Xiaodong Zhang

Summary

Affiliation: Imperial College
Country: UK

Publications

  1. pmc Crystal structures of multidrug binding protein TtgR in complex with antibiotics and plant antimicrobials
    Yilmaz Alguel
    Centre for Structural Biology and Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, UK
    J Mol Biol 369:829-40. 2007
  2. pmc Organization of an activator-bound RNA polymerase holoenzyme
    Daniel Bose
    Division of Molecular Biosciences, Centre for Structural Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
    Mol Cell 32:337-46. 2008
  3. pmc Essential roles of three enhancer sites in sigma54-dependent transcription by the nitric oxide sensing regulatory protein NorR
    Nicholas P Tucker
    Department of Molecular Microbiology, John Innes Center, Colney, Norwich, NR4 7UH, UK
    Nucleic Acids Res 38:1182-94. 2010
  4. pmc Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy
    Heidi O Yeung
    Centre for Structural Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
    Open Biol 4:130142. 2014
  5. pmc The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins
    Xiaodong Zhang
    Division of Molecular Biosciences, Centre for Structural Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW72AZ, UK
    Nat Struct Mol Biol 15:1223-7. 2008
  6. pmc Structural insights into the activity of enhancer-binding proteins
    Mathieu Rappas
    Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK
    Science 307:1972-5. 2005
  7. pmc Coupling sigma factor conformation to RNA polymerase reorganisation for DNA melting
    Patricia C Burrows
    Division of Biology, Department of Life Sciences, Faculty of Natural Sciences, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
    J Mol Biol 387:306-19. 2009
  8. pmc Sigma54-dependent transcription activator phage shock protein F of Escherichia coli: a fragmentation approach to identify sequences that contribute to self-association
    Patricia Bordes
    Department of Biological Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
    Biochem J 378:735-44. 2004
  9. ncbi request reprint Mechanisms of ATPases--a multi-disciplinary approach
    Mathieu Rappas
    Centre for Structural Biology, Department of Biological Sciences, Imperial College London, Flowers Building, South Kensington London SW7 2AZ, UK
    Curr Protein Pept Sci 5:89-105. 2004
  10. ncbi request reprint Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF
    Mathieu Rappas
    Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
    J Mol Biol 357:481-92. 2006

Collaborators

Detail Information

Publications50

  1. pmc Crystal structures of multidrug binding protein TtgR in complex with antibiotics and plant antimicrobials
    Yilmaz Alguel
    Centre for Structural Biology and Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, UK
    J Mol Biol 369:829-40. 2007
    ..The results presented here highlight the importance and versatility of regulatory systems in bacterial antibiotic resistance and open up new avenues for novel antimicrobial development...
  2. pmc Organization of an activator-bound RNA polymerase holoenzyme
    Daniel Bose
    Division of Molecular Biosciences, Centre for Structural Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
    Mol Cell 32:337-46. 2008
    ....
  3. pmc Essential roles of three enhancer sites in sigma54-dependent transcription by the nitric oxide sensing regulatory protein NorR
    Nicholas P Tucker
    Department of Molecular Microbiology, John Innes Center, Colney, Norwich, NR4 7UH, UK
    Nucleic Acids Res 38:1182-94. 2010
    ..We also find that site-specific DNA binding per se promotes oligomerisation but the DNA flanking the three sites is needed to further stabilise the functional higher order oligomer of NorR at the enhancers...
  4. pmc Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy
    Heidi O Yeung
    Centre for Structural Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
    Open Biol 4:130142. 2014
    ..A comparison of conformations reveals inter-ring rotations upon nucleotide binding and hydrolysis that may be linked to the remodelling of target protein complexes. ..
  5. pmc The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins
    Xiaodong Zhang
    Division of Molecular Biosciences, Centre for Structural Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW72AZ, UK
    Nat Struct Mol Biol 15:1223-7. 2008
    ..The reasons for this level of control of the ATPase activity are discussed in the context of the biological processes catalyzed by AAA+ proteins...
