In enzymology, glutamate racemase (MurI with a capital i) (EC 5.1.1.3) is an enzyme that catalyzes the chemical reaction
L-glutamate ⇌ {\displaystyle \rightleftharpoons } D-glutamate Hence, this enzyme RacE has one substrate, L-glutamate, and one product, D-glutamate. This enzyme belongs to the family of isomerases, specifically those racemases and epimerases acting on amino acids and derivatives, including proline racemase, aspartate racemase, and diaminopimelate epimerase. This enzyme participates in glutamate metabolism that is essential for cell wall biosynthesis in bacteria. Glutamate racemase performs the additional function of gyrase inhibition, preventing gyrase from binding to DNA. Glutamate racemase (MurI) serves two distinct metabolic functions: primarily, it is a critical enzyme in cell wall biosynthesis, but also plays a role in gyrase inhibition. The ability of glutamate racemase and other proteins to serve two distinct functions is known as "moonlighting".
Moonlighting background
Before the discovery of moonlighting proteins, it was generally believed by scientists that an enzyme only had one function which led to the concept of "one gene, one enzyme". However, this concept no longer applies in science after the discovery that some proteins consist of both major and minor functions. This led to numerous studies attempting to relate the two functions to each other. The minor functions of these unique enzymes are called moonlighting functions, in which a protein can have a secondary functions not dependent upon the main function. These two functions of the moonlighting protein are found in a single polypeptide chain. Proteins that are multifunctional are not included due to gene fusion, families of homologous proteins, splice variants or promiscuous enzyme activities. The enzyme glutamate racemase (MurI) is an example of a moonlighting protein, functioning both in bacterial cell wall biosynthesis as well as in gyrase inhibition.
Structure The dimensions of MurI is approximately 35 Å × 40 Å × 45 Å and consists of two compact domains of α/β structure. With the active site in between the two domains, the N-terminal domain contains residues 1-97 and 207-264 while the C-terminal domain includes residues 98-206. This allows the enzyme to produce L-isomer from D-glutamate. Also, the N-domain is composed of five-stranded β-sheets compared to four-stranded β-sheets of C-domain. These structural specifications are not identical between MurI of different species; S. pyogenes and B. subtilis actually possess the most structurally similar MurI enzymes yet found. It is also not rare to find MurI as a dimer. The active site, as it is evenly between the N-domain and C-domain, is also between the two cysteine residues. It is accessible to solvents, as several water molecules, such as W1, are found in the active site. In some species, the active site also incorporates sulfate ions to undergo hydrogen bonding on the amide backbone and the side chains.
Function
Bacterial wall synthesis
Glutamate racemase is a bacterial enzyme that is encoded by the murI gene. This enzyme is most commonly known as being responsible for the synthesis of bacterial cell walls. Through experimentation it was found that this enzyme is able to construct these cell walls by synthesizing D-glutamate from L-glutamate through racemization. D-glutamate is a monomer of the peptidoglycan layer in prokaryotic cell walls. Peptidoglycan is an essential structural component of the bacterial cell wall. The peptidoglycan layer is also responsible for the rigidity of the cell wall. This process, in which MurI helps catalyze the interconversion of glutamate enantiomers, like L-Glutamate, into the essential D-glutamate, is also cofactor independent. As such it can proceed without needing an additional source, which would bind to an allosteric site, altering the enzyme shape to assist in catalyzing the reaction. Murl involves a two-step process to catalyze the glutamate enantiomers to D-glutamate. The first step is a deprotonation of the substrate to form an anion. Subsequently, the substrate gets reprotonated. Once the glutamate is in the active site of the enzyme it undergoes a very large conformational change of its domains. This change helps superimpose the two catalytic cysteine residues, Cys73 and Cys184, located on either sides of the substrate at equal positions. Those domains mentioned earlier are symmetric and this symmetry suggests that this racemase activity of the protein may have evolved from gene duplication. Due to this main function of biosynthesis of bacterial cell walls MurI has been targeted as an antibacterial in drug discovery.
… excerpt ends here. Continue reading the full article.
