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1 doi: /nature11541 Supplementary Figure 1. Genome-wide analysis of the phylogenetic relationships Phylogenetic tree of NDH-2s from Prokaryota, Protista, Plantae, Fungi and Metazoa. The 1
2 RESEARCH SUPPLEMENTARY INFORMATION phylogenetic tree of 136 NDH-2s from 61 species is shown. Protein names are corresponding to locus tags, except for Smi1, 2, 3 and Sba1, 2, 3 identified from draft genomes of Saccharomyces mikatae and Saccharomyces bayanus, respectively. Species followed by locus tags from Prokaryota, Protista, Plantae, Fungi and Metazoa are colored in blue, brown, green, black and orange, respectively. The numbers at nodes of the phylogenetic tree are bootstrap values. The numbers of NDH-1 subunits in each species are provided in parentheses. Supplementary Figure 2. The unique CTD of Ndi1 is highly conserved. Phylogenetic tree (left) and partial sequence alignment (right) of NDH-2s from different species. Protein sequences are designated by locus tags. Species names in parentheses from Prokaryota, Protista, Plantae, Fungi, and Metazoa are colored as indicated. The numbers at nodes of the phylogenetic tree are bootstrap values. The numbers of NDH-1 subunits in each species are provided in square brackets. Conserved residues in the partial sequence alignment are shaded in colors. Secondary structural elements of Ndi1 are indicated above the sequences. 2
3 RESEARCH Supplementary Figure 3. Amino acids involved in FAD binding are essential for yeast growth. a. Ribbon representation of the FAD binding pocket. The FAD is shown as magenta sticks, interacting residues as yellow sticks, magnesium ions as gray spheres, and the hydrogen bonds as dashed lines. b. Mutations of the residues interacting with FAD could cause growth defect of yeast cells. Yeast cells were spotted on corresponding positions by serial 10-fold dilutions on SG-URA medium. WT, the BY4742 strain. Ndi1, mutants, and Vector: pyes2-ndi1, pyes2-ndi1 mutants, and pyes2 vector-expressing ndi1 cells, respectively. 3
4 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 4. Detailed interactions between the CTD and the rest of Ndi1. a. Ribbon representation showing the interactions. Residues mediating the interactions are shown as sticks, colored yellow and orange, for those from the CTD and the rest of Ndi1, respectively. Hydrogen bonds are represented by red dashed lines. b. The interface of the interaction. The CTD is shown in cartoon and the rest of the protein is represented as an electrostatic surface model. Supplementary Figure 5. Detailed interactions on the dimer interface. a. Stereo view of part of the interface in the Ndi1 homodimer. Interacting residues from the two protomers are shown as yellow and magenta sticks, respectively. Hydrogen bonds are shown as dashed lines. b. Closer view of the environment around R490. The protein is colored and marked in the same scheme as in Fig. S5a, yet viewed from a reverse orientation. c. Mutations affecting dimer formation could cause growth defect of yeast cells. The data is presented as described in Fig. S3b. 4 W W W. N A T U R E. C O M / N A T U R E
5 RESEARCH Supplementary Figure 6. Ndi1 forms a homodimer in solution. a. Ndi1 forms a stable homodimer in solution. The gel filtration profiles of Ndi1 and the molecular markers on Superdex-200 column are shown. The sizes of the molecular markers are marked on top of the peaks. The bottom panel shows the SDS-PAGE gel of the samples of Ndi1. b. Activities of the enzyme under different enzyme concentrations. Supplementary Figure 7. The binding sites of Triton X-100 molecules. Ribbon representation shows the binding of the Triton X-100 molecules on the membrane attachment side. Ndi1 is shown as in Fig. 2a. Triton X-100 molecules are shown as marine sticks. 5
