SASDFD6: Protein kinase YopO - cytoplasmic 1 actin complex (Protein kinase...

Basic information

• Entry: Database: SASBDB / ID: SASDFD6

Sample

Protein kinase YopO - cytoplasmic 1 actin complex

• Protein kinase YopO (protein), YopO, Yersinia enterocolitica
• Actin, cytoplasmic 1 (protein), Actin, Homo sapiens

Function / homology

Function:

positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport / nBAF complex / brahma complex / morphogenesis of a polarized epithelium / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / Formation of the dystrophin-glycoprotein complex (DGC) / GBAF complex / Formation of annular gap junctions / Tat protein binding / regulation of G0 to G1 transition / Gap junction degradation / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / regulation of nucleotide-excision repair / regulation of double-strand break repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / apical protein localization / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / regulation of norepinephrine uptake / transporter regulator activity / apical junction complex / nitric-oxide synthase binding / positive regulation of double-strand break repair / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of synaptic vesicle endocytosis / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / brush border / kinesin binding / negative regulation of cell differentiation / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / calyx of Held / axonogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / adherens junction / positive regulation of cell differentiation / actin filament / FCGR3A-mediated phagocytosis / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / Schaffer collateral - CA1 synapse / B-WICH complex positively regulates rRNA expression / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinetochore / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / tau protein binding / VEGFA-VEGFR2 Pathway / platelet aggregation / cytoplasmic ribonucleoprotein granule / nuclear matrix / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / UCH proteinases / Signaling by BRAF and RAF1 fusions / nucleosome / cell-cell junction / lamellipodium / actin cytoskeleton / presynapse / Clathrin-mediated endocytosis / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / regulation of apoptotic process

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 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide 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:

Actin, cytoplasmic 1 / YopO

• Biological species: Yersinia enterocolitica (bacteria); Homo sapiens (human)
• 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 #2981: ; Type: atomic / Comment: PELDOR/SAXS refinement without clash penalty / Chi-square value: 1.098 / P-value: 0.013370; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2980: ; Type: atomic / Comment: PELDOR/SAXS refinement with clash penalty / Chi-square value: 1.123 / P-value: 0.003355; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2982: ; Type: atomic; Comment: Model ignoring the Kinase 113 – Actin 374 restraint; Chi-square value: 1.075 / P-value: 0.013370; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Protein kinase YopO - cytoplasmic 1 actin complex / Specimen concentration: 5.52 mg/ml / Entity id: 1636 / 1637
• Buffer: Name: 10 mM Tris-HCl, 50 mM NaCl / pH: 8

Entity #1636

Name: YopO / 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

Entity #1637

Name: Actin / Type: protein / Description: Actin, cytoplasmic 1 / Formula weight: 41.737 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P60709
Sequence:

MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT HTVPIYEGYA LPHAILRLDL AGRDLTDYLM KILTERGYSF TTTAEREIVR DIKEKLCYVA LDFEQEMATA ASSSSLEKSY ELPDGQVITI GNERFRCPEA LFQPSFLGME SCGIHETTFN SIMKCDVDIR KDLYANTVLS GGTTMYPGIA DRMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWISKQ EYDESGPSIV HRKCF

Experimental information

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

Scan

Title: Protein kinase YopO - cytoplasmic 1 actin complex / 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	0.1331	7.2669

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 761 /

	Min	Max
Q	0.133146	2.22243
P(R) point	1	761
R	0	12.33

Result

Type of curve: sec /

	Experimental	Porod
MW	109.1 kDa	82.1 kDa
Volume	-	147 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	615.1	3.1	611	1
Radius of gyration, Rg	3.658 nm	-	3.6 nm	0.1

	Min	Max	Error
D	-	12.33	0.6
Guinier point	1	84	-