SASDFC6: Wild type protein kinase YopO (Protein kinase YopO, YopO)

基本情報

• 登録情報: データベース: SASBDB / ID: SASDFC6

試料

Wild type protein kinase YopO

• Protein kinase YopO (protein), YopO, Yersinia enterocolitica

機能・相同性

分子機能:

3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / ATP binding / metal ion binding / cytoplasm

ドメイン・相同性:

Serine/threonine protein kinase, yersinia-type / YpkA, Rac1-binding domain / Rac1-binding domain, C-terminal / Rac1-binding domain, N-terminal / Rac1-binding domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily

構成要素:

YopO

• 生物種: Yersinia enterocolitica (腸炎エルシニア)
• 引用: ジャーナル: Structure / 年: 2019; タイトル: Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology.; 著者: Martin F Peter / Anne T Tuukkanen / Caspar A Heubach / Alexander Selsam / Fraser G Duthie / Dmitri I Svergun / Olav Schiemann / Gregor Hagelueken / ; 要旨: The type-III secretion effector YopO helps pathogenic Yersinia to outmaneuver the human immune system. Injected into host cells, it functions as a Ser/Thr kinase after activation by actin binding. This activation process is thought to involve large conformational changes. We use PELDOR spectroscopy and small-angle X-ray scattering in combination with available crystal structures to study these conformational transitions. Low-resolution hybrid models of the YopO/actin structure in solution were constructed, where the kinase domain of YopO is tilted "backward" compared with the crystal structure, thus shortening the distance between actin and the kinase active site, potentially affecting the substrate specificity of YopO. Furthermore, the GDI domain of the hybrid models resembles a conformation that was previously observed in a crystal structure of the isolated GDI domain. We investigate possible structural reasons for the inactivity of the apo state, analyze its flexibility and discuss the biological implications.

登録者

• Anne Tuukkanen (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

モデル

• モデル #2978: ; タイプ: atomic / カイ2乗値: 0.979 / P-value: 0.102700; 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: Wild type protein kinase YopO / 試料濃度: 5.52 mg/ml
• バッファ: 名称: 10 mM Tris-HCl, 50 mM NaCl / pH: 8

要素 #1636

名称: YopO / タイプ: protein / 記述: Protein kinase YopO / 分子量: 63.387 / 分子数: 1 / 由来: Yersinia enterocolitica / 参照: UniProt: Q93KQ6
配列:

KPQTELPLGW KGKPLSGAPD LEGMRVAHIS IIERLVAKIG HLFAELEAYK HIYKTAGKHP NLANVHGMAV VPYGNRYYYA LLMDEVDGWR CSDTLRSLAD SWKQGKINSE AYWGTIKFIA HRLLDVTNHL AKAGIVHNDI KPGNVVFDRA SGEPVVIDLG LHSRSGEQPK GFTESFKAPE LGVGGASEKS DVFLVVSTLL HGIEGFEKDP EIKPNQGLRF ITSEPAHVMD ENGYPIHRPG IAGVETAYTR FITDILGVSA DSRPDSNEAR LHEFLSDGTI DEESAKQILK DTLTGEMSIT PYYLRELSDL LRTHLSSAAT KQLDMGVVLS DLDTMLVALD KAEREGGVDK DQLKSFNSLI LKTYSVIGAY ILSIVEPSLQ RIQKHLDQTH SFSDIGSLMR AHKHLETLLE VLVTLSQQGQ PVSSETYSFL NRLAEAKVTL SQQLNTLQQQ QESAKAQLSI LINRSGSWAD VARQSLQRFD STRPVVKFGT EQYTAIHRQM MAAHAAITLQ EVSEFTDDMR NFTADSIPLL IQLGRSSLMD EHLVEQREKL RELTTIAERL NRLEREWM

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
• 検出器: 名称: Pilatus 2M

スキャン

タイトル: Wild type protein kinase YopO / 測定日: 2017年5月6日 / 保管温度: 10 °C / セル温度: 20 °C / 照射時間: 1 sec. / フレーム数: 3600 / 単位: 1/nm /

	Min	Max
Q	0.1112	7.2669

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 830 /

	Min	Max
Q	0.113903	2.39287
P(R) point	1	830
R	0	11.45

結果

カーブのタイプ: sec /

	実験値	Porod
分子量	68.8 kDa	66.2 kDa
体積	-	119 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	270	1.4	267.5	0.7
慣性半径, Rg	3.419 nm	-	3.34 nm	0.1

	Min	Max	Error
D	-	11.45	0.6
Guinier point	2	102	-