  6. pmc Structural insights into the activity of enhancer-binding proteins
    Mathieu Rappas
    Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK
    Science 307:1972-5. 2005
    ..Comparing enhancer-binding structures in different nucleotide states and mutational analysis led us to propose nucleotide-dependent conformational changes that free the loops for association with sigma54...
  7. pmc Coupling sigma factor conformation to RNA polymerase reorganisation for DNA melting
    Patricia C Burrows
    Division of Biology, Department of Life Sciences, Faculty of Natural Sciences, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
    J Mol Biol 387:306-19. 2009
    ....
  8. pmc Sigma54-dependent transcription activator phage shock protein F of Escherichia coli: a fragmentation approach to identify sequences that contribute to self-association
    Patricia Bordes
    Department of Biological Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
    Biochem J 378:735-44. 2004
    ....
  9. ncbi request reprint Mechanisms of ATPases--a multi-disciplinary approach
    Mathieu Rappas
    Centre for Structural Biology, Department of Biological Sciences, Imperial College London, Flowers Building, South Kensington London SW7 2AZ, UK
    Curr Protein Pept Sci 5:89-105. 2004
    ..We will therefore discuss them in greater details in order to describe the wide range techniques being utilised...
  10. ncbi request reprint Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF
    Mathieu Rappas
    Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
    J Mol Biol 357:481-92. 2006
    ..Striking similarities in nucleotide-specific conformational changes and atomic switch exist between PspF and the large T antigen helicase, suggesting conservation in the origin of those events amongst AAA(+) proteins...
  11. pmc Distinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy
    Cecilia Bebeacua
    Centre for Structural Biology and Centre for Biomolecular Electron Microscopy, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
    Proc Natl Acad Sci U S A 109:1098-103. 2012
    ..Our results suggest a model for substrate remodeling by p97 and also explains how p97-Ufd1-Npl4 could form other complexes in a hierarchical model of p97-cofactor assembly...
  12. ncbi request reprint Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation
    Jorg Schumacher
    Division of Biology, Imperial College London, London, SW7 2AZ, UK
    J Struct Biol 156:190-9. 2006
    ..Parallels with the substrate binding elements near the central pore of other AAA+ members are drawn. We propose a structural model of EBPs in complex with a sigma(54)-RNAP-promoter complex...
  13. doi request reprint Mechanism of homotropic control to coordinate hydrolysis in a hexameric AAA+ ring ATPase
    Jorg Schumacher
    Division of Biology, Imperial College London, London SW7 2AZ, UK
    J Mol Biol 381:1-12. 2008
    ..Homotropic coordination is functionally important to remodel the sigma(54) promoter. We propose a structural symmetry-based model for homotropic control in the AAA(+) characteristic ring architecture...
  14. doi request reprint Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins
    Daniel Bose
    Division of Molecular Bioscience, Faculty of Natural Sciences, Imperial College London, South Kensington, London, SW7 2AZ, U K
    Biochem Soc Trans 36:83-8. 2008
    ..In the present article, we review some of the key nucleotides, mutations and techniques used and how they have contributed towards our understanding of the function of bEBPs...
  15. ncbi request reprint Coupling nucleotide hydrolysis to transcription activation performance in a bacterial enhancer binding protein
    Nicolas Joly
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
    Mol Microbiol 66:583-95. 2007
    ..In addition, we show the importance of this glutamate residue in sigma(54).DNA conformation sensing, permitting the identification of new intermediate stages within the transcription activation pathway...
  16. pmc Analysis of nucleotide binding to P97 reveals the properties of a tandem AAA hexameric ATPase
    Louise C Briggs
    Division of Molecular Biosciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
    J Biol Chem 283:13745-52. 2008
    ..ATPgammaS binding triggers a downstream cooperative conformational change of at least three monomers, which involves conserved arginine fingers and is necessary for ATP hydrolysis...
