John Kuriyan

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc A Ras-induced conformational switch in the Ras activator Son of sevenless
    Tanya S Freedman
    Department of Molecular and Cell Biology, California Institute for Quantitative Biomedical Research, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 103:16692-7. 2006
  2. pmc Macromolecular juggling by ubiquitylation enzymes
    Sonja Lorenz
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    BMC Biol 11:65. 2013
  3. pmc A structural role for the PHP domain in E. coli DNA polymerase III
    Tiago Barros
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    BMC Struct Biol 13:8. 2013
  4. pmc A Src-like inactive conformation in the abl tyrosine kinase domain
    Nicholas M Levinson
    Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Biol 4:e144. 2006
  5. pmc The mechanism of ATP-dependent primer-template recognition by a clamp loader complex
    Kyle R Simonetta
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 137:659-71. 2009
  6. pmc Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex
    Steven L Kazmirski
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 101:16750-5. 2004
  7. ncbi request reprint A dimeric kinase assembly underlying autophosphorylation in the p21 activated kinases
    Michelle Pirruccello
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, Department of Chemistry, University of California, Berkeley, CA 94720, USA
    J Mol Biol 361:312-26. 2006
  8. ncbi request reprint Mapping the interaction of DNA with the Escherichia coli DNA polymerase clamp loader complex
    Eric R Goedken
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Nat Struct Mol Biol 12:183-90. 2005
  9. pmc Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms
    Natalia Jura
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Mol Cell 42:9-22. 2011
  10. pmc Structural basis for activation of ZAP-70 by phosphorylation of the SH2-kinase linker
    Qingrong Yan
    Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
    Mol Cell Biol 33:2188-201. 2013

Collaborators

Detail Information

Publications81

  1. pmc A Ras-induced conformational switch in the Ras activator Son of sevenless
    Tanya S Freedman
    Department of Molecular and Cell Biology, California Institute for Quantitative Biomedical Research, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 103:16692-7. 2006
    ..These results indicate that RasGRF1 lacks the allosteric activation switch that is crucial for Sos activity...
  2. pmc Macromolecular juggling by ubiquitylation enzymes
    Sonja Lorenz
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    BMC Biol 11:65. 2013
    ..This enables the efficient, directed and regulated handover of ubiquitin from one carrier to the next one. We review some of these conformational transformations, as revealed by crystallographic studies. ..
  3. pmc A structural role for the PHP domain in E. coli DNA polymerase III
    Tiago Barros
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    BMC Struct Biol 13:8. 2013
    ..In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive...
  4. pmc A Src-like inactive conformation in the abl tyrosine kinase domain
    Nicholas M Levinson
    Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Biol 4:e144. 2006
    ..Our results suggest that interconversion between distinctly different inactive conformations is a characteristic feature of the Abl kinase domain...
  5. pmc The mechanism of ATP-dependent primer-template recognition by a clamp loader complex
    Kyle R Simonetta
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 137:659-71. 2009
    ..By stabilizing a conformation of the clamp loader that is consistent with the ATPase spiral observed upon DNA binding, psi binding promotes the clamp-loading activity of the complex...
  6. pmc Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex
    Steven L Kazmirski
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 101:16750-5. 2004
    ....
  7. ncbi request reprint A dimeric kinase assembly underlying autophosphorylation in the p21 activated kinases
    Michelle Pirruccello
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, Department of Chemistry, University of California, Berkeley, CA 94720, USA
    J Mol Biol 361:312-26. 2006
    ..Mutations at the predicted dimerization interface block dimerization and reduce the rate of autophosphorylation, supporting the role of this interface in PAK activation...
  8. ncbi request reprint Mapping the interaction of DNA with the Escherichia coli DNA polymerase clamp loader complex
    Eric R Goedken
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Nat Struct Mol Biol 12:183-90. 2005
    ..These results provide evidence for the recognition of DNA within an inner chamber formed by the spiral organization of the ATPase domains of the clamp loader...
