The School of Crystallography at Birkbeck has a regular programme of research seminars held on Monday lunchtimes during term. Many of these describe recent developments in protein structure, and, from time to time, I will be reporting these here and linking in to course material where relevant. This week's seminar was by Adrian Lapthorn, a protein crystallographer based at Glasgow University, who just happens also to be the external examiner for the MSc in Structural Molecular Biology as well as the second year module TSMB. Adrian's research is concerned with solving the structures of enzymes, including those involved in the biosynthesis of the amino acid histidine.
Histidine is known as an essential amino acid; that is, it cannot be synthesised de novo in humans, but must be supplied from the diet. However, bacteria, fungi and plants all have enzymes that enable them to synthesise histidine from simple chemical precursors. The enzymes in the histidine synthesis pathway are therefore, at least potentially, good targets for novel antibiotics and herbicides as there are no equivalent human enzymes for them to inhibit, so they should be relatively free of side effects.
In bacteria, the histidine synthesis pathway consists of 10 steps, catalysed by a total of eight enzymes (some of which are bifunctional). The first step in this pathway is synthesised by an enzyme called HisG (or ATP-phosphyribosyltransferase) which catalyses the following reaction:
ATP + PRPP ---> PR-ATP
(PRPP is Phosphoribosyl pyrophosphate; PR-ATP is phosphoribosyl-ATP. The action of the enzyme is, therefore, to transfer a phosphoribose group on to the ATP molecule.
This enzyme is interesting for several reasons, besides the pharmaceutical and biotechnological interest in its inhibition. For one thing, unusually, there are no specific active site residues; the substrate is stabilised in the active site cleft by binding to magnesium ions.
Adrian's talk was subtitled "the long and the short of it", because some bacteria have a "short" form of this enzyme, and others a "long" form with an extra 80-odd residues at its C-terminus. All bacteria with the short form also have an additional enzyme, HisZ, which binds to HisG in an equivalent position to the C-terminal domain of the long form during catalysis. The long form of the enzyme consists of three discrete folded units called domains. There are two similar ones at the N terminus, followed by a long alpha helix and the C terminal domain, which is absent in the short form and has a similar structure to that of the small protein ferredoxin. The active site is between the two similar domains.
You will learn much more about domains and their folds in the next section, Towards Tertiary Structure. For now, look at this structure (PDB 1Q1K) of the long form of HisG (from E.coli) and try to identify the three domains and the active site. You might find it helpful to look at a single chain only.