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基本情報
登録情報 | データベース: PDB / ID: 2bev | ||||||
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タイトル | Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch | ||||||
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![]() | OXIDOREDUCTASE / OXIDATIVE DECARBOXYLATION / MAPLE SYRUP URINE DISEASE / THIAMINE DIPHOSPHATE / PHOSPHORYLATION / CONFORMATIONAL SWITCH | ||||||
機能・相同性 | ![]() Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / branched-chain 2-oxo acid dehydrogenase activity / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of MSUD / Branched-chain ketoacid dehydrogenase kinase deficiency / branched-chain amino acid catabolic process ...Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / branched-chain 2-oxo acid dehydrogenase activity / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of MSUD / Branched-chain ketoacid dehydrogenase kinase deficiency / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / carboxy-lyase activity / response to glucocorticoid / response to cAMP / response to nutrient / lipid metabolic process / mitochondrial matrix / protein-containing complex binding / nucleolus / mitochondrion / nucleoplasm / metal ion binding 類似検索 - 分子機能 | ||||||
生物種 | ![]() SYNTHETIC CONSTRUCT (人工物) | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Machius, M. / Wynn, R.M. / Chuang, J.L. / Tomchick, D.R. / Brautigam, C.A. / Chuang, D.T. | ||||||
![]() | ![]() タイトル: A Versatile Conformational Switch Regulates Reactivity in Human Branched-Chain Alpha-Ketoacid Dehydrogenase. 著者: Machius, M. / Wynn, R.M. / Chuang, J.L. / Li, J. / Kluger, R. / Yu, D. / Tomchick, D.R. / Brautigam, C.A. / Chuang, D.T. #1: ![]() タイトル: Crosstalk between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine 著者: Li, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / Karthikeyan, S. / Tomchick, D.R. / Chuang, D.T. #2: ![]() タイトル: Roles of His291-Alpha and His146-Beta in the Reductive Acylation Reaction Catalyzed by Human Branched-Chain Alpha-Ketoacid Dehydrogenase: Refined Phosphorylation Loop Structure in the Active Site 著者: Wynn, R. / Machius, M. / Chuang, J. / Li, J. / Tomchick, D. / Chuang, D. #3: ジャーナル: J.Biol.Chem. / 年: 2001 タイトル: Roles of Active Site and Novel Potassium Ion- Binding Site Residues in Human Mitochondrial Branched-Chain Alpha-Ketoacid Decarboxylase- Dehydrogenase 著者: Wynn, R.M. / Ho, R. / Chuang, J.L. / Chuang, D.T. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 182.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 142 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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Components on special symmetry positions |
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詳細 | THIS PROTEIN IS A ALPHA-BETA TETRAMER, BUT INTHE PRESENT ENTRY, THEY ARE IN COMPLEX WITH A PEPTIDECHAIN C, THEREBY MAKING THE WHOLE ASSEMBLY A HEXAMERCHAIN C IS A FRAGMENT OF CHAIN B. IT IS NOT CLEAR WHETHERTHIS FRAGMENT IS AN ALTERNATIVE CONFORMATION OF THE CORRESPONDINGRESIDUES IN CHAIN B OF THE SAME MOLECULE OR OF A NEIGHBORING,SYMMETRY-RELATED MOLECULE. IT COULD ALSO COME FROM PROTEOLYSIS,BUT THE AUTHORS DO NOT HAVE ANY EVIDENCE FOR THAT. |
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要素
-2-OXOISOVALERATE DEHYDROGENASE ... , 2種, 2分子 AB
#1: タンパク質 | 分子量: 45571.098 Da / 分子数: 1 / 断片: RESIDUES 46-445 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: P12694, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) |
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#2: タンパク質 | 分子量: 37902.270 Da / 分子数: 1 / 断片: RESIDUES 51-392 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) |
-タンパク質・ペプチド , 1種, 1分子 C
#3: タンパク質・ペプチド | 分子量: 409.461 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) SYNTHETIC CONSTRUCT (人工物) |
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-非ポリマー , 6種, 701分子 










#4: 化合物 | ChemComp-THY / | ||||||||
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#5: 化合物 | #6: 化合物 | ChemComp-MN / | #7: 化合物 | #8: 化合物 | #9: 水 | ChemComp-HOH / | |
-詳細
構成要素の詳細 | CATALYTIC ACTIVITY: 3-METHYL-2-OXOBUTANOATE + [DIHYDROLIPOYLLYSINE-RESIDUE (2-METHYLPROPANOYL) ...CATALYTIC ACTIVITY: 3-METHYL-2-OXOBUTANOA |
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配列の詳細 | CHAIN C IS A FRAGMENT OF CHAIN B. IT IS NOT CLEAR WHETHER THIS FRAGMENT IS AN ALTERNATIVE ...CHAIN C IS A FRAGMENT OF CHAIN B. IT IS NOT CLEAR WHETHER THIS FRAGMENT IS AN ALTERNATIV |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.5 Å3/Da / 溶媒含有率: 53.4 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法 / pH: 5.5 詳細: CRYSTALS WERE GROWN AT 20C VIA THE VAPOR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (20-25 MG/ML IN 50 MM HEPES/NAOH, PH 7.5, 250 MM KCL, 0.5 MM PMSF, 1 MM BENZAMIDINE AND 5% (V/V) ...詳細: CRYSTALS WERE GROWN AT 20C VIA THE VAPOR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (20-25 MG/ML IN 50 MM HEPES/NAOH, PH 7.5, 250 MM KCL, 0.5 MM PMSF, 1 MM BENZAMIDINE AND 5% (V/V) GLYCEROL) WITH WELL SOLUTION (1.4- 1.6 M AMMONIUM SULFATE, 0.1 M NA-CITRATE PH 5.8, 20 MM B-MERCAPTOETHANOL). SERIALLY DILUTED CRUSHED CRYSTALS WERE USED FOR MICRO-SEEDING ONE DAY AFTER THE DROPS WERE SET UP. CRYSTALS APPEARED ONE DAY AFTER SEEDING AND GREW TO A MAXIMUM SIZE OF 120 X 800 UM WITHIN 10 DAYS. CRYSTALS WERE STABILIZED FOR 12 HOURS BY TRANSFER TO FRESH WELL SOLUTION. THEY WERE THEN CRYO-PROTECTED BY STEP-WISE TRANSFER INTO CRYO-BUFFER CONTAINING 1.6 M AMMONIUM SULFATE, 50 MM HEPES, PH 7.5, 100 MM NA-CITRATE, PH 5.8, 100 MM KCL, 50 MM DTT AND UP TO 20% (V/V) GLYCEROL. IT WAS FOUND THAT MANGANESE IONS COULD REPLACE THE MAGNESIUM REQUIRED FOR THE BINDING OF THDP TO THE ENZYME. |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: CUSTOM / 検出器: CCD / 日付: 2003年6月25日 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1.00691 Å / 相対比: 1 |
反射 | 解像度: 1.8→32.05 Å / Num. obs: 77268 / % possible obs: 100 % / Observed criterion σ(I): -3 / 冗長度: 6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.7 |
反射 シェル | 解像度: 1.8→1.83 Å / 冗長度: 5.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3 / % possible all: 100 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 1OLS 解像度: 1.8→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.616 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.091 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 13.26 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.8→30 Å
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拘束条件 |
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