  9. pmc Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms
    Natalia Jura
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Mol Cell 42:9-22. 2011
    ..This mechanism, which involves the stabilization of the active conformation of an α helix, has features in common with mechanisms operative in several other kinases...
  10. pmc Structural basis for activation of ZAP-70 by phosphorylation of the SH2-kinase linker
    Qingrong Yan
    Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
    Mol Cell Biol 33:2188-201. 2013
    ..This difference is due to the ability of Tyr 319 to suppress ZAP-70 activity even when the SH2 domains are dislodged from the kinase domain, providing stringent control of ZAP-70 activity downstream of Lck...
  11. pmc Conformational coupling across the plasma membrane in activation of the EGF receptor
    Nicholas F Endres
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 152:543-56. 2013
    ..We conclude that EGF binding removes steric constraints in the extracellular module, promoting activation through N-terminal association of the transmembrane helices...
  12. ncbi request reprint Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding
    Eric R Goedken
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    J Mol Biol 336:1047-59. 2004
    ....
  13. pmc Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations
    Markus A Seeliger
    Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkely, USA
    Cancer Res 69:2384-92. 2009
    ..Importantly, several of the DSA compounds block the growth of Ba/F3 cells harboring imatinib-resistant BCR-ABL mutants, including the Thr315Ile "gatekeeper" mutation, but do not suppress the growth of parental Ba/F3 cells...
  14. pmc Structure of a sliding clamp on DNA
    Roxana E Georgescu
    Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, Box 228, New York, NY 10021, USA
    Cell 132:43-54. 2008
    ..The pronounced 22 degrees angle of DNA through beta may enable DNA to switch between multiple factors bound to a single clamp simply by alternating from one protomer of the ring to the other...
  15. pmc Inhibition of the EGF receptor by binding of MIG6 to an activating kinase domain interface
    Xuewu Zhang
    Department of Molecular and Cell Biology, and Howard Hughes Medical Institute, California Institute for Quantitative Sciences, University of California, Berkeley, California 94720, USA
    Nature 450:741-4. 2007
    ..We show that signalling by EGFR molecules that contain constitutively active kinase domains still requires formation of the asymmetric dimer, underscoring the importance of dimer interface blockage in MIG6-mediated inhibition...
  16. pmc The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2)
    Jonathan A Winger
    Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, Howard Hughes Medical Institute, University of California, Berkeley, USA
    BMC Struct Biol 9:7. 2009
    ..Recent screens carried out to find off-target proteins that bind to imatinib identified the oxidoreductase NQO2, a flavoprotein that is phosphorylated in a chronic myelogenous leukemia cell line...
  17. pmc Crystal structure of a DNA polymerase sliding clamp from a Gram-positive bacterium
    Maria A Argiriadi
    Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA
    BMC Struct Biol 6:2. 2006
    ..coli), eukaryotes, archaea, and T4-like bacteriophages are well-known, the structure of a sliding clamp from Gram-positive bacteria has not been reported previously...
  18. pmc Membrane-dependent signal integration by the Ras activator Son of sevenless
    Jodi Gureasko
    Department of Molecular and Cell Biology, and Howard Hughes Medical Institute, QB3 Institute, 176 Stanley Hall, University of California, Berkeley, California 94720, USA
    Nat Struct Mol Biol 15:452-61. 2008
    ....
  19. pmc Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment
    Natalia Jura
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 137:1293-307. 2009
    ..The formation of the activating juxtamembrane latch is prevented by the C-terminal tails in a structure of an inactive kinase domain dimer, suggesting how alternative dimers can prevent ligand-independent activation...
  20. pmc Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation
    Luke H Chao
    Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
    Nat Struct Mol Biol 17:264-72. 2010
    ..Our results show that a simple coincidence-detection model cannot be operative and point to the importance of kinetic dissection of the frequency-response mechanism in future experiments...
