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Methylerythritol Synthetase Involved in Mevalonate-Independent Isoprenoid Biosynthesis

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Methylerythritol Synthetase Involved in Mevalonate-Independent Isoprenoid Biosynthesis © 2001 Nature Publishing Group http://structbio.nature.com articles Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate-independent isoprenoid biosynthesis Stéphane B. Richard1, Marianne E. Bowman1, Witek Kwiatkowski1, Ilgu Kang2, Cathy Chow2, Antonietta M. Lillo2, David E. Cane2 and Joseph P. Noel1 The YgbP protein of Escherichia coli encodes the enzyme 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME) synthetase, a member of the cytidyltransferase family of enzymes. CDP-ME is an intermediate in the mevalonate- independent pathway for isoprenoid biosynthesis in a number of prokaryotic organisms, algae, the plant plastids and the malaria parasite. Because vertebrates synthesize isoprenoid precursors using a mevalonate pathway, CDP-ME synthetase and other enzymes of the mevalonate-independent pathway for isoprenoid production represent attractive targets for the structure-based design of selective antibacterial, herbicidal and antimalarial drugs. The high-resolution structures of E. coli CDP-ME synthetase in the apo form and complexed with both CTP–Mg2+ and CDP-ME–Mg2+ reveal the stereochemical principles underlying both substrate and product recognition as well as catalysis in CDP-ME synthetase. Moreover, these complexes represent the first experimental structures for any cytidyltransferase with both substrates and products bound. Isopentenyl diphosphate (IPP) and the isomeric compound, dimensional structures of CDP-ME synthetase both in the apo dimethylallyl diphosphate (DMAPP), are the fundamental form and complexed to CTP–Mg2+ and CDP-ME–Mg2+, respec- building blocks of isoprenoids in all organisms. The isoprenoids tively. These structures reveal active site features responsible for include >23,000 naturally occurring molecules of both primary the stereochemical control of the cytidyltransferase reaction and and secondary metabolism. Isoprenoids include hopane tri- serve as three-dimensional templates for future efforts directed at © http://structbio.nature.com Group 2001 Nature Publishing terpenes, ubiquinones and menaquinones in bacteria; structure-based inhibitor design and evaluation. carotenoids, plastoquinones, mono-, sesqui-, di- and tri- terpenes and the prenyl side chains of chlorophylls in plants; and Overall three-dimensional architecture quinones, dolichols, steroids and retinoids in mammals1. IPP CDP-ME synthetase organizes as a homodimer with each sub- was generally assumed to be derived solely from mevalonate syn- unit related by a crystallographic two-fold axis. We have refined thesized from the condensation of three molecules of acetyl- the ‘apo’ form of CDP-ME synthetase to 1.55 Å resolution, the CoA. However, independent studies demonstrated the existence complex with CTP-Mg2+ to 1.5 Å resolution (Fig. 2a) and the of a novel, mevalonate-independent pathway for IPP synthesis complex with CDP-ME–Mg2+ to 1.8 Å resolution (Fig. 2b). The known as the 1-deoxy-D-xylulose 5-phosphate / 2-C-methyl-D- ‘apo’ form of CDP-ME synthetase was crystallized in the pres- erythritol 4-phosphate (DXP/MEP) pathway. This mevalonate- ence of 10 mM MEP but showed no extra electron density in the independent pathway utilizes pyruvate and glyceraldehyde active site after structural elucidation. Each subunit of the 3-phosphate as starting materials for production of IPP2 (Fig. 1). homodimer is comprised of two structurally distinct domains. The DXP/MEP pathway occurs in a variety of eubacteria, The larger core domain (residues 1–136 and 160–236) is globular including several pathogenic species such as Mycobacterium in shape and maintains an α/β structure that resembles a tuberculosis, in algae, in the plastids of plant cells2 and in the api- Rossmann fold8 but which displays a distinct α/β connectivity coplast of Plasmodium falciparum3, the parasite that causes pattern with an insertion of two β-strands, β7 and β10, into a malaria. Given the essential nature of the DXP/MEP pathway in parallel 3-2-1-4-5 β-sheet. The second, much smaller lobe or these organisms and the absence of this pathway in mammals, the subdomain (residues 137–159) resembles a curved arm that enzymes comprising the DXP/MEP pathway represent potential interlocks in trans with its symmetry related arm to mediate targets for the generation of selective antibacterial4, antimalarial3 dimer formation. Moreover, the interlocking arms form part of and herbicidal5 molecules. 