQHVNSNYDIDLFRTLIQAVAKVTGAT-- -EEYEGDERYLEIWNLVFMQYNR--DEN GVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEEVSGKKYG α 6 β 10 β 11 α 7 η 4 α 8 α 8 InsA2 α 9 α NREDERVRRIVAESSKLAGIMGELRGERLNQLRKSVADTVGVSVEELEGIVVPLEKVYSLADHTRCILFMLGDGLVPSNAGAGYLARLMI P.horikoshii IDEK-----ILMENSRLAGMFDIEDLGDLRYLREQVAKRVGITVEELEKAIRPYELIYAIADHTKALTFMLADGVVPSNVKAGYLARLLI YT GKVGAEDADGIDMAYRVLADHARTITVALADGGRPDNTGRGYVLRRIL DLSNKSLRVIADHIRSCAFLIADGVMPSNENRGYVLRRII E KFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRIL α 9 α 11 α 12 α 13 β RRSLRLAEE-LELG-LDLYDLVEMHKKILG---FEFDVPLSTVQEILELEKERYRTTVSKGTRLVER----LVERK-----KKLEKDDLI P.horikoshii RKSIRHLRE-LGLE-VPLSEIVALHIKELHKTFPEFKEMEDIILEMIELEEKKYAETLRRGSDLVRREIAKLKKKG----IKEIPVEKLV RRAVRYAHEKLNASRGFFATLVDVVVQSLGDAFPELKKDPDMVKDIINEEEVQFLKTLSRGRRILDR-K-IQSLGDSK----TIPGDTAW RRAVRHGNM-LGAKETFFYKLVGPLIDVMGSAGEDLKRQQAQVEQVLKTEEEQFARTLERGLALLDE----ELAKLS-GD--TLDGETAF RRAMRFGYK-LGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEKRFIKTLKAGMEYIQE----VIQKALEEGRKTLSGKEVF α 10 α 11 α 12 β 12 α 14 α 15 β 12 α ELYDSHGIPVELAVGIAAEKGAEVEMPKDIYAELAKRHSKAEKVQE------KKITLQN---E P.horikoshii TFYESHGLTPEIVKEIAEKEGVKVNIPDNFYSMVAKEAERTKEEKG------EELVDFELLKD LLYDTYGFPVDLTGLIAEEKGLVVDM--DGFEE-ERKLAQLKSQGKGAGGEDLIMLDIYAIEE RLYDTYGFPVDLTADVCRERNIKVD--EAGFEAAMEEQRRRAREASGFG AD TAYDTYGFPVDLIDEIAREKGLGID--LEGFQCELEEQRERARKHFKVEAKKVKPVY α 13 α 14 β 13 α 15 Fig. S1. Alignments of the AlaRS and AlaX sequences. A total of 249 AlaRS sequences were initially aligned by using the ClustalW program (6), and then were manually adjusted based on the structural information. The sequences of the A. fulgidus, P. horikoshii, Homo sapiens, E. coli, and A. aeolicus AlaRSs are shown. The highly-conserved residues are boxed in red. Secondary structure information is shown above the A. fulgidus sequence. The color codes are the same as those in Fig. 1B. The E. coli residues, which are important for the activity (7 12), are enclosed by sky-blue boxes. (A) The aminoacylation and trna-recognition domains, including the linker. The residues that are involved in the Ala-SA interactions in A. fulgidus AlaRS- C are boxed in green. Secondary structure information from the A. aeolicus AlaRS-N structure is shown in gray, below the A. aeolicus sequence. The residues involved in interactions with the editing domain are marked by gray boxes. (B) The editing and dimerization domains. The sequences of P. horikoshii AlaX-M and AlaX-S are also shown. The zinc-binding residues are highlighted in blue. The serine-interacting residues in AlaX-S are enclosed in yellow boxes. The residues involved in interactions with the aminoacylation/trnarecognition domains are marked by gray boxes. The sky-blue boxes depict hydrophobic residues involved in the HLHZ in the dimerization domain. 2of9

