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Yorodumi- SASDFD6: Protein kinase YopO - cytoplasmic 1 actin complex (Protein kinase... -
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-Basic information
Entry | Database: SASBDB / ID: SASDFD6 |
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Sample | Protein kinase YopO - cytoplasmic 1 actin complex
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Function / homology | Function and homology information positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium ...positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / GBAF complex / postsynaptic actin cytoskeleton / protein localization to adherens junction / Formation of annular gap junctions / regulation of G0 to G1 transition / dense body / Gap junction degradation / Tat protein binding / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of double-strand break repair / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / positive regulation of double-strand break repair / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / apical junction complex / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair via homologous recombination / cortical cytoskeleton / nitric-oxide synthase binding / regulation of cyclin-dependent protein serine/threonine kinase activity / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / brush border / kinesin binding / calyx of Held / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / EPHB-mediated forward signaling / substantia nigra development / axonogenesis / negative regulation of protein binding / cell motility / actin filament / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / regulation of transmembrane transporter activity / positive regulation of cell differentiation / FCGR3A-mediated phagocytosis / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / tau protein binding / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / kinetochore / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / nuclear matrix / VEGFA-VEGFR2 Pathway / 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 / nucleosome / Signaling by BRAF and RAF1 fusions / cell-cell junction / actin cytoskeleton / presynapse / lamellipodium / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / regulation of apoptotic process / blood microparticle Similarity search - Function |
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. ...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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDFD6 |
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-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-External links
Related items in Molecule of the Month |
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-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) |
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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 |
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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 ...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 ...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 synchrotronSynchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3 mm | ||||||||||||||||||||||||||||||||||||
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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 /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 761 /
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Result | Type of curve: sec /
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