SASDAX2: Pyruvate decarboxylase (PDC) from Z. mobilis (Pyruvate decarboxyl...

基本情報

• 登録情報: データベース: SASBDB / ID: SASDAX2

試料

Pyruvate decarboxylase (PDC) from Z. mobilis

• Pyruvate decarboxylase (protein), ZmPDC, Zymomonas mobilis

機能・相同性

分子機能:

pyruvate decarboxylase / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / cytosol

ドメイン・相同性:

: / Thiamine pyrophosphate (TPP)-dependent enzyme / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily

構成要素:

Pyruvate decarboxylase

• 生物種: Zymomonas mobilis (バクテリア)
• 引用: ジャーナル: J Biol Chem / 年: 2000; タイトル: Crystal versus solution structures of thiamine diphosphate-dependent enzymes.; 著者: D I Svergun / M V Petoukhov / M H Koch / S König / ; 要旨: The quaternary structures of the thiamine diphosphate-dependent enzymes transketolase (EC 2.2.1.1; from Saccharomyces cerevisiae), pyruvate oxidase (EC 1.2.3.3; from Lactobacillus plantarum), and pyruvate decarboxylase (EC 4.1.1.1; from Zymomonas mobilis and brewers' yeast, the latter in the native and pyruvamide-activated forms) were examined by synchrotron x-ray solution scattering. The experimental scattering data were compared with the curves calculated from the crystallographic models of these multisubunit enzymes. For all enzymes noted above, except the very compact pyruvate decarboxylase from Z. mobilis, there were significant differences between the experimental and calculated profiles. The changes in relative positions of the subunits in solution were determined by rigid body refinement. For pyruvate oxidase and transketolase, which have tight intersubunit contacts in the crystal, relatively small modifications of the quaternary structure (root mean square displacements of 0.23 and 0.27 nm, respectively) sufficed to fit the experimental data. For the enzymes with looser contacts (the native and activated forms of yeast pyruvate decarboxylase), large modifications of the crystallographic models (root mean square displacements of 0.58 and 1.53 nm, respectively) were required. A clear correlation was observed between the magnitude of the distortions induced by the crystal environment and the interfacial area between subunits.

登録者

• Maxim Petoukhov
• Stephan Koenig

モデル

• モデル #27: ; タイプ: atomic / 対称性: P222 / コメント: This is Xtal model / カイ2乗値: 0.665856 / P-value: 0.005737; 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: Pyruvate decarboxylase (PDC) from Z. mobilis / Sample MW: 244 kDa
• バッファ: 名称: 100 mM Sodium Citrate, 17% Glycerol, 22.5% PEG 1500 / pH: 6 ; コメント: buffer for thiamin diphosphat dependent enzyme; 組成: Glycerol 17.000 %, PEG 1500 22.500 %, Sodium Citrate 100.000 mM

要素 #20

名称: ZmPDC / タイプ: protein / 記述: Pyruvate decarboxylase / 分子量: 60.93 / 分子数: 4 / 由来: Zymomonas mobilis / 参照: UniProt: P06672
配列:

MSYTVGTYLA ERLVQIGLKH HFAVAGDYNL VLLDNLLLNK NMEQVYCCNE LNCGFSAEGY ARAKGAAAAV VTYSVGALSA FDAIGGAYAE NLPVILISGA PNNNDHAAGH VLHHALGKTD YHYQLEMAKN ITAAAEAIYT PEEAPAKIDH VIKTALREKK PVYLEIACNI ASMPCAAPGP ASALFNDEAS DEASLNAAVE ETLKFIANRD KVAVLVGSKL RAAGAEEAAV KFADALGGAV ATMAAAKSFF PEENPHYIGT SWGEVSYPGV EKTMKEADAV IALAPVFNDY STTGWTDIPD PKKLVLAEPR SVVVNGIRFP SVHLKDYLTR LAQKVSKKTG ALDFFKSLNA GELKKAAPAD PSAPLVNAEI ARQVEALLTP NTTVIAETGD SWFNAQRMKL PNGARVEYEM QWGHIGWSVP AAFGYAVGAP ERRNILMVGD GSFQLTAQEV AQMVRLKLPV IIFLINNYGY TIEVMIHDGP YNNIKNWDYA GLMEVFNGNG GYDSGAGKGL KAKTGGELAE AIKVALANTD GPTLIECFIG REDCTEELVK WGKRVAAANS RKPVNKLL

実験情報

• ビーム: 設備名称: DORIS III EMBL X33 / 地域: Hamburg / 国: Germany / 線源: X-ray synchrotron
• 検出器: 名称: 1D Gas detector

スキャン

測定日: 1998年11月3日 / 単位: 1/nm /

	Min	Max
Q	0.2931	4.6896

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 154 /

	Min	Max
Q	0.304824	2.09861
P(R) point	1	154
R	0	11

結果

Experimental MW: 247 kDa / D max: 11 / カーブのタイプ: merged

	Guinier	P(R)
前方散乱 I0	10.2	-
慣性半径, Rg	3.9 nm	3.763 nm