Chemistry Reference
In-Depth Information
known position of anomalous scattering atoms to resolve the phase ambiguity. Most MAD phasing experiments
use proteins in which methionine residues have been replaced by selenomethionine. From a practical point of
view, such experiments can only be carried out at synchrotron beamlines, and since all of the data are collected on
the same sample, systematic sources of error are eliminated and resulting phase angles are more accurate.
The 12-subunit DNA-binding proteins from starved cells (Dps proteins) are yet another form of iron-storage
protein found in bacteria (see Chapter 8). Initial crystallographic studies on the Dps protein of E. coli ledtothe
claim that Dps proteins did not have a ferroxidase centre.
Figure 6.7
shows the structure of Bacillus brevis Dps,
which confirmed that a di-iron ferroxidase centre certainly does exist (
Ren, Tibbelin, Kajino, Asami, &
Ladenstein, 2003
). The ferroxidase centre possesses unique features among all the di-iron proteins identified so
far. Dps does not have a single di-iron site within the four-helix bundle of the subunit. Instead, two neighbouring
dinuclear iron-binding sites are present at the dimer interface inside the dodecamer (
Figure 6.7
c), related by the
local 2-fold axis. They are located in a shallow groove formed by helices
II from one subunit and their
symmetry-related counterparts from the other subunit. One might consider that these helices at the dimer
interface form a special four-helix bundle, which accommodates not one but two di-iron sites. The ligands to the
pentahedral Fe 1 (
Figure 6.8
) come from two subunits, while the more loosely coordinated Fe 2 has only one
direct protein ligand, the bridging carboxylate Glu 62 (B) with additional water-mediated contacts to Glu 47 (A)
and His 43 (A).
a
Iand
a
REFERENCES
Arnesano, F., Banci, L., & Piccioli, M. (2005). NMR structures of paramagnetic proteins. Quarterly Reviews of Biophysics, 38, 167
219.
Banci, L., Bertini, I., Cantini, F., Felli, I. C., Gonnelli, L., Hadjiliadis, N., et al. (2006). The Atx1-Ccc2 complex is a metal-mediated protein-
protein interaction. Nature Chemical Biology, 2, 367
e
368.
Bertini, I., Luchinat, C., Parigi, G., & Pierattelli, R. (2005). NMR spectroscopy of paramagnetic metalloproteins. Chembiochem, 6,
1536
e
1549.
Campbell, I. D., & Dwek, R. A. (1984). Biological spectroscopy. Menlo Park, Calif.: Benjamin/Cummings Publishing Co., Inc. pp. 404.
Carette, N., Hagen, W., Bertrand, L., de Val, N., Vertommen, D., Roland, F., et al. (2006). Optical and EPR spectroscopic studies of
demetallation of hemin by L-chain apoferritins. Journal of Inorganic Biochemistry, 100, 1426
e
1435.
Crichton, R. R. & Louro, R. O. (Eds.), (2012). Practical approaches to biological inorganic chemistry. Elsevier.
Ealick, S. E. (2000). Advances in multiple wavelength anomalous diffraction crystallography. Current Opinion in Chemical Biology, 4,
495
e
499.
Fragai, M., Luchinat, C., & Parigi, G. (2006). “Four-dimensional” protein structures: examples from metalloproteins. Accounts of Chemical
Research, 39, 909
e
917.
Hagen, W. R. (2006). EPR spectroscopy as a probe of metal centres in biological systems. Dalton Transactions, 37, 4415
e
4434.
Neese, F. (2003). Quantum chemical calculations of spectroscopic properties of metalloproteins and model compounds: EPR and M¨ssbauer
properties. Current Opinion in Chemical Biology, 7, 125
e
135.
Que, L., Jr. (2000). Physical methods in bioinorganic chemistry: Spectroscopy and magnetism. Sausalito, Ca: University Science Books.
pp. 59
e
120.
Ren, B., Tibbelin, G., Kajino, T., Asami, O., & Ladenstein, R. (2003). The multi-layered structure of Dps with a novel di-nuclear ferroxidase
center. Journal of Molecular Biology, 329, 467
e
477.
Strange, R. W., & Feiters, M. C. (2008). Biological X-ray absorption spectroscopy (BioXAS): a valuable tool for the study of trace elements
in the life sciences. Current Opinion in Structural Biology, 18, 609
e
616.
Toussaint, L., Cuypers, M. G., Bertrand, L., Hue, L., Rom˜o, C. V., Saraiva, L. M., et al. (2009). Comparative Fe and Zn K-edge X-ray
absorption spectroscopic study of the ferroxidase centres of human H-chain ferritin and bacterioferritin from desulfovibrio desulfuricans.
Journal of Biological Inorganic Chemistry, 14,35
e
49.
Ubbink, M., Worrall, J. A. R., Canters, G. W., Groenen, E. J. J., & Huber, R. (2002). Paramagnetic resonance of biological metal centers.
Annual Review of Biophysics and Biomolecular Structure, 31393
e
31422.
Ward, R. J., Ramsey, M., Dickson, D. P., Hunt, C., Douglas, T., Mann, S., et al. (1994). Further characterisation of forms of haemosiderin in
iron-overloaded tissues. European Journal of Biochemistry, 225, 187
e
194.
e