  21. pmc The tyrosine kinase Csk dimerizes through Its SH3 domain
    Nicholas M Levinson
    Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
    PLoS ONE 4:e7683. 2009
    ..The formation of this dimer would therefore block the recruitment of tyrosine phosphatases and may have important implications for the regulation of Src kinase activity...
  22. ncbi request reprint Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex
    Jacqueline M Gulbis
    Laboratory of Molecular Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
    Eur J Biochem 271:439-49. 2004
    ..The base of the clamp-loader complex has an open C-shaped structure, and the shape of the chi:psi complex is suggestive of a loose docking within the crevice formed by the open faces of the delta and delta' subunits of the clamp-loader...
  23. ncbi request reprint Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III
    Meindert H Lamers
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology and Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Cell 126:881-92. 2006
    ..The structure also suggests a model for interaction of Pol III with the sliding clamp and DNA...
  24. ncbi request reprint Organization of the SH3-SH2 unit in active and inactive forms of the c-Abl tyrosine kinase
    Bhushan Nagar
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA
    Mol Cell 21:787-98. 2006
    ..This alternative conformation of Abl is likely to prolong the active state of the kinase by preventing it from returning to the autoinhibited state...
  25. ncbi request reprint c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty
    Markus A Seeliger
    Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
    Structure 15:299-311. 2007
    ..Two mutations that are expected to destabilize the inactive Src/CDK conformation increase drug sensitivity 15-fold, suggesting that the free-energy balance between different inactive states is a key to imatinib binding...
  26. pmc Stability of an autoinhibitory interface in the structure of the tyrosine kinase ZAP-70 impacts T cell receptor response
    Sebastian Deindl
    Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 106:20699-704. 2009
    ..Taken together, our results directly correlate the stability of the autoinhibitory interface with the activation of these key events in the T cell response...
  27. ncbi request reprint Structural basis for the autoinhibition of c-Abl tyrosine kinase
    Bhushan Nagar
    Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 112:859-71. 2003
    ....
  28. pmc Regulation of the catalytic activity of the EGF receptor
    Nicholas F Endres
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Curr Opin Struct Biol 21:777-84. 2011
    ..New insights into the allosteric mechanisms utilized by intracellular regulators of EGFR provide hope that allosteric sites could be used as targets for drug development...
  29. pmc Analysis of the role of PCNA-DNA contacts during clamp loading
    Randall McNally
    Department of Molecular and Cell Biology, Department of Chemistry, California Institute for Quantitative Biosciences QB3, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
    BMC Struct Biol 10:3. 2010
    ..In an ATP-dependent reaction, clamp loader complexes, such as the Replication Factor-C (RFC) complex in eukaryotes, open the clamp and load it around primer-template DNA...
  30. pmc Role of the histone domain in the autoinhibition and activation of the Ras activator Son of Sevenless
    Jodi Gureasko
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 107:3430-5. 2010
    ....
  31. ncbi request reprint Oligomerization states of the association domain and the holoenyzme of Ca2+/CaM kinase II
    Oren S Rosenberg
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3202, USA
    FEBS J 273:682-94. 2006
    ....
  32. pmc Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3
    Natalia Jura
    Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 106:21608-13. 2009
    ....
  33. ncbi request reprint Structural basis for the inhibition of tyrosine kinase activity of ZAP-70
    Sebastian Deindl
    Department of Molecular and Cell Biology, Department of Chemistry, and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Cell 129:735-46. 2007
    ..These interactions are inconsistent with ITAM binding, suggesting that destabilization of this autoinhibited ZAP-70 conformation is the first step in kinase activation...
  34. pmc Probing the function of heme distortion in the H-NOX family
    Charles Olea
    Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
    ACS Chem Biol 3:703-10. 2008
    ..These results show a clear link between the heme conformation and Tt H-NOX structure and demonstrate that heme distortion is an important determinant for maintaining biochemical properties in H-NOX proteins...