3 B P.horikoshii PhoAlaX-M 1-53 β 13 β 14 β 15 β 16 β 17 -YPATEKLYYDDPTLL EFEAEVIGVEGD FVILNRSAFYPESGGQDNDVGYLIA------NG -LPDTRRLYYEDPFMK EFDAKVLRVIKD WVILDATAFYPEGGGQPYDTGVLIV------NG -LRARG-LEVTDDSPKYNYHLDSSGSYVFENTVATVMALRR-EK-MFVEEVSTGQECGVVLDKTCFYAEQGGQIYDEGYLVKVDDSSEDK -YNAMIRVDSASEFKGY-DHLELN-----GKVTALFV--DG-KAVDAINAGQ---EAVVVLDQTPFYAESGGQVGDKGELKGA------N -SHLKELG-KTSAFVGY-EHMEWES-----QVVGLVKGEG---LVSELKEGE---EGEVVLKETPFYPEGGGQIGDAGIIES------DK MINMTRKLYYEDAYLK EAKGRVLEIRDN AILLDQTIFYPTGGGQPHDRGTI NG P.horikoshii PhoAlaX-M PhoAlaX-S 1-46 β 18 β 19 β 20 β 21 α 17 β 22 β 23 GKFEVVDVLEAD-GVVLHVVKGAKP--EVGTKVKGVIDSDVRWRHMRHHSATHVLLYSLQKVLGNHV-WQAGARKEFS--KARLDVTHFR REVKVTNVQKVG-KVIIHKVEDPGA-FKEGMIVHGKIDWKRRIQHMRHHTGTHVLMGALVRVLGRHV-WQAGSQLTTD--WARLDISHYK TEFTVKNAQVRG-GYVLHIGTI-YGDLKVGDQVWLFIDEPRRRPIMSNHTATHILNFALRSVLG-EA-DQKGSLVAPD--RLRFDFTAKG FSFAVEDTQKYG-QAIGHIGKLAAGSLKVGDAVQADVDEARRARIRLNHSATHLMHAALRQVLGTHV-SQKGSLVNDK--VLRFDFSHNE ALFKVEDTQKPTEGIIVHIGKVLKGTLKVGDTVHARVDKERRWDIMRNHTATHLLHAALRNVLGEHV-RQAGSLVADK--YLRFDFTHFS --VEVLDVYKDEEGNVWHVVKEPEKF-KVGDEVELKIDWDYRYKLMRIHTGLHLLEHVLNEVLGEGN-WQLVGSG-MSVEKGRYDIAYPE MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGN--KGVLIVKFDR P.horikoshii PhoAlaX-M PhoAlaX-S α 18 β 24 α 19 η 4 β 25 β 26 RPSEEEIKEIEMLANREILANKPIKWEWMDRIEAERKFGFRLYQGGVPPG--RKIRVVQVGD DVQACGGTHCR RISEEELKEIEMLANRIVMEDRKVTWEWLPRTTAEQKYGFRLYQGGVVPG--REIRVVKIEDW DVQACGGTHLP AMSTQQIKKAEEIANEMIEAAKAVYTQDCPLAAAKAIQGLRAVFDETYP---DPVRVVSIGVPVSELLDDPSGPAGSLTSVEFCGGTHLR AMKPEEIRAVEDLVNTQIRRNLPIETNIMDLEAAK-AKGAMALFGEKYD---ERVRVLSMGD FSTELCGGTHAS ALTEEELKRVEELVNEKIRENLPVNVMEMAYDEAL-KTGAIAIFEEKYG---ERVRVISCG EFSKELCGGTHVS NLNK-YKEQIISLFNKYVDEGGEVKIWWE GDRRYTQIRDF EVIPCGGTHVK KPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDW NVNACNKEHTK P.horikoshii PhoAlaX-M PhoAlaX-S η 5 β 26 β STGEIGMLKILKVESIQ-DGVIRFEFAAGEA STGLVGPIKILRTERIQ-DGVERIIFACGEA NSSHAGAFVIVTEEAIA-KGIRRIVAVTGAE RTGDIGLFRIISESGTA-AGVRRIEAVTGEG ATGDIGYFKIISESSVG-AGVRRIVAQTGRW DIKEIGHIKKLKRSSIG-RGKQRLEMWLE-- TTGEIGPIKIRKVRFRKSKGLLEIHFELLE- P.horikoshii α 20 α 21 AIEAVEEMERLLREASSILRVE PAKLPKTVER-----FFEEWK-DQRKEIERLKSVIADLWADILMERAEE- AIREWQKERDLLKKASNVLRVP PEKLPETAER-----FFNEWK-EARKEVDKLKKELARLLVYELESKMQK- AQKALRKAESLKKCLSVMEAKVKAQTAPNKDVQREIADLGE-ALATAVIPQWQKDELRETLKSLKKVMDDLDR-ASKADVQKRVLEKTKQ AIATVHADSDRLSEVAHLL KGDSN--NLADKVR------SVLERTRQLEKELQQLKE---QAAAQE---SANLS SVETAFKEHQTLKKASS ALGVGEEEVIQKIE------ELKEEIKDREREIQRLKQELLKLQIRE V β P.horikoshii β 29 α 22 β 30 β 31 α 23 β 32 FDS MKVVAEVVDADMQALQKLAERLAE---KGAVGCLMAKGEG--KVFVVTFSGQK----YDARELLREIGRVAKGSGGGRKD IGS IEFIGEVVEGSMEDLRELVEKLKK---PKRVVVLISRD----GYFAVSVGSEV---GVEANELAKKITLIAGGGGGGRRD FIDSNPNQ-PLVILEMESGASAKALNEALKLFKMHSPQTSAMLFTVDNEAGKITCLCQVPQNAANRGLKASEWVQQVSGLMDGKGGGKDV SKAIDVNGVKLLVSELSGV-EPKMLRTMVDDLKNQLG-STIIVLAT-VVEGKVSLIAGVSKDVTDR-VKAGELIGMVAQQVGGKGGGRPD VKEENVGDFTLHYGVFEEV-EPEELRNLADMLRQRTK-KDVVFIASRKGD-KINFVIGVSKEISDK-VNAKEVIREVGKVLKGGGGGRAD P.horikoshii β 33 α 24 VAQGAVQQLLDREEMLDVIFRFLSEHEG---- IAQGKVKDISKAKDVIESIKSMFS SAQATGKNVGCLQEALQLATSFAQLRLGDVKN MAQAGGTDAAALPAALASVKGWVSAKLQ---- LAQGGGKAPDKFPEAVKLLKEILSG Fig. S1. (continued) 3of9

