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2 Ṟ ሾ ᮮ ㅨ ࢰ ࢠ ࡗ 㸡ᵋ ᶭ よᯊ ࡖࡒࠊ ይ Ⳟ ࢰ ࢠ ࡗ ୯ ᶭ㛭 1000 㢦 w ࢰ ࢠ ࢪ ᵋ ኬ㔖 㞗୯ 㸡 ࢪ 300 㢦௧ ࢰ ࢠ ࢦ ᶭ㛭 ࡊ よᯊ ౩ࡌ ࡆ 㸡ࢡ ධ మ ࡊ ຝ ࡂスങ ㈠ᮞ Ὡ ࡊࡒࠊ ࡒ ᣈⅤ ᖲ ࡊ ㅨ ࢰ ࢠ ࡗ ᵋ ᶭ よᯊ 㐅 ࡒࠊ ᵋ ᶭ よᯊ ᠺᯕ ࡊ 㸡ḗ ᣪࡅ ࡆ ࡀ ࠊ & Ꮥ㛭 ฦ㔕 ࢰ ࢠ & Ț ࢡ ࢰ ࢨࢪ ᠺ㓕 ᅒ& 㸯 Ț-ࢡ ࢰ ࢨࢪ ᠺ㓕 (GCS) 㸡ࢡ ࢰ ࢲ ᠺࡌ 㝷 ᚂ ṹ㝭 ཬᚺ㸝ࢡ ࢰ 㓗㸠ࢨࢪ 㸞 り፳ࡊ㸡మහ ࢡ ࢰࢲ ಕࡖ ࠊࡊ ࡊ㸡ᐞ ཋ 㸡ࢡ ࢰࢲ 㓗 ࢪ ࢪ㜭ᚒࢨࢪ ᝇ ࡌ ࡆ ࡖ ኣ ᛮ ᚋࡊ ࠊኬ Ⳟ ᮮ GCS ᵋ 㐼 ࢡ 々 మ ᬏᵋ Ử ࡊࡒ ᯕ㸡ᚉᮮ 㒼า ῼ ࡖࡒࢨࢪ ᵕᘟ ཬᚺᶭᵋ ᥆ ྊ ࡖࡒࠊGCS Ὡᛮ ຝᯕ ᢒโࡌ スゝ ࡀ ࠉ ຝ ᢘᐞ ཋ ᢘ 㛜 ࡗ ᙽࡈ 㸡 ぞ㜴ᐐ モ㥺 㛜ጙࡊ ࠊ & ᆵࢬ ࢬ ࢭ ᅒ& 㸯 D-ࢬ 㸡୯ᯙ NMDA ࢬ ࢰ ࡌ ࢥ ࢪ 㸡 㧏ḗᶭ ࡖ 㔔さ ᙲ ᯕࡒࡊ ࠊࢬ ࢬ ࢭ (SerR) L-ࢬ D-ࢬ ᠺࡌ 㓕 㸡 ᅂ㸡ฦ 㓕ẍ SerR ᬏᵋ Ử ࡊࡒࠊࡐ Ὡᛮ㒂న 㸡 り፳ᇱ ࢨ ࢰ B6 㛣 D- ᯣᶣࡊࡒಞ㣥ᵋ ᣚࡖ ࡒࠊ ࡒ㸡ATP open-closed ᵋ ን 㐅ࡌ ࡆ SerR Ὡᛮ ࡌ ࡆ ࡖࡒࠊࡆ ሒ 㸡SerR 㜴ᐐ ୯ ንᛮ ᝀ ᑊࡌ ࡊ 㛜 ࡌ 㐠 㛜ࡄࡒࠊ & ࢲࢱ ࢭ㸝ᅒ & 㸞 㸯 ཋⳞ 㒂 㸡 ࢲࢱ ࢭ ⓮ ࢤ ࢣ ฦよࡊ ᰜ㣬 ࡌ ࠊ ᅂ㸡ṉ Ⳟ ࢬ ࢲ Ⳟ㸝 ぜវ ཋᅄⳞ ࡗ㸞 ᮮ ࢲࢱ ࢭ మᵋ Ử ࡊࡒࠊᇱ 㜴ᐐ ࡊࡒ㓕 Ὡᛮ㒂న レ よᯊ ᇱࡘ 㸡㜴ᐐ 㛜 ࡊࡒࠊⳞ ᰜ㣬ᦜ ᚂ ᛮ ࢲࢱ ࢭ 㜴ᐐ ࡌ ࡆ ࡖ 㸡 ࠔඹ ᨯ ࠕ Ⳟ 㜴ᐐ ࡆࡌࡆ ࡀ ࠊᢘ ᛮ ၡ 㢗 ࡖ ᅹ㸡ᮇ㓕 ᑊࡌ 㜴ᐐ ᚉᮮ ᢘ ᶭᵋ ᢘⳞ 㛜 ࢠࢪ ᛦ ࠊ & ࢪ ࢥ ࢭ㸯 ཋᛮ ᙁ Ⳟ ᨲฝࡌ ࢪ ࢥ ࢭ 㸡 ୯ ฦよࡊ ㉝ ቪࡌ Ὡᛮ ࡌࠊ ᅂ㸡ࢬ ࢪⳞ ࢪ ࢥ ࢭ ᬏᵋ Ử ࡊ㸡ࡐ 㓕 Ὡᛮ ᑊࡌ 㔘ᒌ ᙲ ࡊࡒࠊࡆ ᯕ 㸡 ᛮ 㛜 ࡗ ࠊ ࡒ㸡ᮇ㓕 ష ࡖ ࡋ ࢬ ⓮ み ᒒ ኣࡂ㸡 ࡒ ᛮ⓮ ⅎ 㛭 ࡌ ࡆ ࠊ ࡖ 㸡 ຝᯕ 㧏 ဗ 㛜 ࡌ ࠊ & ࢲ ࢨ ࢭ㸯 ࢲ ࢨ ࢭ, Ⰵ ᠺ 㛭 㔔さ 㓕 ࡒ 㸡ࡐ 㜴ᐐ ဗ ࡊ ࡀ ࠊ ᅂ㸡 Ⰵ 㧏 ࡌ ᨲ Ⳟ ᮮ ࢲ ࢨ ࢭ㸝Ὡᛮ 㖙 ᚪ㡪㸞 㸝ࢲ ࢨ ࢭ 㖙 㐘 㸞 々 మ ᵋ Ử ࡊࡒࠊᚉᮮ㸡 ࢤ ࢩ㓗 ࢲ ࢨ ࢭ㜴ᐐ ࡊ ࡀࡒ, ᛮ ࡆ ሒ ࡈ, ୯Ḿ ࡖࡒࠊ ᅂ ᵋ ᇱࡘ スゝࡈ ࡒࢲ ࢨ ࢭ㜴ᐐ 㸡Ꮽධᛮ 㧏 ぞ 㛜 ࡗ ࠊ Ț ࢡ ࢰ ࢨࢪ ᠺ㓕 ᆵࢬ ࢬ ࢭ ࢲࢱ ࢭ & & & & ࢨ㓏㓗 ࢣ ࢭ㸝ᅒ & 㸞 㸯 ᑺ 㸡 㓗 ㅨ ஸ㐅 ࡋ ࢢ మ ࢨ ࢨࢪ ࡊ ណㆉ㝸ᐐ ᣅࡂࡒ 㸡 ୯ࢢ మ ᗐ ࢰ ࡌ ᚪさ ࠊ3- ࢨ㓏㓗 ࢣ ࢭ 㸡3- ࢨ㓏㓗 ࢬ 㓉㓗㸝 ࡍ ࢢ మ㸞 Ề ཬᚺ り፳ࡌ 㓕 㸡 ᑺ チ ࡊ ࡈ ࠊᮇ㓕 ᬏᵋ 㓕 NADH ࡊࡒ 㓕 ࡗ Ử ࡊࡒࠊ 462