6 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 8. The binding sites of NADH molecules. Ribbon representation shows the binding of the NADH molecules. The CTD (residues 439 to 513) of one protomer is colored in hot pink, and the rest in cyan. The other is colored in orange and lime, for its CTD and the rest, respectively. Two FADs and two NADHs are shown in sticks. 6
7 RESEARCH Supplementary Figure 9. Amino acids involved in NADH binding are essential for yeast growth. a. Ribbon representation of the NADH binding pocket in the Ndi1-NADH complex. The NADH and FAD are shown as orange and magenta sticks, respectively. Residues interacting with NADH are shown as yellow sticks. The hydrogen bonds are shown as dashed lines. b. Structural alignment between apo-ndi1 and Ndi1-NADH complex. Ndi1, FAD and NADH in the Ndi1-NADH complex are all colored as in Fig. S9a. In apo-ndi1, Ndi1 and FAD are both colored pink. Residues undergoing conformational changes upon NADH binding are shown as sticks, colored in yellow and pink, in accordance with their respective color scheme. c. Mutations of the residues interacting with NADH could cause growth defect of yeast cells. The data is presented as described in Fig. S3b. 7
8 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 10. The UQ binding sites are essential both for Ndi1 s activity and yeast survival. a. Close view of the UQ binding pocket. Ndi1 is represented as an electrostatic surface model. The two UQ molecules are marked and colored as slate sticks. b. Ribbon representation showing the UQ binding pocket. Interacting residues from the CTD and the rest of Ndi1 are shown as yellow and orange sticks, respectively. The hydrogen bond is shown as a dashed line. c. Plots of the initial rates of Ndi1 WT, Ndi1 Y482F, and Ndi1 M485E-catalyzed NADH oxidation versus the NADH concentration. The solid line is the best fitting result according to the Michaelis-Menten equation for each plot except Ndi1 M485E whose activity is too low to be fitted. d. Mutations of the residues interacting with UQ could cause growth defect of yeast cells. The data is presented as described in Fig. S3b. 8
9 RESEARCH Supplementary Figure 11. The distance between FAD and UQ II is in the range of electron transfer. Structural alignment between Ndi1-UQ complex and Pdr-Pdx complex (PDB: 3LB8). Ndi1 is colored as in Fig. S10b. The C terminal part of Pdr is colored in yellow, and the rest in salmon. The Pdx is colored in green. The [2Fe-2S] cluster is shown in spheres. 9
10 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Figure 12. UQ I acts as a co-factor with FAD Structural alignment of the reaction center between the Ndi1-NADH-UQ and Ndi1-UQ complexes. In the structure of Ndi1-UQ complex, FAD and UQ molecules are shown as in Fig. S10b. In the Ndi1-NADH-UQ complex, NADH, FAD, and UQ are all shown as orange sticks. Supplementary Figure 13. Electrostatic surface model of the Ndi1 dimer Ndi1 homodimer viewed from the matrix side, perpendicular to the mitochondrial inner membrane plane. Two FADs are indicated. 10
11 RESEARCH Supplementary Table 1. NADH dehydrogenases used to construct the ML tree. Classfication Species Locus, tags Fungi Saccharomycetaceae Saccharomyces cerevisiae S288C YDL085W(NDE2), YML120C(NDI1), YMR145C(NDE1) Saccharomyces bayanus MCYC 623 Sba1, Sba2, Sba3 Saccharomyces mikatae IFO 1815 Smi1, Smi2, Smi3 Candida glabrata CBS138 CAGL0B02431g, CAGL0I00748g Kluyveromyces lactis NRRL Y 1140 KLLA0A08316g, KLLA0C06336g, KLLA0E21891g Ashbya gossypii ATCC AGOS_ADR262C, AGOS_AFR447C Saccharomycetales Candida albicans SC5314 CaO (NDE2), CaO19.339(NDE1), CaO (NDE2) Debaryomyces hansenii CBS767 DEHA2D07568g Pichia stipitis CBS 6054 PICST_66598(NDE1) Yarrowia lipolytica CLIB122 YALI0E05599g, YALI0F25135g Candida tropicalis MYA 3404 CTRG_02112, CTRG_02605 Clavispora lusitaniae ATCC CLUG_04257 Lodderomyces elongisporus NRRL YB 4239 LELG_00216, LELG_02069 Meyerozyma guilliermondii ATCC 6260 PGUG_02433, PGUG_04603 Ascomycota Neurospora crassa OR74A NCU00153, NCU05225, NCU11397 