Asp242 Arg128 Val214 Met147 Asp131 Phe145 Thr212 Glu209 Gly246 Leu142 Glu248 Val210 Arg249 Fig. S2. The aminoacylation site of A. fulgidus AlaRS.

4 Asp242 Arg128 Val214 Met147 Asp131 Phe145 Thr212 Glu209 Gly246 Leu142 Glu248 Val210 Arg249 Fig. S2. The aminoacylation site of A. fulgidus AlaRS. The bound Ala-SA is shown as a yellow stick model. An annealed F o F c omit electron density map, contoured at 3, is superposed on the refined model. The residues interacting with Ala-SA are shown in white stick models. 4of9

5 A B Fig. S3. Different orientations of Mid2 between the A. fulgidus and A. aeolicus structures. (A) The aminoacylation and trna recognition domains of A. fulgidus and A. aeolicus AlaRSs are superposed by the aminoacylation domain and Mid1 (stereoview). The two models were colored as in Fig. 2. Mid2 in A. fulgidus AlaRS- C and A. aeolicus AlaRS- are colored cyan and gold, respectively. (B) A closeup view of the Mid2 subdomains in A. 5of9

A AlaRS B P.horikoshii AlaX-S Glycine-rich loop His600 His9 Thr603 His120 His13 Thr33 His707 Cys703 His604 Gln620 Cys116 Thr30 Gln701 Gln682 Asn114 Asp92 Fig. S4.

