Crystal structure of LeuA from Mycobacterium tuberculosis, a key enzyme in leucine biosynthesis

Abstract

The leucine biosynthetic pathway is essential for the growth of Mycobacterium tuberculosis and is a potential target for the design of new anti-tuberculosis drugs. The crystal structure of α-isopropylmalate synthase, which catalyzes the first committed step in this pathway, has been determined by multiwavelength anomalous dispersion methods and refined at 2.0-Å resolution in complex with its substrate α-ketoisovalerate. The structure reveals a tightly associated, domain-swapped dimer in which each monomer comprises an (α/β)8 TIM barrel catalytic domain, a helical linker domain, and a regulatory domain of novel fold. Mutational and crystallographic data indicate the latter as the site for leucine feedback inhibition of activity. Domain swapping enables the linker domain of one monomer to sit over the catalytic domain of the other, inserting residues into the active site that may be important in catalysis. The α-ketoisovalerate substrate binds to an active site zinc ion, adjacent to a cavity that can accommodate acetyl-CoA. Sequence and structural similarities point to a catalytic mechanism similar to that of malate synthase and an evolutionary relationship with an aldolase that catalyzes the reverse reaction on a similar substrate. Mycobacterium tuberculosis remains one of mankind's deadliest pathogens, responsible for approximately 2 million deaths worldwide every year and estimated to infect one-third of the world's population (World Health Organization, www.who.int/gtb/). Although effective drugs exist, current therapy requires prolonged treatment with three to four drugs, leading to compliance problems and the emergence of multidrug resistance (1). Two features of the organism combine to make it one of the most serious disease-causing agents. First, it has a thick, waxy cell wall that is rich in novel lipids, glycolipids, and polysaccharides and provides a challenging barrier to drugs and other small molecules (2). Second, it can survive for many years in a dormant or persistent state within activated macrophages, to be reactivated as active tuberculosis (TB) later in life (3). The latter phenomenon has led to a deadly synergy with HIV/AIDS. Large-scale transposon mutagenesis and in vitro growth studies have identified many essential biosynthetic pathways in M. tuberculosis (4). Among them are those for the synthesis of the branched-chain amino acids leucine, isoleucine, and valine. These pathways, which share common intermediates, are present in plants and microorganisms, but not humans, and are likely to be particularly important for the survival of M. tuberculosis inside macrophages, in the absence of an exogenous source of nutrients. In support of this notion, leucine auxotrophy (by insertional mutation of leuD) has been shown to attenuate both Mycobacterium bovis and M. tuberculosis, reducing their capacity to establish infections in mice, in vivo, and in macrophages, in vitro (5–7). M. tuberculosis also has shown sensitivity to inhibitors of acetolactate synthase (8), which catalyzes reactions required for the biosynthesis of all three branched-chain amino acids. Leucine biosynthesis occurs via the isopropylmalate (IPM) pathway, starting with the formation of α-IPM from acetyl-CoA and α-ketoisovalerate (α-KIV), which is also the immediate precursor for valine biosynthesis. This aldol condensation-type reaction is catalyzed by α-IPM synthase (α-IPMS), encoded by leuA. Subsequent reactions in this pathway are catalyzed by α-IPM isomerase, which is encoded by leuC/D, and β-IPM dehydrogenase, which is encoded by leuB. Biochemical studies of α-IPMS have been limited to a few microorganisms, notably Salmonella typhimurium (9), Corynebacterium glutamicum (10), and Saccharomyces cerevisiae (11). The enzyme is dimeric (S. cerevisiae) or tetrameric (S. typhimurium), with a monomer molecular mass of 60–70 kDa, a divalent metal ion dependence, and an alkaline pH optimum. As is common for enzymes that catalyze the first committed step in a biosynthetic pathway (12, 13), it is subject to feedback inhibition by the end-product leucine (14). Despite its key role in this important pathway, no 3D structure is yet available for α-IPMS. In this article we describe the crystal structure for α-IPMS from M. tuberculosis. The observation of bound substrate (α-KIV) and metal cofactor (Zn2+) identifies the active site and key residues within it, and structural similarities to several other enzymes that act on analogous substrates indicate previously unrecognized functional and evolutionary relationships. From these comparisons, we suggest a possible biochemical mechanism. The 3D structure also allows us to address other aspects of α-IPMS function, including the leucine feedback inhibition site, and provides a basis for inhibitor design directed toward the development of new anti-TB drugs.