In the case of the single polypeptide chain of pyruvate kinase there are four domains; the central TIM-barrel is the catalytic domain, whereas the other three play no direct role in enzymatic activity. However, the small N-terminal domain of 42 residues is involved in inter-subunit contacts when four copies associate to form a homo-tetramer.
E.coli produces a bifunctional enzyme which performs both the isomerisation of phospho-ribosyl anthranylate AND the synthesis of indole-glyceryl phosphate, two steps in tryptophan biosynthesis. It comprises two very similar eight-stranded alpha/beta barrels, each barrel acting as a separate enzyme. Examine the text-head of the pdb file.
Sometimes, we find that several domains are found in a single enzyme complex, either in a single polypeptide chain, or as an association of separate chains.
Often the domains have related functions, for instance, where one domain will be responsible for binding, another for regulation, and a third for enzymatic activity. Take a glimpse at a delightful study of cellobiohydrolase.
Two (further) steps in the biosynthetic pathway of tryptophan (in S.typhimirium) are catalysed by tryptophan synthase which consists of two separate chains, designated alpha and beta, each of which is effectively a distinct enzyme. The biologically active unit is a hetero-tetramer comprised of 2 alpha and 2 beta units. Again you will recognise the TIM-barrel fold. Study the text-head of the pdb file.
We sometimes find slightly different versions of the same protein associating. Thus, haemoglobin has both an A-chain and a B-chain, which come together to form a hetero-dimer. Two copies of this then associate to form the normal haemoglobin tetramer. Which is equivalent to an A-dimer associating with a B-dimer. Or is it?
In a naturally occurring mutant haemoglobin, we find a higher level of
association, where fibres of the tetramer grow to distort the red blood
cell (erythrocyte). See what the OMIM database has to say about
Sickle-cell anaemia. Find out why it has a higher prevalence amongst
ethnic groups of African origin. Identify the mutation in the
structure and develop the causal explanation.
The reason for this is now thought to be the allosteric cooperativity that results in increased catalytic efficiency, effectively a `sharing' of the small conformational changes that accompany substrate binding and catalytic activity. A good well-studied example is the `breathing motion' observed in the haemoglobin tetramer.
Another interesting case study is found with the growth factors where we see dimers formed in 3 different ways, corresponding to two-fold axes in different directions.
We usually find that hetero and especially homo-multimers exhibit symmetry, a subject worthy of study in itself.
Examples of symmetrical enzyme multimers in the form usually found in cells have been especially prepared and archived at Brookhaven in a directory dedicated to these biological units. It may be accessed by anonymous ftp to ftp.pdb.bnl.gov and going to directory /user_group/biological_units/ The contents and associated README are worth a look.
The entries in the PDB biological units directory may be arranged to MIME-invoke a molecular viewer such as HIV protease, the viral (aspartic) protease responsible for excising the separate proteins from the single polyprotein that the virus produces once inside the cell;
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John Walshaw & Alan Mills, Birkbeck College, Apr'95