Four ligand amino acid residues and a water molecule are depicted as white stick models and a red sphere, respectively.

6 A AlaRS B P.horikoshii AlaX-S Glycine-rich loop His600 His9 Thr603 His120 His13 Thr33 His707 Cys703 His604 Gln620 Cys116 Thr30 Gln701 Gln682 Asn114 Asp92 Fig. S4. The editing active site. (A) The editing active site of A. fulgidus AlaRS. The active-center zinc ion is shown as a silver sphere. Four ligand amino acid residues and a water molecule are depicted as white stick models and a red sphere, respectively. Thr-603, Gln-620, Gln-682, and Gln-701 protrude into the cavity. The glycine-rich loop is shown as a yellow tube. (B) The editing site of AlaX-S shown in the same orientation. The zinc ion, serine, and their interacting residues are shown. 6of9

7 α α Val744 Met747 Leu750 Leu751 Ala754 Ile757 Leu758 Val760 Pro762 Leu765 Pro766 Val769 Phe772 Phe773 Trp776 Ile783 Leu786 Val789 Ile790 Leu793 Ile797 Met747 Val744, Met747, Leu751 Pro766 Met747, Leu751, Pro762, Leu765 Leu765, Pro766, Val769 Val769, Ile757 Val769, Phe773, Ile757, Val769 Leu758, Leu765 Leu751 Ala754, Ala754, Val760, Pro766, Val769 Leu750, Ala754, Leu765 Ala754, Ile757, Leu758, Leu758, Leu765 Phe773, Trp776 Leu758, Phe772, Phe773, Trp776, Trp776 Phe772, Phe773, Phe773 Ile783, Leu786 Ile783, Leu786 Ile790 Leu786, Val789 Ile790, Leu793 Ile797 Fig. S5. A diagram summarizing the hydrophobic interactions in the HLHZ. Amino acid residues of the helical subdomain in 1 molecule are shown in the left column (colored red), and the residues within 4 Å from them are listed on the right. Red-colored residues denote those in the reference molecule (intramolecular interactions), while black-colored residues denote those in the counterpart (intermolecular interactions). 7of9

Ala-SA Ala-SA InsA2 InsA2 1 2 Arg731 1 2 Arg731 Val460 Mid2

8 Ala-SA Ala-SA InsA2 InsA2 1 2 Arg Arg731 Val460 Mid2 Arg371 Val460 Mid2 Arg371 Fig. S6. The stereoview of Fig. 5. 8of9

9 Table S1. Data collection, phasing, and refinement statistics AlaRS- C AlaRS-C PDB ID 2ZTG 2ZVF Data collection Beamline Photon Factory BL17A SPring8 BL41XU Space group C2 P222 1 Unit cell a 160.4, b 49.1, c 98.0 Å, 108 a 124.1, b 131.7, c Å Wavelength (Å) Resolution (Å) ( ) ( ) Completeness (%) 99.4 (95.2) 98.7 (91.3) Redundancy 7.3 (6.3) 9.7 (4.2) I/ (I) 24.0 (2.2) 18.4 (2.2) R sym * (0.510) (0.386) Phasing Se sites identified Phasing power FOM FOM after DM R Cullis Refinement Resolution (Å) No. reflections 37,067 37,899 R work /R free / / No. atoms Protein 5,894 10,707 Zn ion 2 - Sulfate ion - 30 rmsd Bond lengths (Å) Bond angles ( ) The statistics in the highest-resolution shell are given in parentheses. FOM, figure of merit. *R sym I I / I, where I is the observed intensity of reflections. R work, free F obs F calc / F obs. Free reflections consist of 5% of the total number of reflections. The previous data (3) were reprocessed. 9of9

Table 1. Crystallographic data collection, phasing and refinement statistics. Native Hg soaked Mn soaked 1 Mn soaked 2

Table 1. Crystallographic data collection, phasing and refinement statistics Native Hg soaked Mn soaked 1 Mn soaked 2 Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell