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PNAS | November 6, 2001 | vol. 98 | no. 23 | 12896-12901
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Biochemistry
 Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis

Jeffrey B. Bonanno*,dagger ,Dagger , Carme Edo*,Dagger , Narayanan Eswar*, Ursula Pieper*, Michael J. Romanowski*, Valentin Ilyin*, Sue Ellen Gerchman§, Helen Kycia§, F. William Studier§, Andrej Sali*, and Stephen K. Burley*,dagger ,

* Laboratories of Molecular Biophysics, dagger  Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021; and § Biology Department, Brookhaven National Laboratory, Upton, NY 11973

Contributed by F. William Studier, September 4, 2001

X-ray structures of two enzymes in the sterol/isoprenoid biosynthesis pathway have been determined in a structural genomics pilot study. Mevalonate-5-diphosphate decarboxylase (MDD) is a single-domain alpha /beta protein that catalyzes the last of three sequential ATP-dependent reactions which convert mevalonate to isopentenyl diphosphate. Isopentenyl disphosphate isomerase (IDI) is an alpha /beta metalloenzyme that catalyzes interconversion of isopentenyl diphosphate and dimethylallyl diphosphate, which condense in the next step toward synthesis of sterols and a host of natural products. Homology modeling of related proteins and comparisons of the MDD and IDI structures with two other experimentally determined structures have shown that MDD is a member of the GHMP superfamily of small-molecule kinases and IDI is similar to the nudix hydrolases, which act on nucleotide diphosphatecontaining substrates. Structural models were produced for 379 proteins, encompassing a substantial fraction of both protein superfamilies. All three enzymes responsible for synthesis of isopentenyl diphosphate from mevalonate (mevalonate kinase, phosphomevalonate kinase, and MDD) share the same fold, catalyze phosphorylation of chemically similar substrates (MDD decarboxylation involves phosphorylation of mevalonate diphosphate), and seem to have evolved from a common ancestor. These structures and the structural models derived from them provide a framework for interpreting biochemical function and evolutionary relationships.

Dagger J.B.B. and C.E. contributed equally to this work.

To whom reprint requests should be addressed. E-mail: burley{at}rockvax.rockefeller.edu.

www.pnas.org/cgi/doi/10.1073/pnas.181466998
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