Download Symmetry

Symmetry is the concept of repetitive arrangements of similar objects in
space. In three dimensions, objects may be arranged in a large number of
ways - many of these are exhibited in crystal forms. Each possible
arrangement is achieved by a combination of simple, basic operations.
These include translation, rotation, screw-rotation, mirror, inversion,
inversion-rotation, and glide-reflection. The total number of possible
ways of arranging copies of the same object to form a repeating lattice in
3D-space is 230. These are the `Space Groups' familiar to
crystallographers.
Proteins are chiral objects, and cannot be mirror-inverted while
remaining the same. Their mirror reflection is different. Thus, many of
these arrangements are actually precluded. In fact, proteins may only
adopt 65 of the 230 possible 3D space groups. Many of these are
observed when we crystallize proteins.
In the case of naturally occurring multimers of proteins, other
constraints occur which limit the possible arrangements. We are
speaking here of individual assemblies of monomer units, creating
(usually soluble) complexes which exhibit internal symmetry.
Thus, the monomers must associate with van der Waals contact
interfaces between the sub-units of the assembly. That is, the sub-units
can touch but not intersect. They may interpenetrate only in so far as
there exist corresponding `holes' into which `knobs' can be fit.
Furthermore, axes of rotational symmetry may not actually pass
`through' a protein monomer
An icosahedral symmetry, designated
I/532 has 60 identical units related by six 5-,
ten 3- and fifteen 2-fold rotational axes.
Horse liver alcohol dehydrogenase exists as a homodimer or heterodimerthere are two different types of monomer, denoted E and S. However these
two forms are near-identical (both consisting of 374 amino acids), as there
are only six residues which are different. None of these six occur in the
interface region between the two. There are three possible combinations of
the subunits: EE, SS and ES; these are therefore isozymes (or
isoenzymes). When isolated from liver, 40-60% of the enzyme is of the EE
form.
Each of the two subunits of the horse enzyme has one binding site for
NAD+ and two binding sites for Zn2+. Only one of the zinc ions is involved
directly in catalysis. It is ligated by the side chains of Cys 46, His 67, Cys
174 and a water molecule which hydrogen bonds to Ser 48. (If you wish to
view this water molecule, download the 8adh PDB structure, which is a
monomer without NAD+, as the 6adh dimer includes no water molecules.)
The zinc ion is situated at the junction of two binding sites: one of these is
a pocket which binds NAD+, while the other is a cleft which binds the
substrate (which is one of a variety of aromatic and aliphatic alcohols).
Horse liver alcohol dehydrogenase
TRAP Trp attenuation protein of Bacillus subtilis
The biological unit of this
protein is an undecamer (11mer), exhibiting C11 symmetry;
however in this particular crystal
(1wap) the rings pack back-toback, and there are two rings in
the asymmetric unit. Therefore
the appearance is of D11
symmetry.. Diagram courtesy of
The Protein Structure Group,
Chemistry Department,
University of York.
serum amyloid P-component