4-diphosphocytidyl-2-C-methylery- the MEP binding site and organize portions of the catalytic sur- thritol (CDP-ME) synthetase6,7 (alternatively known as MEP face responsible for cytidyltransferase activity (Fig. 2b). cytidyltransferase) encoded by the ygbP open reading frame of Escherichia coli catalyzes the formation of CDP-ME from MEP Relationship to other cytidyltransferases and CTP. This reaction constitutes the third step of the DXP/MEP A search for related three-dimensional structures in the Protein pathway of isoprenoid biosynthesis. We now report the three- Data Bank9 using the DALI10 server retrieved a number of 1Structural Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA. 2Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA. Correspondence and requests for materials should be addressed to J.P.N. email: [email protected] nature structural biology • volume 8 number 7 • july 2001 641 © 2001 Nature Publishing Group http://structbio.nature.com articles Fig. 1 Biosynthesis of the isoprenoid precursor isopen- tenyl diphosphate (IPP, 8) via the alternative, meval- onate-independent DXP/MEP pathway. All reactions are depicted in the forward direction. The synthesis of the C5 IPP skeleton begins with the condensation of a C2 moiety from the decarboxylation of pyruvate (1) and a C3 moiety from glyceraldehyde 3-phosphate (2) to form 1-deoxy-D-xylulose 5-phosphate (DXP, 3) through the action of DXP synthase32,33 (DXPS or DXS). Next, DXP is converted into 2-C-methyl-D-erythritol 4- phosphate (MEP, 4) by DXP reductoisomerase34,35 (DXPR or DXR) and subsequently transformed into 4-diphos- phocytidyl-2-C-methyl-D-erythritol (CDP-ME, 5) by CDP- ME synthetase6,7 (YgbP protein). Fosmidomycin acts as an effective inhibitor of DXPR3. CDP-ME is phosphory- lated on the 2-hydroxy group to form 4-diphospho- cytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-MEP; 6) in an ATP-dependent reaction by the enzyme CDP- ME kinase encoded by the ychB gene of E. coli36,37. Subsequent formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (7) is catalyzed by the enzyme MECDP synthase encoded by the gene ygbB17,38. Additional steps, which remain to be elucidated, ulti- mately form IPP (8). cules in each enzyme are arranged in opposite fashions. In contrast, alignments of the two struc- tures using the bound CTP molecules as a guide reveals an internal pseudosymmetry in the core α/β fold of both GCT and CDP-ME synthetase (Fig. 2c). Although the cytidine base and ribose exhibit nearly identical orientations in GCT and CDP- ME synthetase, the curved triphosphate ends of the bound CTP molecules pucker in opposite directions. These alternative orientations of the © http://structbio.nature.com Group 2001 Nature Publishing triphosphate tail of CTP position each of the α-phosphates of the CTP substrates for nucle- ophilic attack by MEP in CDP-ME synthetase or glycerol 3-phosphate in GCT. The structure of CMP-NeuAc synthetase was solved in the apo form and complexed to a partially disordered enzyme cores containing a nucleotide binding fold. Currently, CDP molecule, which serves as a mimic of the true CTP substrate. three cytidyltransferase structures, which contain a core Structural alignments of E. coli CDP-ME synthetase or Neisseria nucleotide binding domain, have been described and include meningitidis CMP-NeuAc synthetase13 (data not shown) with capsule specific CMP:2-keto-3-deoxy-manno-octonic acid syn- GCT reveal that the catalytic machinery of CDP-ME synthetase thetase11 (K-CKS), CTP:glycerol-3-phosphate cytidyltrans- and CMP-NeuAc synthetase are spatially conserved with GCT ferase12 (GCT) and, most recently, CMP acylneuraminate but not shared at the primary amino acid level with GCT14. The synthetase13 (CMP-NeuAc synthetase). spatial correspondence includes the putative catalytic residues CDP-ME synthetase, CMP-NeuAc synthetase and GCT share His 14 and His 17 of GCT15 with Lys 27 and Lys 213 of CDP-ME similarly folded cores. However, the five parallel β-strands of synthetase and Lys 21 and Asp 209 of CMP-NeuAc synthetase13. GCT, which maintain a 3-2-1-4-5 topology, are interrupted in CDP-ME synthetase and CMP-NeuAc synthetase by the insertion Active site architecture of two antiparallel β-strands (β7 and β10) between β-strands 4 CTP and CDP-ME are sequestered in the active site of CDP-ME and 5 (β6 and β11) of the core β-sheet (Fig. 2c). This insertion synthetase by a glycine-rich loop spanning Pro 13–Arg 20. extends the central β-sheet and leads to a structural alteration of Selectivity for the pyrimidine base is achieved through hydrogen the nucleotide binding region and subsequent formation of a dis- bonding interactions and steric constrictions in the base-binding tinct and spatially nonoverlapping CTP binding motif in CDP- pocket that do not allow for the sequestration of larger purine ME synthetase and CMP-NeuAc synthetase. The coordinates for bases. This selectivity is specifically achieved through hydrogen K-CKS have yet to be deposited in the PDB, making a detailed bonds formed between the backbone amides of Ala 14 and Ala 15, comparison of K-CKS with either CMP-NeuAc synthetase or the carbonyl oxygens of Gly 82 and Asp 83, and the hydroxyl CDP-ME synthetase impossible at this stage. group of Ser 88. The cytosine base is stacked between the flexible By superimposing GCT and CDP-ME synthetase to constrain loop spanning β1 and β2, and the methylene portion of the the connectivity pattern of the central β-sheets and the sur- Arg 85 side chain projecting outward from the β5–αE catalytic rounding α-helices, the GCT and CDP-ME synthetase active loop.
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