3 & ࢠ ࢲ ࢭ㸝ᅒ & 㸞㸯 ᶭ ᗃ ᰕ 㸡ࢠ ࢲ ฦよࡌ ࢠ ࢲ ࢭ ࡊࡒῼ ᗀࡂ ࠊ㔕 ᆵ ࢠ ࢲ ࢭ Ὡᛮ㒂న 㸧 ல㕼 ᣚࡗ㔘ᒌ㓕 ࠉ ᾦ ᯊࡌ 㸡Ὡᛮ ࡌ Ꮽ ᛮ ቌࡊࡒࠊ మᵋ Ử ࡊࡒ ࡆ ࠉ Ὡᛮᆵ㓕 ᪁ ல㕼 ᥦࡈ ࡆ ࡖࡒࠊ ᗃ ᰕモ 㧏 Ꮽ ᛮ ị ࡒ 㸡ᮇ ᅹ ᥦᆵ㓕 チ モ ࡊ ࡈ ࠊ & ᑺ㓗㓗 㓕 㸝ᅒ & 㸞㸯 మහ ᑺ㓗 㔖 㐛 㸡ᑺ㓗 ᬏ మහ ỷ ࡊ 㢴 ష ᘤࡀ ࡆࡊࡒ 㸡 ࡖ 㝸ᐐ ࡆࡌࠊࡐ ࡒ 㸡㧏ᑺ㓗 㢴 ష ๑ṹ㝭 ࡀࡒ 㸡 ᅹ Ὡ 㸝 ࢰ ࢠࢨ 㸞 㸦ࡗ ᣞᵾ ࡊ ࠊ ᅂ㸡ᑺ㓗 ᗃฦᯊ ᑺ㓗㓗 㓕 మᵋ Ử ࡊ㸡ࡐ ᯕ ᇱࡘ ฦᏄ スゝ 㸡 Ꮽ ᛮ 20Υ ࡈࡎ ࡆ ᠺ ࡊࡒࠊᚉᮮ Ꮽ モ 㓕 ࡊ ᴏ භ ᐁ ᒈ㛜 ᅒࡖ ࠊ & ࡐ 㸯 ࢦ ࢯ ᆵ ฦᒪ㙈 㓗 ᇱ 㓕 ࢲ 㸝 㸞 々 మ㸡 ࢬ ࢭ㸝ᢘ ᵾ 㸞 㸡 ࢨ 㸸㸝ᢘ 㸞 ࢰ ࢠ 㸡 ࢨ Ⳟ ࢰẐ Ia ᠺฦ㸡 ࢪ ࢯ ࢰ ࢠ Dsg1 ࡗ 㸡ᵋ ᶭ よᯊ ࡖࡒࠊ ࢨ㓏㓗 ࢠ ࢲ ࢭ ᑺ㓗㓗 㓕 ࢣ ࢭ & & & ' ይ ᛮ Ⳟ ࢰ ࢠ ' ぞ 1 ࢣ ࢭ ᅒ' 㸯 Ⰵ ౪Ꮛᛮ ࢣ ࢭ 㸡 ᕝⰅ 㞹Ꮔ ᐖ మ ࡊ 㸡 㓗 㓗 㑇ඔཬᚺ り፳ࡌ 㓕 㸡ᶭ 㞹ᴗᆵ ࢬ ࢦ ࡀ ࠊⰅ ౪Ꮛᛮ ࢣ ࢭ ࡊ ይ Ⳟ ぜ ࡓࡈ ࡒ L- ࢣ ࢭ ᵋ ᶭ よᯊ 㸡ࡐ ᵋ ཬᚺᶭᵋ ධࡂ ࡊ ࢰ ࡆ よ ࡊࡒࠊࡈ ᮇ㓕 ᅖ ࡊ ࡒ㞹ᴗ ᗐ 㞹ᴗᚺ ῼ ࡀ ࡆ ࡊࡒࠊࡆ 㸡Ꮽ ይ Ⳟ ᮮ 㓕 ࢬ ࢦ ຝ ࡀ ࡆ ࡊࡒ ࠊ ᅂ మᵋ Ử ࡖ 㸡 ࢠ ࢬ ࢦ ࡈ 㧏ᛮ ྊ ࡖࡒࠊ ' 3&) ౪Ꮛᛮࢡ ࢰ 㓗 ࢣ ࢭ ᅒ' 㸯 ይ Ⳟ ᮮ ࢡ ࢰ 㓗 ࢣ ࢭ (GluDH) 㧏 Ꮽ ᛮ 㸡ᖏῺ ᮮ GluDH ࢦ හ ࢦ 㛣 ࡄ ᩐ ኣ ࡆ ಘࡋ ࡀࡒࠊࡊ ࡊ㸡 ᅂỬ ࡊࡒ㸡 ࡒ ይ ᛮ Ⳟ ᮮ GluDH ᬏᵋ ᖏῺ ᮮ GluDH Ẓ 㸡ࢦ හ ᩐ ࡋࡓ 㸡 ࢦ 㛣 ᩐ ᑛ ࡖࡒࠊ 㸡ࢦ 㛣 Ềᛮ பష ᙁࡂ ࡆ ฦ ࡖࡒࠊࡆ ᯕ 㸡 ይ Ⳟ ᮮ ࡋࢰ ࢠ 㸡 ᡋ ࡖ ྊ ᛮ ࡊ ࠊ ࡒ㸡ᮇ㓕 NAD㸝NADP Ꮽ౮㸞 㓕 ࡌ ࡒ 㸡GluDH ࡊ ࡒ Ꮛ ࢬ ࢦ ࢤࢪ ࡀ ࠊ ぞ 1 ࢣ ࢭ ' 3&) ౪Ꮛᛮࢡ ࢰ 㓗 ࢣ ࢭ ' ' ࢨ ) ࢪ 㓗 ࢭ㸯 Aeropyrum pernix ይ ᛮ ᮮ ࢨ ) ࢪ 㓗 ࢭ (DERA) మᵋ Ử ࡊࡒࠊ ይ Ⳟ ᮮ DERA 㧏 Ꮽ ᛮ ࡗ 㸡 ᶭ ፳ 㧏 ᛮ ࡊࡒࠊࡆ ᚡ ᴏ ࡀ ᛮ 㧏 ࡂ㸡 ࢪ 㓕 㜴ᐐ ࢨ ࢪㄇᑙమ 㸡 㓗㛭 ဗཋ 㓕 463