  17. ncbi request reprint Detailed structural insights into the p97-Npl4-Ufd1 interface
    Rivka L Isaacson
    Division of Molecular Biosciences, Imperial College London, Biochemistry Building, South Kensington, London SW7 2AZ, United Kingdom
    J Biol Chem 282:21361-9. 2007
    ..We calculated a structural model for the p97 N-Npl4 UBD complex, and a comparison with the p97-p47 adaptor complex reveals subtle differences in p97 adaptor recognition and specificity...
  18. pmc Structural insights into the p97-Ufd1-Npl4 complex
    Valerie E Pye
    Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
    Proc Natl Acad Sci U S A 104:467-72. 2007
    ....
  19. ncbi request reprint Sensor I threonine of the AAA+ ATPase transcriptional activator PspF is involved in coupling nucleotide triphosphate hydrolysis to the restructuring of sigma 54-RNA polymerase
    Jorg Schumacher
    Division of Biology, Imperial College London, London SW7 2AZ, UK
    J Biol Chem 282:9825-33. 2007
    ..We propose that hydrolysis is relayed via Thr(148) to loop 2 creating motions that provide mechanical force to the GAFTGA loop 1 that contacts sigma(54)...
  20. pmc The ATP hydrolyzing transcription activator phage shock protein F of Escherichia coli: identifying a surface that binds sigma 54
    Patricia Bordes
    Department of Biological Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
    Proc Natl Acad Sci U S A 100:2278-83. 2003
    ....
  21. ncbi request reprint ATP-dependent transcriptional activation by bacterial PspF AAA+protein
    Jorg Schumacher
    Department of Biological Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
    J Mol Biol 338:863-75. 2004
    ..Substitution of this arginine residue results in nucleotide-independent formation of hexameric rings, structurally linking the putative R-finger and, by inference, a specific nucleotide interaction to the control of PspF oligomerisation...
  22. ncbi request reprint Going through the motions: the ATPase cycle of p97
    Valerie E Pye
    Division of Molecular Biosciences, Centre for Structural Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
    J Struct Biol 156:12-28. 2006
    ....
  23. ncbi request reprint The crystal structure of murine p97/VCP at 3.6A
    Trevor Huyton
    Department of Biological Sciences, Imperial College London, South Kensington SW7 2AZ, UK
    J Struct Biol 144:337-48. 2003
    ..The linker between the D1 and D2 domains is partially disordered, suggesting a flexible nature. Normal mode analysis of the crystal structure suggests anti-correlated motions and distinct conformational states of the two AAA domains...
  24. pmc Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein
    Patricia C Burrows
    Department of Life Sciences, Division of Biology, Imperial College London, London, UK
    Mol Microbiol 73:519-33. 2009
    ....
  25. doi request reprint Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor
    Sivaramesh Wigneshweraraj
    Department of Microbiology, Division of Investigative Sciences, Faculty of Medicine and Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK
    Mol Microbiol 68:538-46. 2008
    ..Here, we summarize our current understanding of the interactions the sigma(54) factor makes with the bacterial transcription machinery...
  26. doi request reprint Structural and functional implications of phosphorylation and acetylation in the regulation of the AAA+ protein p97
    Caroline A Ewens
    Division of Molecular Biosciences, Centre for Structural Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
    Biochem Cell Biol 88:41-8. 2010
    ..This review describes the known phosphorylation and acetylation sites on p97 and discusses their possible structural and functional implications...
  27. pmc Conformational changes in the AAA ATPase p97-p47 adaptor complex
    Fabienne Beuron
    Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, South Kensington, UK
    EMBO J 25:1967-76. 2006
    ....
  28. pmc Trapping of a transcription complex using a new nucleotide analogue: AMP aluminium fluoride
    Nicolas Joly
    Division of Biology, Sir Alexander Fleming Building, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
    J Mol Biol 375:1206-11. 2008
    ....