Magnaporthe oryzae MGG_04140, MGG_04999, MGG_06276 Gibberella zeae PH 1 FG , FG , FG Aspergillus fumigatus Af293 AFUA_1G11960, AFUA_1G14520, AFUA_2G05450 Aspergillus clavatus NRRL 1 ACLA_020920, ACLA_023620, ACLA_ Schizosaccharomyces pombe 972h SPAC3A11.07, SPBC947.15c Basidiomycota Laccaria bicolor S238N H82 LACBIDRAFT_192207, LACBIDRAFT_306184, LACBIDRAFT_ Cryptococcus neoformans JEC21 CNA07650, CNG00750 Ustilago maydis 521 UM , UM , UM metazoa Ciona intestinalis Nematostella vectensis NEMVE_v1g Hydra magnipapillata , Trichoplax adhaerens TRIADDRAFT_2088 Plantae Chlamydomonas reinhardtii CHLREDRAFT_133334(NDA2), CHLREDRAFT_189359(NDA5), CHLREDRAFT_195711(NDA3), CHLREDRAFT_195719(NDA1) Cyanidioschyzon merolae 10D CMF056C, CMM178C, CMQ432C Physcomitrella patens subsp. Patens PHYPADRAFT_130383, PHYPADRAFT_133264, PHYPADRAFT_178164, PHYPADRAFT_179555, PHYPADRAFT_183387, PHYPADRAFT_ Oryza sativa ssp. japonica cultivar Nipponbare , , Arabidopsis thaliana AT2G20800(NDB4), AT2G29990(NDA2), AT4G05020(NDB2), AT4G21490(NDB3), AT4G28220(NDB1) Glycine max , , , , , , Selaginella moellendorffii SELMODRAFT_107483, SELMODRAFT_176951, SELMODRAFT_231541, SELMODRAFT_
12 RESEARCH SUPPLEMENTARY INFORMATION Protista Eubacteria Archaea Trypanosoma brucei TREU927 Dictyostelium discoideum Plasmodium falciparum 3D7 Plasmodium vivax SaI 1 Cryptosporidium parvum Iowa II Toxoplasma gondii ME49 Phytophthora infestans T30 4 Thalassiosira pseudonana CCMP1335 Acidobacterium capsulatum ATCC Candidatus Nitrospira defluvii Chloroflexus sp. Y 400 fl Rhodopirellula baltica SH 1 Bacteroides fragilis NCTC 9343 Mycobacterium tuberculosis H37Rv Leptospira interrogans serovar Lai Escherichia coli K 12 MG1655 Bacillus subtilis 168 Candidatus Protochlamydia amoebophila UWE25 Gemmatimonas aurantiaca T 27 Deinococcus radiodurans R1 Aquifex aeolicus VF5 uncultured methanogenic archaeon RC I Methanobacterium sp. SWAN 1 Halobacterium salinarum R1 Sulfolobus islandicus L.S.2.15 Sulfolobus solfataricus P2 Halophilic archaeon DL31 SELMODRAFT_ Tb10.6k DDB_G , DDB_G , DDB_G PFI0735c PVX_ cgd7_1900 TGME49_009150, TGME49_ PITG_14863 THAPSDRAFT_36673, THAPSDRAFT_38312, THAPSDRAFT_38602, THAPSDRAFT_6361, THAPSDRAFT_687 ACP_1313, ACP_2469 NIDE0026(ndh) Chy400_0148, Chy400_3620 RB5766(ndh) BF1612(ndh) Rv0392c(ndhA), Rv1812c, Rv1854c(ndh) LB_036(ndh) b1109(ndh) BSU12290(ndh), BSU32100(yumB), BSU32200(yutJ) pc1809(ndh) GAU_0395(ndh) DR_0950 aq_788 RCIX501(ndh) MSWAN_2349 OE2307F(ndh) LS215_1304, LS215_2385 SSO1010, SSO2960, SSO3148 Halar_2594, Halar_
13 RESEARCH Supplementary Table 2. Statistics of data collection and structures refinement. Data collection Se-SAD(apo) NADH UQ NADH + UQ Space Group C222 1 C222 1 C222 1 C222 1 Unit Cell (Å) , , , , , , , , Wavelength (Å) Resolution (Å) 50~2.39 (2.48~2.39) ( ) ( ) ( ) Rmerge (%) 10 (41.3) 11.8(64.8) 11.3(64.4) 11.4(75.3) I/σ 10.4 (2.1) 11.6(2.0) 25(2.9) 13.3(1.98) Completeness (%) 96.9 (83.7) 99.3(95.8) 97.4(78.6) 99.9(99.9) Redundancy 3.8 (3.3) 3.7(3.1) 11.4(9.8) 3.8(3.8) Wilson B factor (Å 2 ) SAD phasing Anomalous scatterers 8Se Figure-of-merit (FOM) FOM after DM FOM after phase combination Refinement R factor R free No. atoms 7812 protein atoms + 10 Mg TRT + 2 FAD 7821 protein atoms + 8 Mg TRT + 2 FAD + 2 NADH 7828 protein atoms + 8 Mg UQ + 2 TRT + 2 FAD 7781 protein atoms + 8 Mg NADH + 2 UQ + 2 TRT + 2 FAD B factors: Overall RMSD bond lengths RMSD bond angles Ramachandran plot Statistics (%) In preferred regions In allowed regions Outliers PDB accession codes 4G6G 4G6H 4G74 4G73 Values in parentheses are for the highest resolution shell. R merge =Σ h Σ i I h,i -I h /Σ h Σ i I h,i, where I h is the mean intensity of the i observations of symmetry related reflections of h. R=Σ F obs -F calc /ΣF obs, where F calc is the calculated protein structure factor from the atomic model (R free was calculated with 5% of the reflections selected). 13
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