4 ᠺ ᐁ ྊ ࡊࡒࠊ ' 㓗ࢨ ࢰ ࢭ㸯 ཋ ࡄ NAD ᠺ ࠉ NAD ᠺ ࡖ ࡒ 㸡ࡐ ࡂ㓕 ぞᢘⳞ 㛜 ࡒ 㔔さ ࢰ ࢣ 㸦ࡗ ࠊ ᅂ㸡 ይ ᛮ Pyrococcus horikoshii ᮮ 㓕 㸡ࡆ ཬᚺ り፳ࡌ 㓗ࢨ ࢰ ࢭ ᬏᵋ Ử ࡊࡒࠊ ' ࢪ ࢬ ࢪ 㓕 㸝 ぞࢨࢪ ᠺ㓕 㸞 㸯 ࢨࢪ 㓗 㸦 㸡 ࢨ ࡐ ࡌ 㝎ཡࡌ ష ࡗࡆ 㸡 ᅗහ ࠔ 㓗ࠕ ࡊ ᕰሔ౮ 㧏ࡂ㸡 ࡐ ㄇᑙమ ᕝᴏ ࠊ ይ ᛮ Ⳟ ࢨࢪ ᠺ㓕 㞫ࡊ よᯊࡊࡒ ᯕ㸡 ᇱ ࡊ O- ࢪ ࢬ ぞ ཬᚺ り፳ࡌ ࡆ ࡖࡒࠊᮇ㓕 Υ 㧏Ὼ ࡂࡓࡄ ࡂ㸡O- ࢪ ࢬ ᇱ ࡊࡒ ࡀ 㓕 㧏 Ὡᛮ ࡊࡒࠊ ࡖ 㸡 り፳ ࡊ ᮇ㓕 ࡌ 㸡㞟Ⳟ Ṣ ᢒ ࡒ ௲ 㸡Ẓ ᗦ౮ ࢪ ࢬ ࢨࢪ 㓕 ᠺࡌ ࡆ ྊ ࠊ ' ࢬ ࢰ ࢠ ࢡ㸯 ࢬ ࢰ ࢠ (SBP56) Ꮛᅹࡊ㸡Se 㐘ᦑ㸡よẐష 㸡ࢥ ࢩమහࢰ ࢠ 㛭 ࡌ ྊ ᛮ ࡈ ᶭ ᮅ ࢰ ࢠ ࡓ 㸡 ྊ ᛮ ሒ ࡈ ࠊ ᅂ㸡 SBP56 ᛮ ࡗ ይ ᛮ Sulfolobus tokodaii ᮮ ࢰ ࢠ 㸝ST0059㸞 X ᬏよᯊ ᠺ ࡊࡒࠊș ᵋ ࡖ 㸡His ࢠ ࢪࢰ ࡗ ࢲ ᣚࡖ ࡒࠊ ᅂỬ ࡊࡒይ Ⳟ㓕 ᵋ 㸡㧏 SBP56 ḗඔᵋ ࢡ ྊ 㸡 ᚃ SBP56 ᶭ よ ኬࡀࡂ ࡀ ࠊ ' ࡐ 㸯 ࢡ ࢨ 㓗 ࢪ ࢭ㸝ࢡ ࢨ 㓗 よẐ㸞 㸡ࢪ ࢣ ࢭ㸡ࢲ ࢨ ࢱ ࢭ㸡 ࢪ 㓗-tRNA ᠺ㓕 㸡 ࢲ ࢨ ࢭ㸡 ᛮ ࢪ ࢭ㸡 ᵋ ᶭ よᯊ ࡖࡒࠊ )*7& ' 㓗ࢨ ࢰ ࢭ ' ࢬ ࢰ ࢠ ࢡ ' ( ᚺ ᙽࡈ 㓕 ( 3 ࢲ 1 㓗 ࢣ ࢭ ᅒ( 㸯 කᏕὩᛮ N- 㓗 㓗 㢦 మ 㸡 ဗ ᠺ୯㛣మ ࡊ 㞺さ ࠊࡆ 㓗㢦 మ ᠺ ᵋ ࡌ ࡆ 㸡 ࢪࢠ ࢡ 㸡Ș-ࢢ 㓗 ࢲ NADPH ౪Ꮛ N- ࢲ -L- 㓗 ᠺࡌ ぞ 㓕 ぜ ࡓࡊࡒࠊ 々 మ 㹍 ᬏよᯊ ᯕ㸡ᮇ㓕 ࡋ ୯ NADPH 㓕 ࡌ ࡆ ᵋ ㄕ ࡀࡒࠊࡈ 㸡ᮇ㓕 NADPH ࡊ ࢡ ࢤ ࢪ ࢣ ࢭ භ ࡈࡎࡒ ᥦ ኬ Ⳟ ฝᾦ 㸡 ຊࡊࡒࡐ ࡑ ᇱ N- ࢲ -L- 㓗 L- ࢤ 㓗㸝ᢘ ᠺᮞ 㸞 㸡㧏 㸡㧏 ක Ꮥ ᗐ ᠺ ࡀ ࡆ ࡊࡒࠊ ( ࢠ 㓗 ࢱࢠࢰ ࢭ ᅒ( 㸯 ᶭ ࢣ 㸡 ᠺཋ ࡊ ᴗ ᗀ ࡗ 㸡 ᚃ Ꮥᕝᴏ ᨥ ᇱ ᢇ ࡊ කᏕฦ Ἢ ຝ 㧏 㓕 ᠺἪ ị ࠊࡐࡆ 㸡 ࢨ 㓗 㝎ⲙ ཋ (S)-2- 㓗 (S2-CPA) ࡌ ᪁Ἢ 㛜 ᣞࡊ ࢪࢠ ࢡ 㸡2-ࢠ ࢠ 㓗(2-CAA) 㑇ඔࡌ ぞ 㓕 ぜ ࡓࡊࡒࠊᵋ よᯊ ᯕ㸡り፳ NADPH ᵋ ࡆ ࡊࡒࠊ ࡈ 㸡ᮇ㓕 ࢡ ࢤ ࢪ ࢣ ࢭ භ ࡈࡎࡒ ᥦ ኬ Ⳟ ฝᾦ 㸡㧏 ࡗ㧏 ᗐ 2-CAA S2-CPA ᠺ ࡀ ࡆ ࡊࡒࠊ ( ࢨ ࢰ ࢭ㸝 ᠺ㓕 㸞 㸯 (R-CN) 㸡 ࢬ 㸝 ፳㸞 ࢠ 㸝 ᠺᶖ 㸡 㸞 㸡ཋ ࡊ Ꮥᕝᴏ ᗀࡂ ࡈ ࠊ 㛭 ᠺ ᵋ ࡌ 㸡 ฦよⳞ ㅨ㛭 㓕 ࡂࡗ ぜ ࡓࡊ ࡒࠊࡐ ࡔ㸡 ᠺ㓕 㸝 ࢨ ࢰ ࢭ㸞 㸡 㒼నࡊࡒ ࢪࢲࢩ ࢨ (R-CHN-OH) ౩ ࡊ Ềཬᚺ り፳ࡌ ぞ 㓕 ࡆ ࡊ ࡒࠊ ࢨ ཋ ࡊࡒ ᠺ ᚺ ᙽ ࡀ ࠊ ( ࢨ ࢨ ᇱ న㓕 㸯 ⰴ ᶫ㸡㉝㸡 㸡㟯 Ⰵ 㸡 ࢨ ࡄࡒ 464