  29. pmc Foot-and-mouth disease virus 2C is a hexameric AAA+ protein with a coordinated ATP hydrolysis mechanism
    Trevor R Sweeney
    Biophysics Section, Blackett Laboratory, Division of Cell and Molecular Biology, Imperial College London, London SW7 2AZ, United Kingdom
    J Biol Chem 285:24347-59. 2010
    ..Our results provide new insights into the structure and mechanism of picornavirus 2C proteins that will facilitate new investigations of their roles in infection...
  30. pmc Crystal structure of TtgV in complex with its DNA operator reveals a general model for cooperative DNA binding of tetrameric gene regulators
    Duo Lu
    Division of Molecular Biosciences, Centre for Structural Biology, Imperial College, London, United Kingdom
    Genes Dev 24:2556-65. 2010
    ....
  31. doi request reprint Visualizing the organization and reorganization of transcription complexes for gene expression
    Patricia C Burrows
    Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, London, UK
    Biochem Soc Trans 36:776-9. 2008
    ....
  32. pmc Activity map of the Escherichia coli RNA polymerase bridge helix
    Milija Jovanovic
    Division of Biology, Faculty of Medicine and Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, United Kindgom
    J Biol Chem 286:14469-79. 2011
    ..coli alanine substitution variants, which we infer results in conformational changes in RNAP that modify RNAP functionality...
  33. pmc The p97-FAF1 protein complex reveals a common mode of p97 adaptor binding
    Caroline A Ewens
    From the Centre for Structural Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom and
    J Biol Chem 289:12077-84. 2014
    ..Characteristics of p97-FAF1 uncovered in this study reveal common features in the interactions of p97, providing mechanistic insight into how p97 mediates diverse functionalities. ..
  34. pmc Nitric oxide-responsive interdomain regulation targets the σ54-interaction surface in the enhancer binding protein NorR
    Matthew Bush
    Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney NR4 7UH, UK
    Mol Microbiol 77:1278-88. 2010
    ..These observations suggest a novel mechanism for negative regulation in bEBPs in which the GAF domain targets the σ(54)-interaction surface to prevent access of the AAA+ domain to the sigma factor...
  35. ncbi request reprint Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription
    Mathieu Rappas
    Centre for Structural Biology, Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
    Curr Opin Struct Biol 17:110-6. 2007
    ....
  36. pmc Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97
    Xuemei Yuan
    Department of Biological Sciences, Wolfson Laboratories, Imperial College London, South Kensington, London, UK
    EMBO J 23:1463-73. 2004
    ..Furthermore, p97 N binding abolishes p47 self-association, revealing the potential interaction surfaces for recognition of other domains within p97 or the substrate...
  37. doi request reprint Insights into adaptor binding to the AAA protein p97
    Heidi O Yeung
    Division of Molecular Biosciences, Centre for Structural Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U K
    Biochem Soc Trans 36:62-7. 2008
    ..In this review, we aim to summarize our current knowledge on adaptor binding to p97...
  38. pmc Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47
    Ingrid Dreveny
    Centre for Structural Biology, Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK
    EMBO J 23:1030-9. 2004
    ..We also propose a classification for ubiquitin-like domains containing or lacking a longer S3/S4 loop...
  39. pmc The role of the N-domain in the ATPase activity of the mammalian AAA ATPase p97/VCP
    Hajime Niwa
    Centre for Structural Biology, Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
    J Biol Chem 287:8561-70. 2012
    ..This leads us to propose a model where the N-domain adopts either of two conformations: a flexible conformation compatible with ATP hydrolysis or a coplanar conformation that is inactive...
  40. doi request reprint Coupling AAA protein function to regulated gene expression
    Nicolas Joly
    Division of Biology, Imperial College London, London, SW7 2AZ, UK
    Biochim Biophys Acta 1823:108-16. 2012
    ..These specialised macromolecular machines remodel their substrates through ATP hydrolysis that ultimately leads to transcriptional activation. We will discuss how AAA proteins are specialised for this specific task...
