SASDDH9: Chloroplastic phosphoribulokinase (collected using SEC-SAXS)

基本情報

• 登録情報: データベース: SASBDB / ID: SASDDH9

試料

Chloroplastic phosphoribulokinase (collected using SEC-SAXS)

• Phosphoribulokinase, chloroplastic (protein), CrPRK, Chlamydomonas reinhardtii

機能・相同性

分子機能:

phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / reductive pentose-phosphate cycle / response to cold / chloroplast / disordered domain specific binding / enzyme binding / protein homodimerization activity / ATP binding

ドメイン・相同性:

Phosphoribulokinase signature. / Phosphoribulokinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleoside triphosphate hydrolase

構成要素:

Phosphoribulokinase, chloroplastic

• 生物種: Chlamydomonas reinhardtii (クラミドモナス)
• 引用: ジャーナル: Proc Natl Acad Sci U S A / 年: 2019; タイトル: and phosphoribulokinase crystal structures complete the redox structural proteome of the Calvin-Benson cycle.; 著者: Libero Gurrieri / Alessandra Del Giudice / Nicola Demitri / Giuseppe Falini / Nicolae Viorel Pavel / Mirko Zaffagnini / Maurizio Polentarutti / Pierre Crozet / Christophe H Marchand / Julien Henri / Paolo Trost / Stéphane D Lemaire / Francesca Sparla / Simona Fermani / ; 要旨: In land plants and algae, the Calvin-Benson (CB) cycle takes place in the chloroplast, a specialized organelle in which photosynthesis occurs. Thioredoxins (TRXs) are small ubiquitous proteins, known to harmonize the two stages of photosynthesis through a thiol-based mechanism. Among the 11 enzymes of the CB cycle, the TRX target phosphoribulokinase (PRK) has yet to be characterized at the atomic scale. To accomplish this goal, we determined the crystal structures of PRK from two model species: the green alga (PRK) and the land plant (PRK). PRK is an elongated homodimer characterized by a large central β-sheet of 18 strands, extending between two catalytic sites positioned at its edges. The electrostatic surface potential of the catalytic cavity has both a positive region suitable for binding the phosphate groups of substrates and an exposed negative region to attract positively charged TRX-f. In the catalytic cavity, the regulatory cysteines are 13 Å apart and connected by a flexible region exclusive to photosynthetic eukaryotes-the clamp loop-which is believed to be essential for oxidation-induced structural rearrangements. Structural comparisons with prokaryotic and evolutionarily older PRKs revealed that both PRK and PRK have a strongly reduced dimer interface and an increased number of random-coiled regions, suggesting that a general loss in structural rigidity correlates with gains in TRX sensitivity during the molecular evolution of PRKs in eukaryotes.

登録者

• Alessandra Del Giudice (Sapienza, Sapienza University Rome, Rome, Italy)

モデル

• モデル #2956: ; タイプ: atomic / ダミー原子の半径: 1.90 A / カイ2乗値: 0.889; 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: Chloroplastic phosphoribulokinase (collected using SEC-SAXS)
• バッファ: 名称: Tris-HCl 50 mM 150 mM KCl / pH: 7.5

要素 #1177

名称: CrPRK / タイプ: protein / 記述: Phosphoribulokinase, chloroplastic / 分子量: 38.908 / 分子数: 2 / 由来: Chlamydomonas reinhardtii / 参照: UniProt: P19824
配列:

GSHMDKDKTV VIGLAADSGC GKSTFMRRMT SIFGGVPKPP AGGNPDSNTL ISDMTTVICL DDYHCLDRNG RKVKGVTALA PEAQNFDLMY NQVKALKEGK SVDKPIYNHV SGLIDAPEKI ESPPILVIEG LHPFYDKRVA ELLDFKIYLD ISDDIKFAWK IQRDMAERGH SLESIKSSIA ARKPDFDAYI DPQKKDADMI IQVLPTQLVP DDKGQYLRVR LIMKEGSKMF DPVYLFDEGS TISWIPCGRK LTCSFPGIKM FYGPDTWYGQ EVSVLEMDGQ FDKLEELIYV ESHLSNTSAK FYGEITQQML KNSGFPGSNN GTGLFQTIVG LKVREVYERI VKKDVVPV

実験情報

• ビーム: 設備名称: ESRF BM29 / 地域: Grenoble / 国: France / 線源: X-ray synchrotron / 波長: 0.099 Å / スペクトロメータ・検出器間距離: 2.872 mm
• 検出器: 名称: Pilatus 1M / タイプ: Dectris / Pixsize x: 172 mm

スキャン

タイトル: Chloroplastic phosphoribulokinase (collected using SEC-SAXS)
測定日: 2016年2月15日 / 保管温度: 4 °C / セル温度: 4 °C / 照射時間: 1 sec. / フレーム数: 80 / 単位: 1/nm /

	Min	Max
Q	0.1224	3.5023

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 506 /

	Min	Max
Q	0.12243	2.503
P(R) point	1	506
R	0	11.3

結果

カーブのタイプ: sec
コメント: Additional SEC parameters: Column type: Superdex 200 10/300 GL (GE Healthcare); Flow rate: 0.5 ml/min; Sample injection concentration: 6.1 mg/ml; Injection volume: 100 µl.

	実験値	Standard	Standard error	Porod
分子量	70 kDa	70 kDa	0.2	72 kDa
体積	-	-	-	115 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	42.42	0.06	42	0.1
慣性半径, Rg	3.548 nm	0.008	3.43 nm	0.01

	Min	Max
D	-	11.3
Guinier point	1	55