5 N- L- L- 10% L (1)PDB (2) PDB (3) (1) (2)

6 (3) (4) (5) DNA 1-B-1 DERA 1-B-3 1-B-2 N--L-1-C-1 heterofructosaccharide 1-B-2 DERA 1-B-3 L- 1-B-1 N- N--L- N- -L-1-C-1 AIST 1-B-5 4-(2)-(3) DNA 6-N ,6-4-- GDP-D- GMP 17 GMP GDP- 466

7 N- -, SPring-8 3 N N N Streptomyces (1) (2) (3) (3) ab initio ACORN, SHARP, warp 1.9 Å ab initio 1.6 Å SPring-8 SPring

8 directed evolution X B6 O- β, γ D- (DAO) D- DAO D- D- PI3K-Akt PI3K-Akt PI3K-Akt CKIP-1 Aki1 Akt-1 PDK1 CKIP-1 Akt Aki1 Akt Akt

9 : 469

10 10 SPring-8PF X SPring-8 ( 11 N Hoseki, J. et al. (2003) Biochemistry 42, , , , , ,000 1,407,600 () 89,612 17,249 26,290 38,229 9, ,123 () 24, ,236 88,601 84,989 71, ,130 () 177, , , , , ,387 () 15,046 18,065 31,303 29,955 27, ,

11 PDB ID Gln25- T1 1IYY Released 1999/10/6 L- 1UKJ Released 2000/10/18 (2000) (2000) 1ULZ Released 2000/3/8 1OA5 Released 1999/8/27 1OA6 Released 1999/8/27 (2000) 1GXV Released 1999/3/26 (2000) 1GXX Released 1999/3/26 Carboxyl transferase subunit of archaeal propionyl-coa carboxylase -CoA CT 1X0U Released 2002/7/3 SshEstI(Sulfolobus shibatae ) 1WZJ Est 1(Sulfolobus shibatae ) H274A mutant at ph 4.2 Est 1(Sulfolobus shibatae ) H274E mutant at ph 7.0 Est 1(Sulfolobus shibatae ) H274E mutant at ph 4.0 Est 1(Sulfolobus shibatae ) H274E mutant at ph 4.2 Est 1(Sulfolobus shibatae ) H274D mutant at ph4.2 1WZP 1WZQ 1WZR 1WZS 1WZT on hold Aspartate aminotransferase (Mesorhizobium spi ) 2D5E on hold 2D4V Released 2002/11/13 471

12 2D4W Released 2002/11/13 Aspartate aminotransferase E.coli, MC+ IVA 2D5Y Aspartate aminotransferase E.coli, MA+ MAE Aspartate aminotransferase E.coli, MA+ IVA Aspartate aminotransferase E.coli, MABC+ IVA Aspartate aminotransferase E.coli, MABC Aspartate aminotransferase E.coli, MAB Aspartate aminotransferase E.coli, MA Aspartate aminotransferase E.coli, + MAE 2D61 2D63 2D64 Released 2002/11/13 2D65 2D66 2D7Y 2D7Z Salt torelant glutaminase 2DFW Released 2002/7/17 Sulerythrin 1J30 Released 1999/10/13 Nitrile hydratase mutants + n-butylate 1UGP Nitrile hydratase mutants, apo enzyme Nitrile hydratase mutants, T109S mutant 1UGQ 1UGR Released 2000/6/16 Nitrile hydratase mutants, Y114T mutant 1UGS 472

