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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 4d06 | ||||||
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タイトル | Bacterial chalcone isomerase complexed with naringenin | ||||||
![]() | CHALCONE ISOMERASE | ||||||
![]() | ISOMERASE / BACTERIAL CHALCONE ISOMERASE / FLAVONOIDS / NARINGENIN | ||||||
機能・相同性 | Chalcone isomerase, N-terminal / Chalcone isomerase N-terminal domain / chalcone isomerase / chalcone isomerase activity / NARINGENIN / Chem-X8W / Chalcone isomerase![]() | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Thomsen, M. / Palm, G.J. / Hinrichs, W. | ||||||
![]() | ![]() タイトル: Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase. 著者: Maren Thomsen / Anne Tuukkanen / Jonathan Dickerhoff / Gottfried J Palm / Hanna Kratzat / Dmitri I Svergun / Klaus Weisz / Uwe T Bornscheuer / Winfried Hinrichs / ![]() 要旨: Flavonoids represent a large class of secondary metabolites produced by plants. These polyphenolic compounds are well known for their antioxidative abilities, are antimicrobial phytoalexins ...Flavonoids represent a large class of secondary metabolites produced by plants. These polyphenolic compounds are well known for their antioxidative abilities, are antimicrobial phytoalexins responsible for flower pigmentation to attract pollinators and, in addition to other properties, are also specific bacterial regulators governing the expression of Rhizobium genes involved in root nodulation (Firmin et al., 1986). The bacterial chalcone isomerase (CHI) from Eubacterium ramulus catalyses the first step in a flavanone-degradation pathway by ring opening of (2S)-naringenin to form naringenin chalcone. The structural biology and enzymology of plant CHIs have been well documented, whereas the existence of bacterial CHIs has only recently been elucidated. This first determination of the structure of a bacterial CHI provides detailed structural insights into the key step of the flavonoid-degradation pathway. The active site could be confirmed by co-crystallization with the substrate (2S)-naringenin. The stereochemistry of the proposed mechanism of the isomerase reaction was verified by specific (1)H/(2)H isotope exchange observed by (1)H NMR experiments and was further supported by mutagenesis studies. The active site is shielded by a flexible lid, the varying structure of which could be modelled in different states of the catalytic cycle using small-angle X-ray scattering data together with the crystallographic structures. Comparison of bacterial CHI with the plant enzyme from Medicago sativa reveals that they have unrelated folds, suggesting that the enzyme activity evolved convergently from different ancestor proteins. Despite the lack of any functional relationship, the tertiary structure of the bacterial CHI shows similarities to the ferredoxin-like fold of a chlorite dismutase and the stress-related protein SP1. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 722.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 606 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 2.8 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.8 MB | 表示 | |
XML形式データ | ![]() | 83.5 KB | 表示 | |
CIF形式データ | ![]() | 121.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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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Components on special symmetry positions |
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非結晶学的対称性 (NCS) | NCS oper:
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要素
-タンパク質 , 1種, 6分子 ABCDEF
#1: タンパク質 | 分子量: 32537.928 Da / 分子数: 6 / 由来タイプ: 組換発現 由来: (組換発現) ![]() 発現宿主: ![]() ![]() |
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-非ポリマー , 5種, 1923分子 ![](data/chem/img/NAR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/X8W.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/X8W.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: 化合物 | ChemComp-NAR / #3: 化合物 | ChemComp-CL / #4: 化合物 | #5: 化合物 | #6: 水 | ChemComp-HOH / | |
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-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: 4.47 Å3/Da / 溶媒含有率: 72.5 % / 解説: DATA WERE PROCESSED WITH FRIEDEL'S LAW - FALSE. |
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結晶化 | pH: 7.5 詳細: 0.1 M HEPES PH 7.5, 0.2 M SODIUM CHLORIDE, 1.6 M AMMONIUM SULFATE, 380 MIKROM NARINGENIN CHALCONE DISSOLVED IN ETHANOL |
-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: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2013年6月6日 / 詳細: MIRROR |
放射 | モノクロメーター: MIRROR / 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: 0.9785 Å / 相対比: 1 |
反射 | 解像度: 2→50 Å / Num. obs: 436945 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / 冗長度: 3.5 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.94 |
反射 シェル | 解像度: 2→2.12 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.9 / % possible all: 98.4 |
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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 4C9S 解像度: 2→49.18 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.809 / SU ML: 0.069 / 交差検証法: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.09 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 24.527 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2→49.18 Å
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拘束条件 |
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