Phillips Group

Simon Phillips

Structure and function of protein-nucleic acid complexes

Simon Phillips is Director of RCaH, Visiting Professor in Molecular Biophysics, University of Oxford and Visiting Professor of Biophysics, University of Leeds
Co-workers: Dr. Stephen Carr

We are working on structural and functional studies of biological macromolecules. We are particularly interested in the critical biological problem of how molecules recognize each other, especially in the case of proteins and nucleic acids. This highly specific molecular recognition underpins the function of all complex biological systems. For instance, some proteins recognize specific DNA sequences that stimulate them to carry out particular functions, such as repairing DNA damage, turning transcription of genes on and off, or transferring genes from one DNA molecule to another in recombination events. The approach is three-dimensional structure determination with X-ray crystallography as the main technique, although other structural techniques are employed, as well as routine protein chemistry and molecular biology.

The Holliday Junction: We are interested in the molecular structure of junctions formed by two DNA molecules as they come together in genetic recombination events. This "Holliday Junction" structure, and the way specific enzymes cleave (resolve) it to produce separate DNA duplexes, is poorly understood at the molecular level. It is a critical intermediate in many genetic processes, such as the transfer of genes between parental chromosomes and in the repair of damaged DNA. We have determined the structure of a simple resolving enzyme, bacteriophage T7 Endonuclease 1, in a complex with a synthetic DNA junction, and are working in understanding the details of its mechanism. We are extending this work to Holliday Junction processing enzymes in humans that are involved with DNA repair

Plasmid replication and antibiotic resistance: In collaboration with Dr. Chris Thomas" group in Leeds, we are studying proteins that control replication of plasmids, small circular DNA molecules that carry foreign genes into bacteria. Such plasmids can harbour genes for antibiotic resistance apart from a few other genes dedicated to their own replication. Antibiotic resistance is becoming a major public health problem. The Rep proteins, which govern replication by binding to the replication origin on a plasmid, are potential targets for new antibiotic compounds, but structural information on members of the Rep protein family is scarce. The long-term goals are to understand the replication-initiation process and provide structural targets for rational design of new generations of antibiotics.

Recent publications

Campeotto I., Carr, S.B., Trinh, C.H., Nelson, A.S., Berry, A., Phillips, S. E.V. and Pearson, A.R. (2009) “Structure of an E. coli N-acetyl-D-neuraminic acid lyase mutant, E192N, in complex with pyruvate at 1.45 Å” Acta Cryst F, 65, 1088-1090.

Sutay Kobacas,D, Pearson,A.R., Phillips,S.E.V., McPherson, M.J. and Trinh, C.H.(2009) “Crystallization and preliminary X-ray analysis of a bi-functional catalase-phenol oxidase from Scytalidium thermophilum" Acta Cryst F, 65, 486-488.

 

Fadouloglou V.E., Bastaki M.N., Ashcroft A.E., Phillips S.E.V., Panopoulos N. J., Glykos, N.M. & Kokkinidis M. (2009) “On the quaternary association of the type III secretion system HrcQB-C protein: Experimental evidence differentiates among the various oligomerization models”J. Struct. Biol. 166, 214-225.

 

Trinh, C., Asipu, A, Bonthron, D.T. and Phillips, S.E.V. (2009) "Crystal structures of alternatively-spliced isoforms of human ketohexokinase". Acta Cryst D, 65, 201-211.

Deacon, S.E., Roach, P.C.J., Postis,V.L.G., Wright, G.S.A., Xia, X., Phillips, S.E.V., Knox, J.P., Henderson, P.J.F., McPherson, M. J. and Baldwin, S.A. (2008) "Reliable scale-up of membrane protein over-expression by bacterial auto-induction: from microwell plates to pilot scale fermentations" Mol. Memb. Biol., 25, 588-598.

Postis,V.L.G., Deacon, S.E., Roach, P.C.J., Wright, G.S.A., Xia, X., Ingram, J.C., Hadden, J.M., Henderson, P.J.F., Findlay, J.B.C., Phillips, S.E.V., McPherson, M. J. and Baldwin, S.A. (2008) "A high-throughput assay of membrane protein stability" Mol. Memb. Biol., 25, 617-624.

Xia, X., Postis,V.L.G., Rahman, M., Wright, G.S.A., Roach, P.C.J., Deacon, S.E., Ingram, J.C., Henderson, P.J.F., Findlay, J.B.C., Phillips, S.E.V., McPherson, M. J. and Baldwin, S.A. (2008) "Investigation of the structure and function of a Shewanella oneidensis arsenical-resistance family transporter" Mol. Memb. Biol,. 25, 691-701.