13 Isocitrate dehydrogenase 1V94 Released 2001/1/24 Fructose-1,6-bisphosphatase UMG Released 2000/7/12 Cumene dioxygenase (CumA1A2) 1WQL Released 2001/3/28 Lipoamide dehydrogenase 1V59 Released 2001/2/14 3-Isopropylmalate dehydrogenase 1V53 Released 2001/2/14 3-Isopropylmalate dehydrogenase S225A, E251L 1V5B Released 2001/2/14 2-Keto-3-deoxygluconate kinase (ST2478) 1WYE Released 2002/7/3 2-Keto-3-deoxygluconate kinase (ST2478) 2D2T on hold Hexokinase 2E2N Hexokinase + ADP 2E2O Released 2003/1/15 Hexokinase + glucose 2E2P Hexokinase + xylose, Mg 2+, and ADP 2E2Q Meta-cleavage product hydrolase (CumD) 2D0D Released 2002/6/5 473

14 Chitosanase, Active form (ph 6.4) 1V5D Released 2000/12/6 Chitosanase, Inactive form (ph 3.7) Pyruvate oxidase with FAD, TPP, pyruvate Pyruvate oxidase with FAD, TPP 1V5C Released 2000/12/6 1V5E Released 2002/6/27 1V5F Released 2002/6/27 Pyruvate oxidase with FAD, TPP and pyruvate 1V5G Released 2002/6/27 Uricase with Na-borate 1VAX Uricase with an inhibitor, 8-azaxthantine Uricase with the substrate, uric acid Uricase with the product, allantoin 1VAY Released 1WRX on hold 2D67 on hold 2002/6/27 Aspartyl-tRNA synthetase trna 1WYD Released 2002/7/3 474

15 1WYA on hold O6-1WRJ Released 2001/12/5 5'--5'- 1WTA Released 2002/2/6 Threonyl-tRNA synthetase 2D5S on hold H 2EX7 on hold Pyrroline-5-carboxylate reductase (ST0646) 2D7A on hold Hypothetical aspartate-semialdehyde dehydrogenase 2DHP on hold Pyruvate oxidase 2DJI Released 2001/6/27 N-acetyl glutamate kinase 2E0U on hold 475

16 N5-carboxyaminoimidazole ribonucleotide synthetase 2E0V on hold Aspergillus oryzae aspartic proteinase 1IZD Released 1999/3/3 Aspergillus oryzae aspartic proteinase + pepstatin A 1IZE Released 1999/3/3 Sulfolobus tokodaii cytochrome P450 1UE8 Released 2000/7/12 Sporobolomyces salmonicolor aldehyde reductase 2 Sporobolomyces salmonicolor aldehyde reductase 2 + NADPH Sporobolomyces salmonicolor aldehyde reductase 2, high resolution 1UJM Released 2000/10/11 1Y1P Released 2001/9/5 1ZZE Released 2001/9/5 Arthrobactoer globiformis glucodextranase 1UG9 Arthrobactoer globiformis glucodextranase + acarbose 1ULV Released 1999/12/8 Aspergillus niger ATCC9642 isoplullanase 1WMR Released 2001/7/18 Iba1 1WY9 () Released 2002/2/20 Iba1 2D58 () Released 2002/10/9 Cyclodextrin binding protein 2DFZ Released 2003/3/5 YgjK 2DS3 on hold 476

17 hypothetical selenium-binding protein, ST0059 2ECE on hold Rhamnose Isomerase 2HCV Rhamnose Isomerase + L-allose 2I56 Rhamnose Isomerase + D-allose 2I57 Released 2002/12/18 Hypothetical molybdenum cofacto biosynthesis protein C, ST0472 2OHD on hold D-tagatose 3-epimerase 2OU4 on hold H. salinarum 1IW6 Released 1998/12/10 K 1IXF Released 1998/12/17 L 1UCQ Released 1999/12/29 M 1IW9 Released 1999/12/22 1X0I Released XOK Released X0S Released (Halorubrum sp. aus-1) 1UAZ Released 1999/4/14-2 (Halorubrum sp. aus-2) 1VGO Released 2001/10/3 a/bii 1VCR Released 2000/3/29 477

18 I Sulfolobus tokodaii ) 1VGM II (Sulfolobus tokodaii ) 1VGP Released 2001/6/27 v8 1WCZ Released 2000/5/31 2E0C on hold 2DHT Released 2003/3/26 2DQL on hold 2E5M on hold 2EI4 on hold Catalytic Domain of N -Acetylmuramoyl- L- Alanine Amidase 1JWQ Released 1999/11/17 Family 30 Carbohydrate Binding Module 1WMX Released 2000/8/2 Family 30 Carbohydrate Binding Module 1WZX Released 2001/3/21 Ubiquitin-Conjugating Enzyme Ubch8 1WZW Released 2001/3/21 478

19 Ubiquitin-Conjugating Enzyme Ubch8 1WZV Released 2001/3/21 Alkaline Mannanase from Bacillus Sp. Strain Jamb-602 1WKY Released 2001/6/14 phospholipase A2 1VKQ Released 2000/8/29 ST2478(2-keto-3-deoxygluconate kinase) 2DCN Released 2002/1/30 D-stereospecific amino-acid amiase (DAA), native 2DRW Released 2002/7/3 D-stereospecific amino-acid amiase (DAA) + D- Phe D-stereospecific amino-acid amiase (DAA) + L- Phe D-stereospecific amino-acid amiase (DAA) + L- Phe-NH2 2DNS Released 2002/5/8 2EFU Released 2003/3/5 2EFX Released 2003/3/5 ST680(transposes) 2EC2 Released 2003/2/26 ) ST0452(glucose-1-phosphate thymidylyltransferase ) ST0452(glucose-1-phosphate thymidylyltransferase ) ST1970(dTDP-6-deoxy-L-xylo-4-hexulose reductase ) ST1969(dTDP-4-dehydrorhamnose 3,5-epimerase 2GGO Released 2003/3/23 2GGQ Released 2003/3/23 2GGS Released 2003/3/23 2B9U Released 2002/10/12 1WTC Released 2001/10/31 1V71 Released 2001/6/13 2-1WLY Released 2001/10/3 479

