The Structure of a Binary Complex between a Mammalian Mevalonate Kinase and ATP

Abstract

Mevalonate kinase catalyzes the ATP-dependent phosphorylation of mevalonic acid to form mevalonate 5-phosphate, a key intermediate in the pathways of isoprenoids and sterols. Deficiency in mevalonate kinase activity has been linked to mevalonic aciduria and hyperimmunoglobulinemia D/periodic fever syndrome (HIDS). The crystal structure of rat mevalonate kinase in complex with MgATP has been determined at 2.4-Å resolution. Each monomer of this dimeric protein is composed of two domains with its active site located at the domain interface. The enzyme-bound ATP adopts an anti conformation, in contrast to the syn conformation reported for Methanococcus jannaschii homoserine kinase. The Mg 2؉ ion is coordinated to both ␤-and ␥-phosphates of ATP and side chains of Glu 193 and Ser 146 . Asp 204 is making a salt bridge with Lys 13 , which in turn interacts with the ␥-phosphate. A model of mevalonic acid can be placed near the ␥-phosphoryl group of ATP; thus, the C5 hydroxyl is located within 4 Å from Asp 204 , Lys 13 , and the ␥-phosphoryl of ATP. This arrangement of residues strongly suggests: 1) Asp 204 abstracts the proton from C5 hydroxyl of mevalonate; 2) the penta-coordinated ␥-phosphoryl group may be stabilized by Mg 2؉ , Lys 13 , and Glu 193 ; and 3) Lys 13 is likely to influence the pK a of the C5 hydroxyl of the substrate. V377I and I268T are the most common mutations found in patients with HIDS. Val 377 is located over 18 Å away from the active site and a conservative replacement with Ile is unlikely to yield an inactive or unstable protein. Ile-268 is located at the dimer interface, and its Thr substitution may disrupt dimer formation.Mevalonate kinase (MK, ATP:mevalonate 5-phosphotransferase, EC 2.7.1.36) 1 catalyzes the transfer of the ␥-phosphoryl group from ATP to the C5 hydroxyl oxygen of mevalonic acid to form mevalonate 5-phosphate, a key intermediate in the biosynthetic pathway for isoprenoids and sterols from acetate. Although the enzyme was discovered in the late 1950s (1, 2), it suffered over three decades of neglect, as research on the isoprenoid pathway was focused on HMG-CoA reductase, which catalyzes the previous step in the pathway, i.e. the formation of mevalonic acid from HMG-CoA. However, interest in MK has been revived recently, because it was recognized that this enzyme, together with HMG-CoA synthase and HMG-CoA reductase, is involved in coordinate regulation of this pathway and therefore may represent a secondary control point. The recent recognition of the involvement of the diverse non-sterol isoprenoid metabolites in various cellular functions (e.g. protein prenylation, protein glycosylation, and cell cycle regulation) has also increased interest in this enzyme. In addition, the significance of MK has been further highlighted by the implication of the enzyme in human inherited diseases, such as mevalonic aciduria and hyperimmunoglobulinemia D/periodic fever syndrome (HIDS, Mendelian Inheritance in Man 260920).The enzyme is found in eukaryotes, archaebacteria, and some eubacteria. Th...

Biochemical Characterization of Pantoate Kinase, a Novel Enzyme Necessary for Coenzyme A Biosynthesis in the Archaea

“…Residues interacting with the adenine base in Mj-MvK are Lys74, Tyr75, and Cys76 (32). Ser135 of the rat MvK has also been identified as a residue interacting with the adenine base, and this residue is conserved in MvK proteins from various sources (6). Residues recognizing the adenine base in Mj-HSK are Asn62, Val63, Lys87, and Ser101, and Asn62 is conserved in HSK proteins from a wide range of organisms (12).…”

MVK mutations and associated clinical features in Italian patients affected with autoinflammatory disorders and recurrent fever

“…The other four novel MVK mutations reported here for the first time, V132I, G171R, V250I and G376V, affect amino-acidic residues which are either conserved in other mammalian species and/or located in close vicinity of stretches of highly conserved residues. 23 Other mutant MVK alleles were found in heterozygous state in six out of the 136 selected patients. With the exception of the case of the common V377I allele, the other five alleles are private variants represented by two synonymous changes (I260I and L308L), a T356 M missense change and two nucleotide substitutions (c.79-62G4A and c.1191 þ 11C4T) in intron 2 and in the 3 0 UTR, respectively.…”

Isolation and Characterization of a Novel trans-Factor for Luteinizing Hormone Receptor mRNA from Ovary

“…Mevalonate kinase is a member of GHMP kinase superfamily, a family of metabolic enzymes with a highly conserved glycine-rich motif (PXGXGLGSSAA) that is implicated in the binding of ATP (41)(42)(43). It might first appear that the presence of an ATP binding site in MVK might make it vulnerable for nonspecific binding to any RNA molecule due to the presence of adenine residues.…”