Engagement of Arginine Finger to ATP Triggers Large Conformational Changes in NtrC1 AAA+ ATPase for Remodeling Bacterial RNA Polymerase

Structure - Tập 18 - Trang 1420-1430 - 2010
Baoyu Chen1, Tatyana A. Sysoeva1, Saikat Chowdhury1, Liang Guo2, Sacha De Carlo3, Jeffrey A. Hanson4,5, Haw Yang4,5, B. Tracy Nixon1
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
2BioCAT at APS/Argonne National Lab, Illinois Institute of Technology, 9700 South Cass Avenue, Argonne, IL 60439, USA
3Chemistry Department and Institute for MacroMolecular Assemblies, Marshak Science Building, City University of New York, NY 10031, USA
4Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA
5Department of Chemistry, Princeton University, Princeton, NJ 08544, USA

Tài liệu tham khảo

Adams, 2010, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol. Crystallogr., D66, 213, 10.1107/S0907444909052925 Batchelor, 2009, Receiver domains control the active-state stoichiometry of Aquifex aeolicus σ54 activator NtrC4, as revealed by electrospray ionization mass spectrometry, J. Mol. Biol., 393, 634, 10.1016/j.jmb.2009.08.033 Bose, 2008, Organization of an activator-bound RNA polymerase holoenzyme, Mol. Cell, 32, 337, 10.1016/j.molcel.2008.09.015 Brunger, 1998, Crystallography and NMR system (CNS): a new software system for macromolecular structure determination, Acta Crystallogr. D Biol. Crystallogr., D54, 905, 10.1107/S0907444998003254 Chen, 2009, KiNG (Kinmage, Next Generation): a versatile interactive molecular and scientific visualization program, Protein Sci., 18, 2403, 10.1002/pro.250 Chen, 2007, ATP ground- and transition states of bacterial enhancer binding AAA+ ATPases support complex formation with their target protein, σ54, Structure, 15, 429, 10.1016/j.str.2007.02.007 Chen, 2009, ADPase activity of recombinantly expressed thermotolerant ATPases may be caused by co-purification of adenylate kinase of Escherichia coli, FEBS J., 276, 807, 10.1111/j.1742-4658.2008.06825.x Davies, 2008, Improved structures of full-length p97, an AAA ATPase: Implications for mechanisms of nucleotide-dependent conformational change, Structure, 16, 715, 10.1016/j.str.2008.02.010 Davis, 2007, MolProbity: all-atom contacts and structure validation for proteins and nucleic acids, Nucleic Acids Res., 35, W375, 10.1093/nar/gkm216 De Carlo, 2006, The structural basis for regulated assembly and function of the transcriptional activator NtrC, Genes Dev., 20, 1485, 10.1101/gad.1418306 Dekker, 2004, A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments, Bioinformatics, 20, 1565, 10.1093/bioinformatics/bth128 Doucleff, 2005, Negative regulation of AAA+ ATPase assembly by two component receiver domains: a transcription activation mechanism that is conserved in mesophilic and extremely hyperthermophilic bacteria, J. Mol. Biol., 353, 242, 10.1016/j.jmb.2005.08.003 Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr., D60, 2126, 10.1107/S0907444904019158 Fischetti, 2004, The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source, J. Synchrotron Radiat., 11, 399, 10.1107/S0909049504016760 Hayward, 1998, Systemic analysis of domain motions in proteins from conformational change; new results on citrate synthase and T4 lysozyme, Proteins, 30, 144, 10.1002/(SICI)1097-0134(19980201)30:2<144::AID-PROT4>3.0.CO;2-N Joly, 2010, Engineered interfaces of an AAA+ ATPase reveal a new nucleotide-dependent coordination mechanism, J. Biol. Chem., 285, 15178, 10.1074/jbc.M110.103150 Joly, 2008, An intramolecular route for coupling ATPase activity in AAA+ proteins for transcription activation, J. Biol. Chem., 283, 13725, 10.1074/jbc.M800801200 Joly, 2006, Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator, J. Biol. Chem., 281, 34997, 10.1074/jbc.M606628200 Keegan, 2007, Automated search-model discovery and preparation for structure solution by molecular replacement, Acta Crystallogr. D Biol. Crystallogr., D63, 447, 10.1107/S0907444907002661 Kozin, 2001, Automated matching of high- and low-resolution structural models, J. Appl. Crystallogr., 34, 33, 10.1107/S0021889800014126 Lee, 2003, Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains, Genes Dev., 17, 2552, 10.1101/gad.1125603 Mosca, 2008, Alignment of protein structures in the presence of domain motions, BMC Bioinformatics, 9, 352, 10.1186/1471-2105-9-352 Mosca, 2008, RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes, Nucleic Acids Res., 36, W42, 10.1093/nar/gkn197 Neuwald, 1999, AAA+: A class of chaperonin-like ATPases associated with the assembly, operation, and disassembly of protein complexes, Genome Res., 9, 27, 10.1101/gr.9.1.27 Radermacher, 1987, Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli, J. Microsc., 146, 113, 10.1111/j.1365-2818.1987.tb01333.x Rappas, 2005, Structural insights into the activity of enhancer-binding proteins, Science, 307, 1972, 10.1126/science.1105932 Rappas, 2006, Structural basis of the nucleotide driven conformational changes in the AAA+ domain of the transcription factor PspF, J. Mol. Biol., 357, 481, 10.1016/j.jmb.2005.12.052 Rappas, 2007, Bacterial enhancer-binding proteins: unlocking σ54-dependent gene transcription, Curr. Opin. Struct. Biol., 17, 110, 10.1016/j.sbi.2006.11.002 Sallai, 2005, Crystal structure of the central and C-terminal domain of the sigma(54)-activator ZraR, J. Struct. Biol., 151, 160, 10.1016/j.jsb.2005.05.006 Schumacher, 2008, Mechanism of homotropic control to coordinate hydrolysis in a hexameric AAA+ ring ATPase, J. Mol. Biol., 381, 1, 10.1016/j.jmb.2008.05.075 Terwilliger, 2000, Maximum likelihood density modification, Acta Crystallogr. D Biol. Crystallogr., D56, 965, 10.1107/S0907444900005072 Theobald, 2008, Accurate structural correlations from maximum likelihood superpositions, PLoS Comput. Biol., 4, e43, 10.1371/journal.pcbi.0040043 Thomsen, 2008, Structural framework for considering microbial protein- and nucleic acid-dependent motor ATPases, Mol. Microbiol., 69, 1071, 10.1111/j.1365-2958.2008.06364.x Tucker, 2007, The AAA+ superfamily—a myriad of motions, Curr. Opin. Struct. Biol., 17, 641, 10.1016/j.sbi.2007.09.012 Xu, 2004, Purification and characterization of the AAA+ domain of Sinorhizobium meliloti DctD, a σ54-dependent transcriptional activator, J. Bacteriol., 186, 3499, 10.1128/JB.186.11.3499-3507.2004 Zhang, 2008, The ‘glutamate switch’ provides a link between ATPase activity and ligand binding in AAA+ proteins, Nat. Struct. Mol. Biol., 15, 1223, 10.1038/nsmb.1501