20 1IX6 1IX7 Released 1998/7/2 1IX8 + glutarate + glutamate 1IYD 1IYE Released 1999/5/5 -CoA 1UDY Released 1999/12/8 1V72 Released 2001/2/28 1VB3 Released 2001/6/20 1Y37 Released 2002/2/ WTJ Released 2001/10/ NADPH 2CWF on hold NADPH + pyrrole-2-carboxylate (substrate analog) 2CWH Released 2001/10/3 480

21 + gabapentin (oxidized form) + gabapentin (reduced form) + 4-methylvalerate (oxidized form) 2COI 2COJ 2COG Released 2001/8/29 + phosphopyridoxyl-l-glutamate 1X28 + phosphopyridoxyl-d-glutamate 1X2A Released 2001/6/13 1X29 2,6-Dihydroxybenzoate Decarboxylase + 2,6- dihydroxybenzoate 2DVU 2,6-Dihydroxybenzoate Decarboxylase + 2,3- dihydroxybenzaldehyde 2DVX Released 2002/7/31 2,6-Dihydroxybenzoate Decarboxylase 2DVT Acyl-CoA oxidase 2DDH Released 2002/3/27 1WKV Released 2001/6/27 1X0R Released 2001/12/19 481

22 2CWR (X-ray) Released 2002/7/10 2CZN (NMR) Released 2002/7/17 Threonine dehydrogenase 2DFV Released 2003/1/15 Chitinase Active Domain 2DSK Released 2003/2/5 ADP- 1L2L Released 1998/12/29 Co-homing endonuclease I-Tsp 061I 2DCH (1VAW) Released 2002/7/5 1V9L Released 2000/12/13 1N7K Released 1999/3/24 1VCV Released 2001/8/1 482

23 1WY6 Released 2000/4/5 L- 1Y56 Released 2001/7/25 1WZU Released 2001/6/6 2D4A Released 2001/10/11 Aspartate dehydrogenase 2DC1 Released 2002/12/25 L-Aspartate oxidase 2E5V on hold 1J2G Released 2000/6/14 - GCS 1V4G Released 2001/1/31 GCS + P2S(transition-state analog) 1VA6 Released 2001/3/7 GCS + AMP-PNP 2D32 GCS + AlF3 2D33 Released 2002/11/13 MexA 1VF7 Released 2000/5/24 483

24 OprM 1WP1 Released 2000/11/1 Glycerol dehydratase-cyanocobalamin complex 1IWP Released 1998/10/1 Diol dehydratase-reactivating factor complexed with ADP and Mg 2+ 2D0O Released 2002/2/27 Diol dehydratase-reactivating factor complexed with ADP and Mg 2+ 2D0P Released 2002/2/27 Iota-Toxin 1GIQ Released 1999/1/13 Iota-Toxin 1GIR Released 1999/1/13 Sphingomyelinase 1WUX on hold HA (C-HA1/) + N-acetylneuramic 2EHI HA (C-HA1/) + N- cetylgalactosamine 2EHM HA (C-HA1/) + galactose 2EHN on hold 484

25 Phosphlipase A 2 from S. violaceoruber 1LWB Released 1998/5/30 Bleomycin-binding protein (BLMT) from transposon Tn5 1MH6 Released 1999/2/18 BLMT complexed with Co(III)-bound bleomycin 1NIQ Released 1999/12/24 Alanine racemase (ALR) from S. lavendulae 1VFH Released 2000/9/13 DCS-bound form of S. lavendulae ALR 1VFS Released 2000/9/13 L-cycloserine (LCS)-bound form of S.lavendulae 1VFT Released 2000/9/13 ALR Cu(II)-free tyrosinase complexed with caddie protein in P WXC Released 2002/1/30 Cu(II)-free tyrosinase complexed with caddie protein in P 2 1WX5 Released 2002/1/30 1 Cu(II)-bound met-form tyrosinase complexed with caddie protein Cu(II)-bound oxy-form tyrosinase complexed with caddie protein obtained by the addition of DTT 1WX3 Released 2002/1/30 1WX4 Released 2002/1/30 Cu(II)-bound oxy-form tyrosinase complexed with 1WX2 Released 2002/1/30 caddie protein obtained by the addition of H 2 O 2 Cu(II)-bound met-formii tyrosinase complexed with caddie protein Cu(I)-bound deoxy-form tyrosinase complexed with caddie protein obtained by the addition of NH OH Mitomycin C-binding protein complexed with metal-free bleomycin Mitomycin C-binding protein complexed with Cu(II)-bound bleomycin 2AHK Released 2002/1/12 2AHL Released 2002/1/12 2A4X Released 2002/6/27 2A4W Released 2002/6/27 Alginate lyase 1J1T Released 2000/2/2 485

26 Pokweed Antiviral Protein (PAP-S1) 1J1Q Pokweed Antiviral Protein (PAP-S1) + Adenine 1J1R Pokweed Antiviral Protein (PAP-S1) + Formycin 1J1S Released 2000/2/2 Ricin A-chain 1J1M Released 2000/2/2 L-Lactate dehydrogenase 1V6A Released 2001/2/14 Subtilisin-like protease Apa1 1V6C Released 2000/12/27 Subtilisin-like protease Apa1 1WVM Released 2002/3/20 1KOL Released 1998/12/10 1J2U Released 2000/1/26 486

27 Mn 1J2T Released 2000/1/26 1V7Z Released 2000/1/26 + Pro-TBODA 1WM1 Released 2003/7/19 + Ala-TBODA 1X2B Released 2002/5/8 + Sar-TBODA 1X2E Released 2002/5/8 D-3-1WMB Released 2001/9/5 D-3- + NAD 1X1T Released 2002/1/9 2D5L Released 2002/9/18 S603A mutated prolyl tripeptidylaminoptidase 2DCM Released 2002/9/18 Aminopeptidase N 2DQ6 Released 2002/7/31 Aminopeptidase N 2DQM Dipeptidyl aminopeptidase IV 2ECF on hold Human D-amino acid oxidase 1ZPJ on hold 487

