Structural Biochemistry/NMP Kinase

A specific enzyme called Nucleoside Monophosphate kinase (NMP kinase) catalyzes the transfer of a terminal phosphate group (ATP in most cases) to the phosphate group on the Nucleoside Monophosphate (NMP). Oftentimes, the transfer of NTP to NMP competes with a hydrolysis reaction in which the phosphate group from NTP transfers to a molecule of water instead. However, the use of the induced fit model allows the enzyme to wrap around the substrate and change the overall conformation of the enzyme-substrate complex in order to solve this problem. The phosphorylation reaction takes on the general form:

ATP + NMP <=====> ADP + NDP

In this reaction, the enzyme NMP binds to the substrate ATP (by induced fit). NMP gains one phosphate group and becomes NDP, whereas the ATP substrate loses one phosphate group and thus becomes ADP.

P-Loop Structures

Through X-ray crystallography, scientists and researchers discovered the structure of many different NMP kinases. Analyzing the three-dimensional structures revealed that these kinases are homologous proteins. Moreover, crystallographic data suggested that the NTP-binding domain was strictly conserved. This domain consists of two alpha helices wrapped around a beta sheet. One distinct feature of this domain is the formation of a loop between the beta strand and the alpha helix (P-Loop). These loops tend to wrap or "loop" around substrates, therefore enclosing them. The P-Loop is unique in the sense that it interacts with phosphate groups on bounded nucleotides.

Magnesium and Manganese Complexes

Studies of NMP kinases and ATP substrates reveal that these kinases are only active in the presence of divalent metal ions such as magnesium or manganese. In this case, the ATP substrate binds to the divalent ion, forming a metal ion-nucleotide complex. This complex is ultimately the true substrate for enzymes like NMP kinase.

Binding of divalent ions like magnesium or manganese increases the enzyme specificity. These ions help stabilize negative charges on phosphate groups. The interactions between the divalent ion and the oxygen atoms in the phosphate group changes the conformation such that it can bind specifically to the enzyme. These divalent ions also produce an interaction between the true substrate complex and the enzyme, therefore increasing the binding energy.

Conformational Changes

By understanding the tertiary structure of adenylate kinase, scientists and researchers discovered that a large conformational change occurs when adenylate kinase binds to an ATP analog. The P-Loop wraps around the phosphate chain, reacting mostly with the beta phosphate group. This allows the domain of the enzyme to shift downward such that a lid forms over the bounded nucleotide. As a result, the gamma phosphate group is positioned directly next to the NMP binding site. This binding induces yet another conformational change.