SBRU

The Structural Biology Research Unit co-ordinates and promotes the experimental determination of biological structure at the University of Cape Town. The Unit is a grant funded entity, operationally located in the Integrative Biomedical Sciences Department in the Health Sciences Faculty. It employs staff, provides a home for post-graduate students and post-doctoral fellows and conducts research. It has members who are UCT academics who wish to conduct structural research and who are prepared to apply for grants to fund research in the Unit. The Unit also has affiliates, either from South Africa or abroad, who participate in the activities of the Unit in a variety of ways – including but not limited to: providing advice and expertise, exchanging materials, providing resources and using the resources of the Unit.

The visualization of the structure of biological objects ranging from cells to macromolecules with microscopic or atomic detail is essential for understanding how living systems work. The knowledge of the structures can be exploited to produce medicines and vaccines, ecologically friendly industrial processes and agricultural products. The unit specializes in determining structures experimentally by electron microscopy and X-ray crystallography and makes extensive use of computer based modelling to extend the results. The unit has access to unique resources for the purification and preliminary characterization of proteins, cryo-electron microscopy and X-ray diffraction at a synchrotron beamline. It plays a pivotal role in South Africa’s BioEconomy strategy by providing the core expertise for establishment of the discipline of Structural Biology in the whole country and applying the technology to a wide range of problems of scientific, medical and industrial interest.

Our structures:

Mycobacterium tuberculosis MshB
Cover of the FEBS Journal, 2007, Vol 274(8)
Cover of Acta Crystallographica Section D, 2007, Vol 63(10)
Cover of the Journal of Molecular Biology, 2006, Vol 361(4)
G. pallidus RAPc8 amidase homohexameric structure
G. sorghi nitrilase helical symmetries
G. pallidus RAPc8 amidase homohexameric structure
G. pallidus RAPc8 amidase homohexameric structure
The catalytic triad
The catalytic triad
G. sorghi nitrilase helical symmetries
G. sorghi nitrilase helical symmetries. The IHRSR algorithm was initiated at the three helical symmetries, predicted by indexing and converged on three stable reconstructions. All the reconstructions are plausible in the sense that the dimeric structure of the repeating unit can be visualised and the interactions appear reasonable based on our limited biochemical knowledge. — See Woodward et al., 2008
Details of the interactions at the interfaces. A stereo diagram of the "A surface" interactions viewed perpendicular to the twofold axis
Details of the interactions at the interfaces. A stereo diagram of the “A surface” interactions viewed perpendicular to the twofold axis. Helices from monomer 1 are coloured green, while those from monomer 2 are coloured blue. The figure shows the methionine packing in α6 and the connection between the interface and the active site through the hydrogen bond between Trp209 and Asn170, which stabilizes the 310-helix on which Cys166 is located. — See Kimani et al., 2007
Details of the interactions at the interfaces
Details of the interactions at the interfaces. The details of the “A surface” interaction between helices α5 viewed parallel to the twofold axis. Arg176 and Glu173 form salt bridges linking the subunits. Trp209 and Asn170 contribute a hydrogen bond to the interface. — See Kimani et al., 2007
Details of the interactions at the interfaces. Interactions of helices α7 and the N-terminal loops in monomers 2 (blue) and 3 (cyan) on the second twofold-related interface.
Details of the interactions at the interfaces. Interactions of helices α7 and the N-terminal loops in monomers 2 (blue) and 3 (cyan) on the second twofold-related interface. This interface is stabilized mainly by electrostatic interactions, with two salt bridges between Asp265 and Arg2 of both subunits. — See Kimani et al., 2007
Electron-density maps around the active-site. A stereo surface rendering of the active-site pocket lying behind Trp138.
Electron-density maps around the active-site. A stereo surface rendering of the active-site pocket lying behind Trp138. The surface is coloured in CPK colours corresponding to the exposed surface atoms. The two magenta patches directly behind the wire rendition of Trp138r epresent the carboxyl O atoms of Glu142. The acyl intermediate formed after reaction with D-lactamide has been modelled and is also illustrated as a wire rendition. The location of the sp2 acyl carbon is indicated by the black arrow. The yellow surface behind the acyl carbon represents the sulfur of Cys166. The acyl oxygen is located in a pocket near Lys134. Glu59 is located directly behind the acyl oxygen and is inaccessible to solvent. It can be seen clearly that the L-actamide enantiomer would produce a clash between the hydroxyl and the carboxyl of Glu142. The image was drawn with UCSF Chimera (Pettersen et al., 2004). — See Kimani et al., 2007
Electron-density maps around the active-site
Electron-density maps around the active-site. A stereoview of the electron-density maps around the active-site residues Glu59, Lys134 and Cys166. The 2Fobs – Fcalc map contoured at 1.3 is shown in blue, while the positive Fobs – Fcalc difference map contoured at 3.0σ is shown in red. The positive difference electron density around the Sγ atom of Cys166 suggests oxidative modification, probably to a mixture of species including sulfinic acid. — See Kimani et al., 2007
The fold of G. pallidus RAPc8 amidase: alpha-Helix and beta-sheet topology of G. pallidus RAPc8 amidase
The fold of G. pallidus RAPc8 amidase: alpha-Helix and beta-sheet topology of G. pallidus RAPc8 amidase. beta-Sheets (labelled 1–14) are shown as purple arrows, while alpha-helices are shown as blue cylinders. The cyan cylinder in the topology diagram is the 3(10)-helix on which the active-site Cys166 resides. The secondary-structure elements are numbered in sequence from the N-terminus. The topology diagram was generated using the program TOPS (Westhead et al., 1999) and manually redrawn in TOPDRAW (Bond, 2003) for simplification. — Kimani et al., 2007
The fold of G. pallidus RAPc8 amidase
The fold of G. pallidus RAPc8 amidase: Stereoview of a cartoon representation of a G. pallidus RAPc8 amidase monomer. The bars indicate the locations of the interacting surfaces seen in the spiral-forming homologues. The green bar indicates the “A surface”, the red bar the “C surface” and the grey bar the “D surface”, following the nomenclature of Sewell et al. (2005). — See Kimani et al., 2007
G. pallidus RAPc8 amidase homohexameric structure. A cylindrical projection of the density of the hexamer, with the cylinder axis and the threefold axis aligned
G.pallidus RAPc8 amidase homohexameric structure: A cylindrical projection of the density of the hexamer, with the cylinder axis and the threefold axis aligned. The density of each monomer was projected separately, coloured and then combined to form the composite image. The monomers are labelled and coloured in a manner consistent with the previous image. The value of the projected density is higher in lighter areas. The conserved “A surfaces” link 1–2, 3–4 and 5–6. A second twofold interacting surface links 1–6, 2–3 and 4–5. — See Kimani et al., 2007