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

Basic information

• Entry: Database: SASBDB / ID: SASDFC6

Sample

Wild type protein kinase YopO

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

Function / homology

Function:

non-specific serine/threonine protein kinase / phosphorylation / protein serine/threonine kinase activity / ATP binding / metal ion binding / cytoplasm

Domain/homology:

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

Component:

YopO

• Biological species: Yersinia enterocolitica (bacteria)
• Citation: Journal: Structure / Year: 2019; Title: Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology.; Authors: Martin F Peter / Anne T Tuukkanen / Caspar A Heubach / Alexander Selsam / Fraser G Duthie / Dmitri I Svergun / Olav Schiemann / Gregor Hagelueken / ; Abstract: 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.

Contact author

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

Models

• Model #2978: ; Type: atomic / Chi-square value: 0.979 / P-value: 0.102700; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Wild type protein kinase YopO / Specimen concentration: 5.52 mg/ml
• Buffer: Name: 10 mM Tris-HCl, 50 mM NaCl / pH: 8

Entity #1636

Name: YopOAnadenanthera peregrina / Type: protein / Description: Protein kinase YopO / Formula weight: 63.387 / Num. of mol.: 1 / Source: Yersinia enterocolitica / References: UniProt: Q93KQ6
Sequence:

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

Experimental information

• Beam: Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3 mm
• Detector: Name: Pilatus 2M

Scan

Title: Wild type protein kinase YopO / Measurement date: May 6, 2017 / Storage temperature: 10 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 3600 / Unit: 1/nm /

	Min	Max
Q	0.1112	7.2669

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 830 /

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

Result

Type of curve: sec /

	Experimental	Porod
MW	68.8 kDa	66.2 kDa
Volume	-	119 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	270	1.4	267.5	0.7
Radius of gyration, Rg	3.419 nm	-	3.34 nm	0.1

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