28 The kexin-type serine protease 2C3R on hold Sphingo Myelinase, 2DDR Released 2002/5/1 Sphingo Myelinase, 2DDS Released 2002/5/8 Sphingo Myelinase, 2DDT Released 2002/5/1 D-amino acid oxidase 2E48 Released 2003/3/5 D-amino acid oxidase + Imino-Serine 2E49 Released 2003/3/5 D-amino acid oxidase + o-aminobenzoate 2E4A Released 2003/3/5 D-amino acid oxidase + Imino-DOPA 2E82 Released 2003/3/5 D-amino acid oxidase + FAD, Benzoate 2DU8 Released 2002/11/20 Iota-toxin/actin complex 2OAV on hold Alanine racemase 2ODO on hold Pyridoxamine-pyruvateaminotransferase 2E04 Pyridoxamine-pyruvateaminotransferase + Pyridoxamine Pyridoxamine-pyruvateaminotransferase + Pyridoxal 2E05 2E06 on hold L-Glutamate Oxidase 2E1M on hold Enzyme Microsensors LLP 488

29 L-Methionine γ-lyase 2O7C on hold 2E1T 2E1U Released 2003/4/9 2E1V Biotin carboxylase domain of pyruvate carboxylase 2DZD on hold GAR synthetase (aq_742, PurD) 2YW2 on hold GAR synthetase (aq_742, PurD) 2YYA on hold AIR carboxylase, ATPase subunit (aq_245, PurK) 2Z04 on hold 489

30 Mihara, H., Kato, S., Lacourciere, G.M., Standman, T.C., Kennedy, R.A.J.D., Kurihara, T., Tokumoto, U., Takahashi, Y., Esaki, N., The iscs gene is essential for the biosynthesis of 2-selenouridine in trna and the selenocysteine containing formate dehydrogenase H. Proc. Natl. Acad. Sci. USA, 99, (2002). Herai, S., Hashimoto, Y., Higashibata, H., Maseda, H., Ikeda, H., Omura, S. & Kobayashi, M. Hyper-inducible expression system for streptomycetes. Proc. Natl. Acad. Sci. USA, 101, (2004). Hibi T., Nii H., Nakatsu T., Kimura A., Kato H., Hiratake J., and Oda J., Crystal structure of g-gltutamyl-cysteine synthetase: Insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis. Proc. Natl. Acad. Sci. USA, 101, (2004). PDB ID: 1V4G, 1VA6. Tamura, T., Yamamoto, S., Takahata, M., Sakaguchi, H., Tanaka, H., Stadtman, T. C., and Inagaki, K., Selenophosphate synthetase genes Sps1 and Sps2 from lung adenocarcinoma cells; Sps1 for recycling L-selenocysteine and Sps2 for selenite assimilation. Proc. Natl. Acad. Sci. USA, 101, (2004). Konishi, K., Ohta, T., Oinuma, K-I., Hashimoto, Y., Kitagawa, T. and Kobayashi, M., Discovery of a reaction intermediate of aliphatic aldoxime dehydratase involving heme as an active center. Proc. Natl. Acad. Sci. USA, 103, (2006). Chen, X., Chong, C.R., Lirong Shi, Yoshimoto, T., Sullivan, D. J. and Liu, J. O., Inhibitors of Plasmodium falciparum methionine aminopeptidase 1b possess antimalarial activity. Proc. Natl. Acad. Sci. USA, 103, (2006). Yoshimoto, T., Tanaka, N., Kanada, N., Inoue, T., Nakajima, Y., Haratake, M., Nakamura, K.T., Yue X., and Ito, K., Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism. J. Mol. Biol., 337, (2004). PDB ID: 1J2U, 1J2T, 1V7Z Ito, K., Nakajima, Y., Ichihara, E., Ogawa, K., Katayama, N., Nakashima, K., and Yoshimoto, T., D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: Molecular cloning of the enzyme gene and crystal structure of the enzyme. J. Mol. Biol., 355, (2006). PDB ID: 1WMB, 1X1T Yoshida, H., Yamada, M., Ohyama, Y., Takada, G., Izumori, K. and Kamitori, S. The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate-specificity. J. Mol. Biol., 365, (2007). PDBID: 2HCV, 2I56, 2I57 Ikeda, H., Ishikawa, J., Hanamoto, A., Shinose, M., Kikuchi, H., Shiba, T., Sakaki, Y., Hattori, M., and Omura, S., Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nature Biotechnol. 21, (2003). 490 Sakaguchi Y, Hayashi, T, Kurokawa K, Nakayama K, Oshima K, Fujinaga Y, Ohnishi M, Ohtsubo E, Hattori M, and Oguma K., The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny. Proc. Natl. Acad. Sci. USA, 102, (2005).