  35. pmc The crystal structure of the catalytic domain of a eukaryotic guanylate cyclase
    Jonathan A Winger
    Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
    BMC Struct Biol 8:42. 2008
    ..The guanylate cyclase catalytic module, for which no structure has been determined at present, is a class III nucleotide cyclase domain that is also found in mammalian membrane-bound guanylate and adenylate cyclases...
  36. ncbi request reprint An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
    Xuewu Zhang
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, 94720, USA
    Cell 125:1137-49. 2006
    ..The CDK/cyclin-like complex formed by two kinase domains thus explains the activation of EGFR-family receptors by homo- or heterodimerization...
  37. ncbi request reprint Structure of the kinase domain of an imatinib-resistant Abl mutant in complex with the Aurora kinase inhibitor VX-680
    Matthew A Young
    Departments of Molecular and Cell Biology and Chemistry, Howard Hughes Medical Institute, The University of California at Berkeley, Berkeley, CA 94720, USA
    Cancer Res 66:1007-14. 2006
    ....
  38. ncbi request reprint DNA polymerase clamp loaders and DNA recognition
    Gregory D Bowman
    Departments of Molecular and Cell Biology and Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    FEBS Lett 579:863-7. 2005
    ..Here, we briefly review the crystal structures of clamp loader complexes and the insights they have provided into the mechanism of the clamp loading process...
  39. pmc How a DNA polymerase clamp loader opens a sliding clamp
    Brian A Kelch
    Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
    Science 334:1675-80. 2011
    ..The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA...
  40. pmc Differences in flexibility underlie functional differences in the Ras activators son of sevenless and Ras guanine nucleotide releasing factor 1
    Tanya S Freedman
    Department of Molecular and Cell Biology, California Institute for Quantitative Biomedical Research, University of California, Berkeley, Berkeley, CA 94720, USA
    Structure 17:41-53. 2009
    ..Our results support the premise that the catalytic domain of Sos has evolved an allosteric activation mechanism that extends beyond the simple process of membrane recruitment...
  41. pmc Tuning a three-component reaction for trapping kinase substrate complexes
    Alexander V Statsuk
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94107, USA
    J Am Chem Soc 130:17568-74. 2008
    ..The combination of these two structural modifications provides for cross-linking of a cysteine-containing substrate to its corresponding kinase in the presence of competing cellular proteins...
  42. pmc Structural basis for the recognition of c-Src by its inactivator Csk
    Nicholas M Levinson
    Department of Molecular and Cell Biology, Department of Chemistry, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences QB3, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 134:124-34. 2008
    ..Csk cannot phosphorylate substrates that lack this docking mechanism because the conventional substrate binding site used by most tyrosine kinases to recognize substrates is destabilized in Csk by a deletion in the activation loop...
  43. pmc A mechanism for tunable autoinhibition in the structure of a human Ca2+/calmodulin- dependent kinase II holoenzyme
    Luke H Chao
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Cell 146:732-45. 2011
    ..This equilibrium between autoinhibited states provides a simple mechanism for tuning the calcium response without changes in either the hub or the kinase domains...
  44. pmc Computational docking and solution x-ray scattering predict a membrane-interacting role for the histone domain of the Ras activator son of sevenless
    Holger Sondermann
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:16632-7. 2005
    ..The orientation and position of the histone domain in the SOS model implicates it as a potential mediator of membrane-dependent activation signals...
  45. ncbi request reprint Protein-protein interactions in the allosteric regulation of protein kinases
    Patricia Pellicena
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Curr Opin Struct Biol 16:702-9. 2006
    ....
  46. pmc Structural insights into the molecular mechanism of H-NOX activation
    Charles Olea
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Protein Sci 19:881-7. 2010
    ..Fe-His ligation is ubiquitous in all H-NOX domains, and therefore, the heme and protein conformational changes observed in this study are likely to occur throughout the H-NOX family when NO binding leads to rupture of the Fe-His bond...