  41. pmc Automated assignment in selectively methyl-labeled proteins
    Yingqi Xu
    Division of Molecular Biosciences, Cross Faculty NMR Centre, Imperial College London, South Kensington, London, SW7 2AZ, UK
    J Am Chem Soc 131:9480-1. 2009
    ..Of the observed methyl groups, 99% can be correctly assigned in a matter of minutes without manual intervention...
  42. doi request reprint Mechanisms for activating bacterial RNA polymerase
    Tamaswati Ghosh
    Department of Life Sciences, Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, London, UK
    FEMS Microbiol Rev 34:611-27. 2010
    ..In this review, we present recent structural studies of the two major bacterial RNAP holoenzymes and focus on mechanistic advances in the transcription initiation process via enhancer-binding proteins...
  43. ncbi request reprint Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantised elastic deformational model
    Fabienne Beuron
    Department of Biological Sciences, Imperial College London, South Kensington Campus, The Flowers Building, Armstrong Road, SW7 2AZ, London, UK
    J Mol Biol 327:619-29. 2003
    ..Together these results allow the identification of functionally important features that offer molecular insights into the dynamics of the proposed p97 chaperone function...
  44. doi request reprint Transcriptional regulation by the dedicated nitric oxide sensor, NorR: a route towards NO detoxification
    Matthew Bush
    Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney NR4 7UH, UK
    Biochem Soc Trans 39:289-93. 2011
    ....
  45. doi request reprint Regulation of p97 in the ubiquitin-proteasome system by the UBX protein-family
    Patrik Kloppsteck
    Division of Molecular Biosciences, Centre for Structural Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
    Biochim Biophys Acta 1823:125-9. 2012
    ..These features allow the regulation, within the UPS, of the competitive interactions on p97, a regulation that is crucial to allow the diverse functionality of p97...
  46. doi request reprint Crystal structure of MexZ, a key repressor responsible for antibiotic resistance in Pseudomonas aeruginosa
    Yilmaz Alguel
    Division of Molecular Biosciences and Centre for Structural Biology, Imperial College London, London SW7 2AZ, United Kingdom
    J Struct Biol 172:305-10. 2010
    ..This work provides a framework for further characterisation of MexZ in order to fully understand its regulation and induction...
  47. pmc Structure-based mechanism of lipoteichoic acid synthesis by Staphylococcus aureus LtaS
    Duo Lu
    Division of Molecular Biosciences, Department of Microbiology, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
    Proc Natl Acad Sci U S A 106:1584-9. 2009
    ..These results will aid in the development of LtaS-specific inhibitors for S. aureus and many other Gram-positive pathogens...
  48. pmc Domain movements of the enhancer-dependent sigma factor drive DNA delivery into the RNA polymerase active site: insights from single molecule studies
    Amit Sharma
    Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
    Nucleic Acids Res 42:5177-90. 2014
    ..Although the coupled promoter recognition and melting steps may be conserved between σ(70) and σ(54), the domain movements of the latter have evolved to require an activator ATPase. ..
  49. pmc A new labeling method for methyl transverse relaxation-optimized spectroscopy NMR spectra of alanine residues
    Rivka L Isaacson
    Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, South Kensington, London, UK
    J Am Chem Soc 129:15428-9. 2007
  50. ncbi request reprint Machinery of protein folding and unfolding
    Xiaodong Zhang
    Centre for Structural Biology, Department of Biological Sciences, Imperial College of Science, Technology and Medicine, Flowers Building, South Kensington, SW7 2AZ, London, UK
    Curr Opin Struct Biol 12:231-8. 2002
    ..The majority of folding/unfolding machines adopt oligomeric ring structures in a cooperative fashion and utilise the conformational changes induced by ATP binding/hydrolysis for their specific functions...