+データを開く
-基本情報
登録情報 | データベース: SASBDB / ID: SASDEF5 |
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試料 | Phosphoketolase (L. lactis) with 1 mM thiaminpyrophosphate and 2% v/v glycerol at pH 7.0
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機能・相同性 | 機能・相同性情報 付加脱離酵素(リアーゼ); C-Cリアーゼ; アルデヒド基の付加脱離 / aldehyde-lyase activity / carbohydrate metabolic process 類似検索 - 分子機能 |
生物種 | Lactococcus lactis subsp. lactis (strain IL1403) (乳酸菌) |
引用 | ジャーナル: J Struct Biol / 年: 2019 タイトル: Crystal structure of a xylulose 5-phosphate phosphoketolase. Insights into the substrate specificity for xylulose 5-phosphate. 著者: A J Scheidig / D Horvath / S E Szedlacsek / 要旨: Phosphoketolases (PK) are TPP-dependent enzymes which play essential roles in carbohydrate metabolism of numerous bacteria. Depending on the substrate specificity PKs can be subdivided into xylulose ...Phosphoketolases (PK) are TPP-dependent enzymes which play essential roles in carbohydrate metabolism of numerous bacteria. Depending on the substrate specificity PKs can be subdivided into xylulose 5-phosphate (X5P) specific PKs (XPKs) and PKs which accept both X5P and fructose 6-phosphate (F6P) (XFPKs). Despite their key metabolic importance, so far only the crystal structures of two XFPKs have been reported. There are no reported structures for any XPKs and for any complexes between PK and substrate. One of the major unknowns concerning PKs mechanism of action is related to the structural determinants of PKs substrate specificity for X5P or F6P. We report here the crystal structure of XPK from Lactococcus lactis (XPK-Ll) at 2.1 Å resolution. Using small angle X-ray scattering (SAXS) we proved that XPK-Ll is a dimer in solution. Towards better understanding of PKs substrate specificity, we performed flexible docking of TPP-X5P and TPP-F6P on crystal structures of XPK-Ll, two XFPKs and transketolase (TK). Calculated structure-based binding energies consistently support XPK-Ll preference for X5P. Analysis of structural models thus obtained show that substrates adopt moderately different conformation in PKs active sites following distinct networks of polar interactions. Based on the here reported structure of XPK-Ll we propose the most probable amino acid residues involved in the catalytic steps of reaction mechanism. Altogether our results suggest that PKs substrate preference for X5P or F6P is the outcome of a fine balance between specific binding network and dissimilar catalytic residues depending on the enzyme (XPK or XFPK) - substrate (X5P or F6P) couples. |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-モデル
モデル #2447 | タイプ: atomic / 対称性: P2 コメント: PDB-ID 6GUA is a tetramer of dimers; the dimer is supposed to be the biological assembly in solution カイ2乗値: 3.244 Omokage検索でこの集合体の類似形状データを探す (詳細) |
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モデル #2448 | タイプ: atomic / 対称性: P1 / カイ2乗値: 1.90 Omokage検索でこの集合体の類似形状データを探す (詳細) |
-試料
試料 | 名称: Phosphoketolase (L. lactis) with 1 mM thiaminpyrophosphate and 2% v/v glycerol at pH 7.0 試料濃度: 8 mg/ml |
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バッファ | 名称: 20mM potassium phosphate 150mM NaCl 0.007 %(w/v) β-octyl glucoside 1mM DTT 1mM MgCl 1mM thiaminpyrophosphate 2 %(v/v) glycerol pH: 7 / コメント: SEC11 buffer |
要素 #1316 | タイプ: protein / 記述: Probable phosphoketolase / 分子量: 95.727 / 分子数: 2 / 由来: Lactococcus lactis subsp. lactis (strain IL1403) / 参照: UniProt: Q9CFH4 配列: MSHHHHHHSM DIEFVDLEGS MTEYNSEAYL KKLDKWWRAA TYLGAGMIFL KENPLFSVTG TPIKAENLKA NPIGHWGTVS GQTFLYAHAN RLINKYDQKM FYMGGPGHGG QAMVVPSYLD GSYTEAYPEI TQDLEGMSRL FKRFSFPGGI GSHMTAQTPG SLHEGGELGY ...配列: MSHHHHHHSM DIEFVDLEGS MTEYNSEAYL KKLDKWWRAA TYLGAGMIFL KENPLFSVTG TPIKAENLKA NPIGHWGTVS GQTFLYAHAN RLINKYDQKM FYMGGPGHGG QAMVVPSYLD GSYTEAYPEI TQDLEGMSRL FKRFSFPGGI GSHMTAQTPG SLHEGGELGY VLSHATGAIL DQPEQIAFAV VGDGEAETGP LMTSWHSIKF INPKNDGAIL PILDLNGFKI SNPTLFARTS DVDIRKFFEG LGYSPRYIEN DDIHDYMAYH KLAAEVFDKA IEDIHQIQKD AREDNRYQNG EIPAWPIVIA RLPKGWGGPR YNDWSGPKFD GKGMPIEHSF RAHQVPLPLS SKNMGTLPEF VKWMTSYQPE TLFNADGSLK EELRDFAPKG EMRMASNPVT NGGVDSSNLV LPDWQEFANP ISENNRGKLL PDTNDNMDMN VLSKYFAEIV KLNPTRFRLF GPDETMSNRF WEMFKVTNRQ WMQVIKNPND EFISPEGRII DSQLSEHQAE GWLEGYTLTG RTGAFASYES FLRVVDSMLT QHFKWIRQAA DQKWRHDYPS LNVISTSTVF QQDHNGYTHQ DPGMLTHLAE KKSDFIRQYL PADGNTLLAV FDRAFQDRSK INHIVASKQP RQQWFTKEEA EKLATDGIAT IDWASTAKDG EAVDLVFASA GAEPTIETLA ALHLVNEVFP QAKFRYVNVV ELGRLQKKKG ALNQERELSD EEFEKYFGPS GTPVIFGFHG YEDLIESIFY QRGHDGLIVH GYREDGDITT TYDMRVYSEL DRFHQAIDAM QVLYVNRKVN QGLAKAFIDR MKRTLVKHFE VTRNEGVDIP DFTEWVWSDL KK |
-実験情報
ビーム | 設備名称: PETRA III EMBL P12 / 地域: Hamburg / 国: Germany / 線源: X-ray synchrotron / 波長: 0.124 Å / スペクトロメータ・検出器間距離: 3 mm | |||||||||||||||||||||||||||||||||
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検出器 | 名称: Pilatus 2M | |||||||||||||||||||||||||||||||||
スキャン | タイトル: Phosphoketolase (L. lactis) with 1 mM thiaminpyrophosphate and 2% v/v glycerol at pH 7.0 測定日: 2017年9月7日 / 保管温度: 20 °C / セル温度: 20 °C / 照射時間: 0.045 sec. / フレーム数: 29 / 単位: 1/nm /
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距離分布関数 P(R) | ソフトウェア P(R): GNOM 5.0 / ポイント数: 800 /
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結果 | カーブのタイプ: single_conc
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