31 Ishikawa, K., Higashi, N., Nakamura, T., Matsuura, T., Nakagawa, A., The first crystal structure of L-threonine dehydrogenase. J. Mol. Biol., 366, (2007). PDB ID: 2DFV Okazaki, S. Suzuki, A., Komeda, H., Yamaguchi, S., Asano, Y., and Yamane, T., Crystal structure and functional characteri zation of a D-stereospecific amino acid amidase from Ochrobactrum anthropi SV3, a new member of the penicillin-recognizing proteins. J. Mol. Biol., 368, (2007). Hayashi H, Mizuguchi H, Miyahara I, Nakajima Y, Hirotsu K, Kagamiyama H, Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis. J. Biol. Chem., 278, (2003). PDB ID: 1IX6, 1IX7, 1IX8 Mizuno, M., Tonozuka, T., Suzuki, S., Uotsu-Tomita, R., Kamitori, S., Nishikawa, A. & Sakano, Y., Structural insights into substrate specificity and function of glucodextranase. J. Biol. Chem., 279, (2004). PDB ID: 1UG9, 1ULV Noda, M., Matoba, Y., Kumagai, T. and Sugiyama, M. Structural evidence that alanine racemase from D-cycloserine-producing-microorganism exhibits resistance to its own product. J. Biol. Chem. 279, (2004). PDB ID: 1VFH, 1VFS, 1VFT Konishi, K., Ishida, K., Oinuma, K-I., Ohta, T., Hashimoto, Y., Higashibata, H., Kitagawa, T. & Kobayashi, M. Identification of crucial histidines involved in carbon-nitrogen triple bond synthesis by aldoxime dehydratase. J. Biol. Chem., 279, (2004). Hayashi, F., Itoh, N., Uzumaki, T., Iwase,R., Tsuchiya, Y., Yamakawa, H., Morishita, M., Onai, K., Itoh, S., and Ishiura, M., Roles of two ATPase-motif-containing domains in cyanobacerial circadian clock protein KaiC. J. Biol. Chem., 279, (2004). Muramatsu H, Mihara H, Kakutani R, Yasuda M, Ueda M, Kurihara T, Esaki N, The putative malate/lactate dehydrogenase from Pseudomonas putida is an NADPH-dependent Delta(1)-piperideine-2-carboxylate/Delta(1)-pyrroline-2-carboxylate reductase involved in the catabolism of D-lysine and D-proline. J. Biol. Chem., 280, (2005). Sakuraba H., Tsuge H., Yoneda K., Katunuma N., Ohshima T. Crystal structure of the NAD biosynthetic enzyme quinolinate synthase. J. Biol. Chem., 280, ( 2005 ). PDB ID: 1WZU Tsuge H., Kawakami R., Sakuraba H., Ago H., Miyano M., Aki K., Katunuma N., Ohshima T. Crystal structure of a novel FAD-, FMN-, and ATP-containing L-proline dehydrogenase complex from Pyrococcus horikoshii. J. Biol. Chem., 280, ( 2005). PDB ID: 1Y56 Goto, M., Muramatsu, H., Mihara, H., Kurihara, T., Esaki, N., Omi, R., Miyahara, I., Hirotsu, K., Crystal structures of Δ 1 -piperideine-2-carboxylate/δ 1 -pyrroline-2-carboxylate reductase belonging to a new family of NAD(P)H-dependent oxidoreductases: conformational change, substrate recognition, and stereochemistry of the reaction. J. Biol. Chem., 491 Tsukatani, R., Miyamoto, Itoh, S., and Oh-oka, H., Function of a PscD subunit in a homodimeric reaction center complex of the photosynthetic green sulfur bacterium Chlorobium tepidum studied by insertional gene inactivation: Regulation of energy transfer and ferredoxin-mediated NADP + reduction on the cytoplasmic side. J. Biol. Chem., 279, (2004).

32 Matoba, Y., Kumagai, T., Yamamoto, A., Yoshitsu, H. and Sugiyama, M. Crystallographic evidence that the dinuclear copper center of tyrosinase is flexible during catalysis. J. Biol. Chem. 281, (2006). PDB ID: 1WXC, 1WX2, 1WX3, 1WX5, 2AHK, 2AHL Kawata, M., Kinoshita, K., Takahashi, S., Ogura, K., Komoto, N., Yamanishi, M., Tobimatsu, T, Toraya, T. Survey of catalytic residues and essential roles of glutamate-alpha170 and aspartate-alpha335 in coenzyme B12-dependent diol dehydratase. J. Biol. Chem. 281, (2006). Ago H., Oda, M., Takahashi, M., Tsuge, H., Ochi, S., Katunuma, N., Miyano, M. and Sakurai, J., Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from bacillus cereus. J. Biol. Chem. 281, (2006). PDB ID: 2DDS, 2DDR, 2DDT Nishimasu, H., Fushinobu, S., Shoun, H. and Wakagi, T., Crystal structure of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii. J. Biol. Chem., 282, (2007). PDB ID: 2E2N, 2E2O, 2E2P, 2E2Q Shibata N, Mori K, Hieda N, Higuchi Y, Yamanishi M, Toraya T, Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor. Structure, 13, (2005). PDB ID: 2D0O, 2D0P Sato, Y., Maeda, Y., Hossain, M. T., Ubukata, S., Suzuki, K., Sekiguchi, T., and Takenaka, A., Crystal structure of non-discriminating aspaertyl-trna synthetase from crenarchaea Sulfolobus tokodaii strain 7 reveals the recognition mechanism of two different trna anticodons. Acta Cryst., D63, in press (2007). PDB ID: 1WYD Hoseki, J., Okamoto, A., Takada, N., Suenaga, A., Funatsugi, N., Konagaya, A., Taiji, M.,Yano, T., Kuramitsu, S., and Kagamiyama, H., Increased rigidity of domain structures enhances the stability of a mutant enzyme created by directed evolution. Biochemistry, 42, (2003). Kaneko, M., Masui, R., Ake, K., Kousumi, Y., Kuramitsu, S., Yamaguchi, M., Kuyama, H., Ando, E., Norioka, S., Nakazawa, T., Okamura, T. A., Yamamoto, H., and Ueyama, N., Rapid and sensitive amino-acid sequencing of cloning Thermus thermophilus HB8 ferredoxin by proteomics. J. Proteome Res, 3, (2004). Okamura, T., Iwamura, T., Ito, A., Kaneko, M., Yamaguchi, M., Yamamoto, H., Ueyama, N., Kuyama, H., Ando, E., Norioka, S., Nakazawa, T., Masui, R., and Kuramitsu, S. Application of bis(terpyridine)ruthenium(ii) to N-terminal amino acid sequencing. Chemistry Letters, 34, (2005). Ito, A., Okamura, T. A., Yamamoto, H., Ueyama, N., Ake, K., Masui, R., Kuramitsu, S., and Tsunasawa, S. Distinction of Leu and Ile using a ruthenium(ii) complex by MALDI-LIFT-TOF/TOF-MS analysis. Anal. Chem., 77, (2005). 280, (2005). PDB ID: 1WTJ, 2CWF, 2CWH 492 Kawazoe, R, Tsuge, H, Pilone, MS, Fukui, K., Crystal structure of human D-amino acid oxidase: context-dependent variability of the backbone conformation of the VAAGL hydrophobic stretch located at the si-face of the flavin ring. Protein. Science, 15, (2006). PDB ID: 2DU8