2vii › Citations

Trapping of a transcription complex using a new nucleotide analogue: AMP aluminium fluoride.

Joly N, Rappas M, Buck M, Zhang X
J Mol Biol 375 1206-11 (2008)
Cited: 15 times
EuropePMC logo PMID: 18082766

Abstract

Mechanochemical proteins rely on ATP hydrolysis to establish the different functional states required for their biological output. Studying the transient functional intermediate states these proteins adopt as they progress through the ATP hydrolysis cycle is key to understanding the molecular basis of their mechanism. Many of these intermediates have been successfully 'trapped' and functionally characterised using ATP analogues. Here, we present a new nucleotide analogue, AMP-AlF(x), which traps PspF, a bacterial enhancer binding protein, in a stable complex with the sigma(54)-RNA polymerase holoenzyme. The crystal structure of AMP-AlF(x)*PspF(1-275) provides new information on protein-nucleotide interactions and suggests that the beta and gamma phosphates are more important than the alpha phosphate in terms of sensing nucleotide bound states. In addition, functional data obtained with AMP-AlF(x) establish distinct roles for the conserved catalytic AAA(+) (ATPases associated with various cellular activities) residues, suggesting that AMP-AlF(x) is a powerful new tool to study AAA(+) protein family members and, more generally, Walker motif ATPases.

Articles - 2vii mentioned but not cited (3)

  1. Regulation of microglial development: a novel role for thyroid hormone. Lima FR, Gervais A, Colin C, Izembart M, Neto VM, Mallat M. J Neurosci 21 2028-2038 (2001)
  2. Receiver domains control the active-state stoichiometry of Aquifex aeolicus sigma54 activator NtrC4, as revealed by electrospray ionization mass spectrometry. Batchelor JD, Sterling HJ, Hong E, Williams ER, Wemmer DE. J Mol Biol 393 634-643 (2009)
  3. Visualizing Synaptic Multi-Protein Patterns of Neuronal Tissue With DNA-Assisted Single-Molecule Localization Microscopy. Narayanasamy KK, Stojic A, Li Y, Sass S, Hesse MR, Deussner-Helfmann NS, Dietz MS, Kuner T, Klevanski M, Heilemann M. Front Synaptic Neurosci 13 671288 (2021)


Reviews citing this publication (4)

  1. The role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription. Bush M, Dixon R. Microbiol Mol Biol Rev 76 497-529 (2012)
  2. Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology. Joly N, Engl C, Jovanovic G, Huvet M, Toni T, Sheng X, Stumpf MP, Buck M. FEMS Microbiol Rev 34 797-827 (2010)
  3. Mechanisms for activating bacterial RNA polymerase. Ghosh T, Bose D, Zhang X. FEMS Microbiol Rev 34 611-627 (2010)
  4. The bacterial enhancer-dependent RNA polymerase. Zhang N, Darbari VC, Glyde R, Zhang X, Buck M. Biochem J 473 3741-3753 (2016)

Articles citing this publication (8)

  1. Regulation of the co-evolved HrpR and HrpS AAA+ proteins required for Pseudomonas syringae pathogenicity. Jovanovic M, James EH, Burrows PC, Rego FG, Buck M, Schumacher J. Nat Commun 2 177 (2011)
  2. An intramolecular route for coupling ATPase activity in AAA+ proteins for transcription activation. Joly N, Burrows PC, Buck M. J Biol Chem 283 13725-13735 (2008)
  3. Coupling sigma factor conformation to RNA polymerase reorganisation for DNA melting. Burrows PC, Joly N, Cannon WV, Cámara BP, Rappas M, Zhang X, Dawes K, Nixon BT, Wigneshweraraj SR, Buck M. J Mol Biol 387 306-319 (2009)
  4. Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein. Burrows PC, Schumacher J, Amartey S, Ghosh T, Burgis TA, Zhang X, Nixon BT, Buck M. Mol Microbiol 73 519-533 (2009)
  5. A key hydrophobic patch identified in an AAA⁺ protein essential for its in trans inhibitory regulation. Zhang N, Simpson T, Lawton E, Uzdavinys P, Joly N, Burrows P, Buck M. J Mol Biol 425 2656-2669 (2013)
  6. Subunit dynamics and nucleotide-dependent asymmetry of an AAA(+) transcription complex. Zhang N, Gordiyenko Y, Joly N, Lawton E, Robinson CV, Buck M. J Mol Biol 426 71-83 (2014)
  7. Comparative analysis of activator-Esigma54 complexes formed with nucleotide-metal fluoride analogues. Burrows PC, Joly N, Nixon BT, Buck M. Nucleic Acids Res 37 5138-5150 (2009)
  8. Mutations in RNA Polymerase Bridge Helix and Switch Regions Affect Active-Site Networks and Transcript-Assisted Hydrolysis. Zhang N, Schäfer J, Sharma A, Rayner L, Zhang X, Tuma R, Stockley P, Buck M. J Mol Biol 427 3516-3526 (2015)


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