ayout 1 - EMBL Grenoble

EMBL Research at a Glance 2009
Paul Tucker
PhD 1972, University of
Essex, Colchester.
Postdoctoral research at the
universities of Groningen,
Leicester, the Australian
National University in
Canberra, and Exeter.
Lecturer in Inorganic
Chemistry, University of the
West Indies.
At EMBL Heidelberg 1985-
1998; at EMBL Hamburg
since 1998.
Structural studies of proteins from pathogens
Previous and current research
A major focus has been trying to understand, at a structural level, the mechanisms by which bacteria
respond to external conditions. We are therefore interested in classical two-component systems
and the way they regulate gene expression by responding to the environment. Mycobacterium
tuberculosis (MtB) continues to pose a global health threat and is our organism of choice because
understanding the way in which the bacteria responds to externally generated stress is a possible
way to the discovery of novel antibiotics. In the last years we have extended our work to investigate
the structure of proteins involved
in regulating the production
of the stress response sigma factor,
σ F . The most interesting results
have been on a protein that contains
four regulatory domains, a
sensor PAS domain, a kinase domain
(the anti-sigma factor), a
phosphatase domain and an antisigma
factor antagonist domain. In
this system we are beginning to understand
the structural basis of the
regulation mechanism, and, from
the structural work, have some
idea as to what signal is used to switch on σ F dependent genes. Two structures
are shown in figure 1.
A second area of study has been on proteins that are involved in replication of the genome of
a variety of RNA viruses. Our goal is still to obtain structural information on the RNA dependent
RNA polymerase domains of the caliciviridae, the flaviviridae and, more importantly,
a vesiculovirus. We have also continued our work on the structural and functional aspects of
single-stranded DNA binding proteins found in the dsDNA viruses, and are interested in how
these proteins interact with other components of the replication machinery (figure 2).
A third focus, largely with Staff Scientist Santosh Panjikar and the Weiss team (opposite), remains
on improving the structure determination process by, for example, developing improved
phasing methods and automating structure determination. Santosh Panjikar is also
actively engaged in elucidated the enzymes of the biosynthetic pathway of various indole alkaloids
in Indian medicinal plants.
Future projects and goals
We will continue our work on the unusual actinobacterial two-component system
(PdtaR/PdtaS) we discovered a few years ago, by determining the structure of the sensor domain
of the (cytosolic) histidine kinase. We will continue our structural work on domains of
the coronavirus NSP3 protein, as part of a comparative analysis of these domains and their organisation
in the different classes of the coronaviridae.
Figure 1: The structures of the PAS (sensor) domain
(blue), the kinase (red) and phosphatase (green)
domains of the Mycobacterium tuberculosis
regulatory protein Rv1364c.
Figure 2: The solution structure
(represented by grey spheres) from
small-angle X-ray scattering of a dimer
of the Epstein-Barr virus single
stranded DNA binding protein BalF2.
Superimposed is a homology model
derived from the equivalent Herpes
Simplex Virus 1 protein, ICP8.
We are expecting to push forward our structural work on lipid binding proteins from nematodes. There is a complete lack of structural information
on this class of proteins and, for parasitic nematodes, they are essential for the viability of the organism in the host.
Selected references
King-Scott, J., Nowak, E., Mylonas, E., Panjikar, S., Roessle, M.,
Svergun, D.I. & Tucker, P.A. (2007). The structure of a full-length
response regulator from Mycobacterium tuberculosis in a stabilised
3D domain-swapped, activated state. J. Biol. Chem., 282, 37717-29
Stockigt, J. & Panjikar, S. (2007). Structural biology in plant natural
product biosynthesis – architecture of enzymes from monoterpenoid
indole and tropane alkaloid biosynthesis. Natural Product Reports,
2, 1382-100
Tucker, P.A., Jens, E.N. & Morth, P. (2007). Two-component systems
of M. tuberculosis: structure-based approaches. Methods Enzymol.,
23, 79-501
Tucker, P.A. & Sallai, L. (2007). The AAA+ superfamily-a myriad of
motions. Curr. Opin. Struct. Biol., 17, 61-652
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