  47. ncbi request reprint Structural analysis of autoinhibition in the Ras activator Son of sevenless
    Holger Sondermann
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology and Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Cell 119:393-405. 2004
    ..The action of the DH-PH unit gates a reciprocal interaction between Ras and SOS, in which Ras converts SOS from low to high activity forms as Ras*GDP is converted to Ras*GTP by SOS...
  48. pmc Clamp loader ATPases and the evolution of DNA replication machinery
    Brian A Kelch
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    BMC Biol 10:34. 2012
    ..We review here the current understanding of the clamp loader mechanism and discuss the implications of the differences between clamp loaders from the different branches of life...
  49. ncbi request reprint Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex
    Gregory D Bowman
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology and Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 429:724-30. 2004
    ....
  50. pmc Tunnels modulate ligand flux in a heme nitric oxide/oxygen binding (H-NOX) domain
    Michael B Winter
    Department of Chemistry, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 108:E881-9. 2011
    ..The findings provide insights on how the flux of biomolecules through protein scaffolds modulates protein chemistry...
  51. pmc Modulating heme redox potential through protein-induced porphyrin distortion
    Charles Olea
    Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, and Division of Physical Biosciences, University of California, Berkeley, Berkeley, California 94720 3220, USA
    J Am Chem Soc 132:12794-5. 2010
    ..Protein-induced porphyrin distortion represents a new strategy to rationally tune the electronic properties of protein-bound porphyrins and could be used to engineer proteins with desired reactivity or functionality...
  52. ncbi request reprint Multiple BCR-ABL kinase domain mutations confer polyclonal resistance to the tyrosine kinase inhibitor imatinib (STI571) in chronic phase and blast crisis chronic myeloid leukemia
    Neil P Shah
    Department of Medicine, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    Cancer Cell 2:117-25. 2002
    ..Multiple independent mutant clones were detected in a subset of relapsed cases. Our data support a clonal selection model of preexisting BCR-ABL mutations that confer imatinib resistance...
  53. doi request reprint A MAPK scaffold lends a helping hand
    Markus A Seeliger
    Department of Molecular and Cell Biology, University of California, Howard Hughes Medical Institute, Berkeley, Berkeley, CA 94720, USA
    Cell 136:994-6. 2009
    ..Good et al. (2009) now reveal that in the budding yeast the scaffold protein Ste5 acts as an allosteric activator of the mitogen-activated protein kinase Fus3, rendering it competent to be a kinase substrate for signal transmission...
  54. ncbi request reprint Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme
    Oren S Rosenberg
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 123:849-60. 2005
    ....
  55. pmc Molecular mechanisms in signal transduction at the membrane
    Jay T Groves
    Departments of Chemistry, University of California, Berkeley, California, USA
    Nat Struct Mol Biol 17:659-65. 2010
    ....
  56. pmc Out-of-plane motions in open sliding clamps: molecular dynamics simulations of eukaryotic and archaeal proliferating cell nuclear antigen
    Steven L Kazmirski
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:13801-6. 2005
    ....
  57. ncbi request reprint The origin of protein interactions and allostery in colocalization
    John Kuriyan
    Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Nature 450:983-90. 2007
    ..Thus, the regulated protein networks of organisms seem to be the inevitable consequence of natural selection operating under physical laws...
  58. ncbi request reprint Clamp loaders and replication initiation
    Mike O'Donnell
    The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10021, USA
    Curr Opin Struct Biol 16:35-41. 2006
    ..Recently determined structures of clamp loader complexes from prokaryotic and eukaryotic sources have revealed exciting new details of how these complex AAA+ machines perform this essential clamp loading function...
  59. ncbi request reprint Tandem histone folds in the structure of the N-terminal segment of the ras activator Son of Sevenless
    Holger Sondermann
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
    Structure 11:1583-93. 2003
    ..Residues that form a contiguous patch on the surface of the histone domain of Sos are conserved from C. elegans to humans, suggesting a potential role for this domain in protein-protein interactions...
