Structural basis of ubiquitin modification by the Legionella effector SdeA

[1]  Donghyuk Shin,et al.  Insights into catalysis and function of phosphoribosyl-linked serine ubiquitination , 2018, Nature.

[2]  D. J. Wasilko,et al.  The mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector , 2018, Nature.

[3]  M. Wirth,et al.  Ubiquitin Chains Modified by the Bacterial Ligase SdeA Are Protected from Deubiquitinase Hydrolysis. , 2017, Biochemistry.

[4]  Nam Ki Lee,et al.  Architecture of the type IV coupling protein complex of Legionella pneumophila , 2017, Nature Microbiology.

[5]  Zhao‐Qing Luo,et al.  Legionella and Coxiella effectors: strength in diversity and activity , 2017, Nature Reviews Microbiology.

[6]  William L. Jorgensen,et al.  LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands , 2017, Nucleic Acids Res..

[7]  William L. Jorgensen,et al.  1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations. , 2017, The journal of physical chemistry. B.

[8]  R. Isberg,et al.  A Single Legionella Effector Catalyzes a Multistep Ubiquitination Pathway to Rearrange Tubular Endoplasmic Reticulum for Replication. , 2017, Cell host & microbe.

[9]  I. Matic,et al.  Phosphoribosylation of Ubiquitin Promotes Serine Ubiquitination and Impairs Conventional Ubiquitination , 2016, Cell.

[10]  M. Rapé,et al.  The increasing complexity of the ubiquitin code , 2016, Nature Cell Biology.

[11]  Zhao‐Qing Luo,et al.  Ubiquitination independent of E1 and E2 enzymes by bacterial effectors , 2016, Nature.

[12]  C. Das,et al.  Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination , 2015, Proceedings of the National Academy of Sciences.

[13]  J. Sexton,et al.  Spatiotemporal Regulation of a Legionella pneumophila T4SS Substrate by the Metaeffector SidJ , 2015, PLoS pathogens.

[14]  Qs Wang,et al.  The macromolecular crystallography beamline of SSRF , 2015 .

[15]  John A. Tainer,et al.  Accurate assessment of mass, models and resolution by small-angle scattering , 2013, Nature.

[16]  Tal Pupko,et al.  Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal , 2013, Proceedings of the National Academy of Sciences.

[17]  M. Rapé,et al.  The Ubiquitin Code , 2012, Annual review of biochemistry.

[18]  Maxim V. Petoukhov,et al.  New developments in the ATSAS program package for small-angle scattering data analysis , 2012, Journal of applied crystallography.

[19]  Masataka Oda,et al.  Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex , 2012, Proceedings of the National Academy of Sciences.

[20]  D. Staiger,et al.  Structure Function Analysis of an ADP-ribosyltransferase Type III Effector and Its RNA-binding Target in Plant Immunity* , 2011, The Journal of Biological Chemistry.

[21]  Zhao-Qing Luo,et al.  Comprehensive Identification of Protein Substrates of the Dot/Icm Type IV Transporter of Legionella pneumophila , 2011, PloS one.

[22]  H. Tsuge,et al.  Clostridium perfringens Iota-Toxin: Structure and Function , 2009, Toxins.

[23]  Charles D Schwieters,et al.  A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements. , 2009, Journal of molecular biology.

[24]  Soichi Wakatsuki,et al.  Ubiquitin-binding domains — from structures to functions , 2009, Nature Reviews Molecular Cell Biology.

[25]  Jan H. Jensen,et al.  Very fast prediction and rationalization of pKa values for protein–ligand complexes , 2008, Proteins.

[26]  H. Tsuge,et al.  Structural basis of actin recognition and arginine ADP-ribosylation by Clostridium perfringens ι-toxin , 2008, Proceedings of the National Academy of Sciences.

[27]  E. D. Cambronne,et al.  The Legionella pneumophila IcmSW Complex Interacts with Multiple Dot/Icm Effectors to Facilitate Type IV Translocation , 2007, PLoS pathogens.

[28]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[29]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[30]  Peter V. Konarev,et al.  ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis , 2007 .

[31]  Federico D. Sacerdoti,et al.  Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters , 2006, ACM/IEEE SC 2006 Conference (SC'06).

[32]  Richard A. Friesner,et al.  Integrated Modeling Program, Applied Chemical Theory (IMPACT) , 2005, J. Comput. Chem..

[33]  Julian Tirado-Rives,et al.  Molecular modeling of organic and biomolecular systems using BOSS and MCPRO , 2005, J. Comput. Chem..

[34]  Jan H. Jensen,et al.  Very fast empirical prediction and rationalization of protein pKa values , 2005, Proteins.

[35]  J Patrick Bardill,et al.  IcmS‐dependent translocation of SdeA into macrophages by the Legionella pneumophila type IV secretion system , 2005, Molecular microbiology.

[36]  E. D. Cambronne,et al.  The Legionella IcmS–IcmW protein complex is important for Dot/Icm‐mediated protein translocation , 2004, Molecular microbiology.

[37]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[38]  William L. Jorgensen,et al.  Accuracy of free energies of hydration using CM1 and CM3 atomic charges , 2004, J. Comput. Chem..

[39]  Zhao-Qing Luo,et al.  Multiple substrates of the Legionella pneumophila Dot/Icm system identified by interbacterial protein transfer. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Dmitri I. Svergun,et al.  PRIMUS: a Windows PC-based system for small-angle scattering data analysis , 2003 .

[41]  Dmitri I. Svergun,et al.  Uniqueness of ab initio shape determination in small-angle scattering , 2003 .

[42]  C. Roy,et al.  Legionella phagosomes intercept vesicular traffic from endoplasmic reticulum exit sites , 2002, Nature Cell Biology.

[43]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[44]  George M Sheldrick,et al.  Substructure solution with SHELXD. , 2002, Acta crystallographica. Section D, Biological crystallography.

[45]  P. Hünenberger,et al.  A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations , 2001, J. Comput. Chem..

[46]  Dmitri I. Svergun,et al.  Automated matching of high- and low-resolution structural models , 2001 .

[47]  J. Tainer,et al.  Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis. , 2001, Journal of molecular biology.

[48]  Alexander Varshavsky,et al.  The ubiquitin system. , 1998, Annual review of biochemistry.

[49]  K D Cowtan,et al.  Density modification for macromolecular phase improvement. , 1999, Progress in biophysics and molecular biology.

[50]  D I Svergun,et al.  Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. , 1999, Biophysical journal.

[51]  D. Svergun,et al.  CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates , 1995 .

[52]  M. Swanson,et al.  Association of Legionella pneumophila with the macrophage endoplasmic reticulum , 1995, Infection and immunity.

[53]  David J. Giesen,et al.  Class IV charge models: A new semiempirical approach in quantum chemistry , 1995, J. Comput. Aided Mol. Des..

[54]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[55]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[56]  Dmitri I. Svergun,et al.  Determination of the regularization parameter in indirect-transform methods using perceptual criteria , 1992 .

[57]  M. Horwitz Formation of a novel phagosome by the Legionnaires' disease bacterium (Legionella pneumophila) in human monocytes , 1983, The Journal of experimental medicine.

[58]  M G Rossmann,et al.  Comparison of super-secondary structures in proteins. , 1973, Journal of molecular biology.

[59]  H. Nagai,et al.  Modulation of the ubiquitination machinery by Legionella. , 2013, Current topics in microbiology and immunology.

[60]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.