ENZYME MECHANISMS, PROTEASES, STRUCTURAL BIOLOGY
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1 Supplementary Information SUBJECT AREAS: ENZYME MECHANISMS, PROTEASES, STRUCTURAL BIOLOGY Correspondence and requests for materials should be addressed to N.T. or W.O. Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity Yasumitsu Sakamoto 1,7, Yoshiyuki Suzuki 2,7, Ippei Iizuka 1, Chika Tateoka 1, Saori Roppongi 1, Mayu Fujimoto 1, Koji Inaka 3, Hiroaki Tanaka 4, Mitsugu Yamada 5, Kazunori Ohta 5, Hiroaki Gouda 6, Takamasa Nonaka 1, Wataru Ogasawara 2, and Nobutada Tanaka 6 1 School of Pharmacy, Iwate Medical University, Nishitokuta, Yahaba, Iwate , Japan; 2 Department of Bioengineering, Nagaoka University of Technology, Kamitomioka, Nagaoka, Niigata , Japan; 3 Maruwa Foods and Biosciences Inc., Tsutsui-cho, Yamatokoriyama, Nara , Japan; 4 Confocal Science Inc., Iwamoto-cho, Chiyoda-ku, Tokyo , Japan; 5 Japan Aerospace Exploration Agency, Sengen, Tsukuba, Ibaraki , Japan; 6 School of Pharmacy, Showa University, Hatanodai, Shinagawa-ku, Tokyo , Japan 7 These authors contributed equally to this work. Supplementary information includes: Supplementary Figures S1-S3 Supplementary Tables S1-S3 1
2 Figure S1 Representative electron density maps of. Contour levels are 1.5 for both cases. The final refined model for each data set is superimposed on the respective electron density maps. (A) Experimentally phased MAD map at 2.5 Å resolution. (B) Final refined 2Fo-Fc map at 1.66 Å resolution. 2
3 Figure S2 Topology diagram of. The secondary structure elements are coloured as described in Figure 2. The active site and oxyanion hole are indicated by a rounded rectangle (cyan) and a circle (green), respectively. 3
4 Figure S3 Representative electron density map of the bound Leu-Glu dipeptide in G675R mutant DAP BII. To exclude a model bias, the structure was refined in the absence of the dipeptide molecule before the map calculation. The amplitude Fc and the phase angle calculated from the partial structure were then used to calculate the Fo Fc omit map. The contour levels are 3.0 σ (blue) and 4.5 σ (red). 4
5 Table S1 Data collection statistics for and G675R mutant DAP BII. Data set Se-Met Peak Se-Met Edge Se-Met Remote Space Ground WT P DAP BII G675R Beamline PF BL17A PF BL17A PF BL17A PF BL17A PF-AR NE3A PF-AR NW12A PF BL17A Wavelength (Å) Detector ADSC Q270 ADSC Q270 ADSC Q270 ADSC Q270 ADSC Q210r ADSC Q210r PILATUS 6M Space group P P P C2221 C2221 P P43212 Asymmetric unit Cell dimensions a (Å) b (Å) c (Å) Resolution (Å) 2.46 ( ) a Total reflections 412,705 (13,522) Unique reflections 62,234 (4,304) ( ) 402,394 (15,714) 57,627 (4,179) ( ) 404,427 (14,397) 59,586 (4,250) 1 subunit (a half dimer) ( ) 656,335 (40,782) 105,914 (7,774) 1 subunit (a half dimer) ( ) 437,251 (12,645) 71,425 (4,928) ( ) 200,486 (21,188) 45,581 (6,818) ( ) 633,364 (48,249) 88,533 (6,460) Rsym (%) 11.2 (59.7) 12.6 (67.4) 12.0 (63.3) 5.1 (74.2) 8.0 (15.5) 6.4 (39.4) 8.4 (73.6) Rpim (%) 5.7 (39.7) 6.4 (43.9) 6.1 (41.7) 2.0 (32.1) 3.1 (10.6) 2.8 (17.3) 3.1 (26.1) I/sig.I 12.6 (2.1) 12.3 (2.1) 12.8 (2.0) 19.8 (2.5) 15.0 (2.4) 28.7 (2.0) 16.3 (3.1) Completeness (%) 99.6 (99.5) 99.9 (99.5) 99.8 (98.2) 99.6 (98.9) 97.5 (92.0) 96.4 (94.0) 99.8 (100) Redundancy 6.6 (3.1) 7.0 (3.8) 6.8 (3.4) 6.2 (5.2) 6.1 (2.6) 4.4 (4.3) 7.2 (7.5) Average mosaicity ( ) Wilson B-factor (Å 2 ) a Highest resolution shell is shown in parenthesis. 5
6 Table S2 Refinement statistics for and G675R mutant DAP BII. Data set Se-Met Peak Se-Met Edge Se-Met Remote Space Ground WT P PDB ID 4Y Y04 4Y02 4XZY 4Y06 DAP BII G675R Resolution (Å) ( ) a ( ) ( ) ( ) ( ) No. reflections 58, ,593 61,427 43,583 84,077 Rwork / Rfree / (0.286/0.327) 0.186/0.224 (0.326/0.340) / (0.263/0.319) 0.181/ (0.259/0.353) / (0.232/0.304) No. of atoms Protein 11,216 5,533 b 5,492 c 11,216 10,756 Peptide Glycerol K Zn Water B-factors Chain A Chain B Peptide in A Peptide in B Glycerol K Zn Water R.m.s d. d Bond lengths (Å) Bond angles ( ) Dihedral angles ( ) Chirality Planarity a Highest resolution shell is shown in parenthesis. b Residues in the C2221 form of the space-grown crystal were disordered. c Residues and in the C2221 form of the ground-grown crystal were disordered. d MOLPROBITY [Acta Crsytallogr. D66, (2010).] 6
7 Table S3 A comparison of structural features of with those of human DPPs I and 4. Enzyme Clan / Family Specificity Catalytic domain Regulatory domain N-term. (P2-N) recognition a P2-C=O recognition a P1-NH recognition P1-C=O recognition PA / S46 P1: Asp/Glu Double -barrel chymotrypsinlike fold -helical COO - (Asp672) C=O b (Asn218) C=O b (Asn333) Pai c (Trp219) NH2 (Asn333) C=O (Phe671) NH (Gly653) NH (Ser655) HsDPP4 SC / S9 P1: Pro / hydrolase fold Eight-bladed -propeller COO - (Glu205) COO - (Glu206) NH2 (Arg125) NH2 (Asn710) NONE NH (Tyr631) OH (Tyr547) HsDPPI (Cathepsin C) CA / C1 NONE + papain-like fold Eight-stranded -barrel COO - (Asp1) C=O (Gly277) Pai c (Phe278) NH(Gly277) C=O (Asn380) a Residues belonging to the regulatory domain are shown in italics. b Side-chain carbonyl group. c Negative center of aromatic-pai electrons. NH (Cys234) NH2 (Gln228) 7
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