  60. pmc Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1
    Jeffrey S Iwig
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
    elife 2:e00813. 2013
    ..These features allow RasGRP1 to be maintained in an inactive state that is poised for activation by calcium and membrane-localization signals. DOI:http://dx.doi.org/10.7554/eLife.00813.001. ..
  61. pmc The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2
    Katherine E Wickliffe
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Cell 144:769-81. 2011
    ..Our studies suggest that monomeric E2s promote linkage-specific ubiquitin chain formation through substrate-assisted catalysis...
  62. ncbi request reprint Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571)
    Bhushan Nagar
    Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
    Cancer Res 62:4236-43. 2002
    ..The structures suggest that PD173955 achieves its greater potency over STI-571 by being able to target multiple forms of Abl (active or inactive), whereas STI-571 requires a specific inactive conformation of Abl...
  63. pmc High yield bacterial expression of active c-Abl and c-Src tyrosine kinases
    Markus A Seeliger
    Department of Molecular and Cell Biology, 16 Barker Hall, University of California, Berkeley, CA 94720 3202, USA
    Protein Sci 14:3135-9. 2005
    ..This method makes practical the use of isotopic labeling of c-Abl and c-Src for NMR studies, and is also applicable for constructs containing the SH2 and SH3 domains of the kinases...
  64. ncbi request reprint Nucleotide-induced conformational changes in an isolated Escherichia coli DNA polymerase III clamp loader subunit
    Marjetka Podobnik
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
    Structure 11:253-63. 2003
    ..This change would break one of the gamma:gamma interfaces seen in the empty clamp loader complex, and may represent one step in the activation process...
  65. pmc Structural studies on the regulation of Ca2+/calmodulin dependent protein kinase II
    Margaret M Stratton
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Curr Opin Struct Biol 23:292-301. 2013
    ..These structures, when combined with other data, allow informed speculation about how CaMKII escapes calcium-dependence when calcium spikes exceed threshold frequencies...
  66. doi request reprint The structure, regulation, and function of ZAP-70
    Byron B Au-Yeung
    Department of Medicine, Rosalind Russell Medical Research Center for Arthritis, Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94143 0795, USA
    Immunol Rev 228:41-57. 2009
    ..Thus, the critical importance of ZAP-70 in TCR signaling and its predominantly T-cell-restricted expression pattern make ZAP-70 an attractive drug target for the inhibition of pathological T-cell responses in disease...
  67. ncbi request reprint C2 can do it, too
    Holger Sondermann
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, Berkeley, California 94720, USA
    Cell 121:158-60. 2005
    ..This new role for the C2 domain links phosphotyrosine recognition directly to serine/threonine kinase activity and reveals an unexpected mechanism for crosstalk between distinct signaling pathways...
  68. pmc Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases
    Patricia Pellicena
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 101:12854-9. 2004
    ....
  69. ncbi request reprint Allostery and coupled sequence variation in nuclear hormone receptors
    John Kuriyan
    Howard Hughes Medical Institute, Departments of Molecular and Cell Biology and of Chemistry, University of California, Berkeley, CA 94707, USA
    Cell 116:354-6. 2004
    ..Such an analysis has been carried out for the nuclear hormone receptors, and the conclusions tested by making mutations that switch the allosteric response to ligands of RXR heterodimers...
  70. ncbi request reprint The conformational plasticity of protein kinases
    Morgan Huse
    Department of Biological Sciences, Stanford University, Palo Alto, California 94305, USA
    Cell 109:275-82. 2002
    ..By contrast, crystal structures of inactive kinases have revealed a remarkable plasticity in the kinase domain that allows the adoption of distinct conformations in response to interactions with specific regulatory domains or proteins...
  71. pmc Activation of tyrosine kinases by mutation of the gatekeeper threonine
    Mohammad Azam
    Karp Research Building, 7th Floor, Division of Pediatric Hematology Oncology, Children s Hospital of Boston, Massachusetts 02115, USA
    Nat Struct Mol Biol 15:1109-18. 2008
    ..These results demonstrate that mutation of the gatekeeper threonine is a common mechanism of activation for tyrosine kinases and provide structural insights to guide the development of next-generation inhibitors...