Pirrat, P. , Smith, M.A. , Pearson, A.R., McPherson, M.J. and Phillips, S.E.V. (2008) "Structure of the xenon derivative of E. coli copper amine oxidase: confirmation of the proposed copper amine oxidase oxygen entry pathway" Acta Cryst F, 64, 1105-1109.

Trinh, C., Hunter, T, Stewart, E.E., Phillips, S.E.V., and Hunter, G.J. (2008) "Purification, crystallization and x-ray structures of the two manganese superoxide dismutases from Caenorhabditis elegans" Acta Cryst F, 64, 1110-1114.

Rogers, M.S., Ram'n Hurtado-Guerrero, R., Firbank, S.J., Halcrow, M.A., Dooley, D.M., Phillips, S.E.V., Knowles, P.F. and McPherson, M.J. (2008) "Crosslink formation of the Cysteine228-Tyrosine 272 catalytic cofactor of Galactose Oxidase does not require dioxygen" Biochemistry 47, 10428-10439.

Uppal, S., Diggle, C.P., Carr, I.M., Fishwick C.W.G., Ahmed, M., Ibrahim, G.H., Helliwell, P.S., Latos-Bielenska A., Phillips, S.E.V., Markham, A.F., Bennett C.P., Bonthron D.T. (2008) "The oldest clinical sign: Genetic insight into the cause of clubbing" Nature Genetics 40,789-793.

Garnett, J.A., Marincs, F., Baumberg, S., Stockley, P.G. and Phillips, S.E.V. (2008) "Structure and function of the arginine repressor-operator complex from Bacillus subtilis" JMB 379, 284-298.

Sutay, D., Bakir, U., Phillips S.E.V., McPherson M.J. and Ogel Z.B. (2008) "Purification, characterization and identification of a novel bifunctional catalase-phenol oxidase from Scytalidium thermophilum. Applied Microbiology and Biotechnology 79, 407-415.

Dunsmore, C.J., Miller, K., Blake, K.L., Patching, S.G., Henderson, P.J. F., Garnett, J.A., Stubbings, W. J., Phillips, S.E.V., Palestrant, D., De Los Angeles, J., Leeds, J.A., Chopra I., and Fishwick C.W.G. (2008) "2-Aminotetralones: Novel Irreversible Inhibitors of MurA and MurZ" Bioorganic and Medicinal Chemistry Letters 18, 1730-1734.

Knowles, P., Kurtis, C., Murray, J., Saysell, C., Tambyrajah, W., Wilmot, C.M., McPherson, M.J., Phillips, S.E.V., Dooley, D.M., Brown, D., Rogers, M. and Mure, M. (2007) "Hydrazine and amphetamine binding to amine oxidases: old drugs with new prospects". Journal of Neural Transmission (Budapest) 114, 743-746.

Syme, N.R., Dennis, C., Phillips, S.E.V. and Homans S.W. (2007) "Origin of heat capacity changes in a "nonclassical" hydrophobic interaction" ChemBiochem 8, 1509-1511.

Garnett, J.A., Baumberg, S., Stockley, P.G. and Phillips, S.E.V. (2007) "Crystal structure of the C-terminal effector-binding domain of AhrC, bound to its corepressor L-arginine" Acta Cryst F, 63, 918-921.

Garnett, J.A., Baumberg, S., Stockley, P.G. and Phillips, S.E.V. (2007) "A high resolution structure of the DNA-binding domain of AhrC, the arginine repressor/activator protein from B. subtilis" Acta Cryst F, 63, 914-917.

Hadden, J.M., D"clais, A-C., Carr, S.B., Lilley D.M.J. and Phillips, S.E.V. (2007) "The structural basis of Holliday junction resolution by T7 endonuclease 1" Nature, 449, 621-624.

Rogers, M.S., Tyler, E.M., Akumanyi, N., Kurtis, C.R., Spooner, R.K, Deacon, S.E., Tamber, S., Firbank, S.J., Mahmoud, K., Knowles, P.F., Phillips, S.E.V., McPherson, M.J. and Dooley, D.M. (2007) "The stacking tryptophan of galactose oxidase: a second coordination sphere residue that has profound effects on tyrosyl radical behavior and enzyme catalysis" Biochemistry, 46, 4606-4618.

Trinh, C.H., Liu, Y., Phillips S.E.V. and Phillips-Jones, M.K. (2007) "Crystal structure of the response regulator VicR DNA-binding domain" Acta Cryst. D, 63, 266-269.