  72. ncbi request reprint Clamp loaders and sliding clamps
    David Jeruzalmi
    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, The University of California, Berkeley, CA 94720, USA
    Curr Opin Struct Biol 12:217-24. 2002
    ..Crystallographic and electron microscopic views of clamp loaders from bacteria, archaebacteria and eukaryotes emphasize their common architecture and have produced models of how ATPbinding might be coupled to clamp opening/loading...
  73. ncbi request reprint The replication factor C clamp loader requires arginine finger sensors to drive DNA binding and proliferating cell nuclear antigen loading
    Aaron Johnson
    Laboratory of DNA Replication, Howard Hughes Medical Institute and Rockefeller University, New York, New York 10021, USA
    J Biol Chem 281:35531-43. 2006
    ..PCNA closure severs contact to RFC subunits D and E (RFC2 and RFC5), and the gamma-phosphate sensor of ATP site C is switched off, resulting in low affinity of RFC for DNA and ejection of RFC from the site of PCNA loading...
  74. ncbi request reprint Analysis of a multicomponent thermostable DNA polymerase III replicase from an extreme thermophile
    Irina Bruck
    Rockefeller University and Howard Hughes Medical Institute, New York, New York 10021, USA
    J Biol Chem 277:17334-48. 2002
    ..Similarities and differences between the A. aeolicus and E. coli pol III systems are discussed, as is application of thermostable pol III to biotechnology...
  75. ncbi request reprint Mechanism of proliferating cell nuclear antigen clamp opening by replication factor C
    Nina Y Yao
    Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    J Biol Chem 281:17528-39. 2006
    ..Interestingly, the Rad.RFC DNA damage checkpoint clamp loader unloads PCNA clamps from DNA. We propose that Rad.RFC may clear PCNA from DNA to facilitate shutdown of replication in the face of DNA damage...
  76. pmc Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp
    Roxana E Georgescu
    The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, P O Box 228, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 105:11116-21. 2008
    ..The results suggest that the small molecule may be useful in the future to probe polymerase function with beta, and that the beta-clamp may represent an antibiotic target...
  77. ncbi request reprint Structural evidence for feedback activation by Ras.GTP of the Ras-specific nucleotide exchange factor SOS
    S Mariana Margarit
    Department of Molecular Genetics and Microbiology, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
    Cell 112:685-95. 2003
    ..These results demonstrate the existence of a positive feedback mechanism for the spatial and temporal regulation of Ras...
  78. ncbi request reprint SAXS and the working protein
    Bhushan Nagar
    Structure 13:169-70. 2005
    ..This work emphasizes the emerging potential of SAXS for visualizing the workings of biological machines in solution...
  79. ncbi request reprint Motors and switches: AAA+ machines within the replisome
    Megan J Davey
    Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nat Rev Mol Cell Biol 3:826-35. 2002
    ..Other AAA+ proteins are also involved in the initiation of DNA replication, and studies of the E. coli clamp loader indicate mechanisms by which these proteins might function...
  80. pmc A reinterpretation of the dimerization interface of the N-terminal domains of STATs
    Xiaomin Chen
    Department of Biochemistry and Molecular Biology, The University of Texas, M D Anderson Cancer Center, Houston 77030, USA
    Protein Sci 12:361-5. 2003
    ..Given the alternative model for the N-domain dimer, the ability of the N-domain to mediate interactions of two STAT dimers on DNA remains unchanged...
  81. ncbi request reprint Crystal structure of a tetradecameric assembly of the association domain of Ca2+/calmodulin-dependent kinase II
    Andre Hoelz
    The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Mol Cell 11:1241-51. 2003
    ..A deep and highly conserved pocket present within the association domain may serve as a docking site for proteins that interact with CaMKII...