We are interested in structural aspects of the mechanisms of hydrolytic metalloenzymes in the arginase-deacetylase family. To date, we have determined the crystal structures of rat arginase I, human arginase I, human arginase II, and arginases from Plasmodium falciparum, Leishmania mexicana, and Schistosoma mansoni. Structural and enzymological data suggest a mechanism for arginine hydrolysis in which both manganese ions activate a bridging hydroxide ion for nucleophilic attack at the guanidinium group of arginine in the first step of catalysis. Based on our structural and mechanistic analyses, we designed and synthesized boronic acid analogues of arginine such as 2-amino-6-boronohexanoic acid (ABH, Kd = 5 nM) [Baggio et al. (1997) J. Am. Chem. Soc. 119, 8107]. The boronic acid moiety of ABH similarly undergoes nucleophilic attack by the metal-bridging hydroxide ion to yield a metal-bound boronate anion that mimics the tetrahedral intermediate and its flanking transition states in catalysis (Figure 1), as shown in X-ray crystallographic studies of rat arginase I [Cox et al. (1999) Nature Struct. Biol. 6, 1043], human arginase I [Di Costanzo et al. (2005) Proc. Natl. Acad. Sci. USA, 102, 13058], P. falciparum arginase [Dowling et al. (2010) Biochemistry 49 5600], and L. mexicana arginase [D' Antonio et al. (2013) Arch. Biochem. Biophys. 535, 163]
Figure 1: Human arginase I-ABH complex. (a) Omit electron density map of ABH bound in the enzyme active site at 1.29 Å resolution. Water molecules appears as red spheres and Mn(II) ions appears as larger pink spheres. (b) Summary of arginase-ABH interactions; manganese coordination interactions are designated by green dashed lines, and hydrogen bonds are indicated by black dashed lines. (c) Stabilization of the tetrahedral intermediate (and flanking transition states) in the arginase mechanism based on the binding mode of ABH.
We have also used ABH as a chemical tool for probing the role of arginase in regulating arginine bioavailability for nitric oxide (NO) biosynthesis in tissues and in live animals. We discovered that arginase inhibition by ABH enhances smooth muscle relaxation in ex vivo organ bath studies. Since smooth muscle relaxation in the corpus cavernosum of the penis is necessary for erection, we concluded that human penile arginase is a potential target for the development of new therapies in the treatment of erectile dysfunction [Cox et al. (1999) Nature Struct. Biol. 6, 1043]. Our subsequent in vivo studies demonstrated that arginase inhibition by ABH enhances erectile function and vasocongestion in the male and female genitalia, so we concluded that both male erectile dysfunction and female sexual arousal disorder are potentially treatable by ABH [Cama et al. (2003) Biochemistry 42, 8445; Christianson (2005) Acc. Chem. Res. 38, 191]. More recent studies show that ABH may also be useful in the treatment of certain cardiovascular disorders such as atherosclerosis [Santhanam et al. (2007) Circulation Res. 101, 692; Ryoo et al. (2008) Circulation Res. 102, 923]. The biopharmaceutical company Arginetix was founded in 2008 based on our arginase inhibitor technology.
Our work with metal-dependant histone deacetylases recently yielded the first crystal structure of a histone deacetylase complexed with a macrocyclic depsipeptide inhibitor (Figure 2) [Cole et al. (2011) J. Am. Chem. Soc. 133, 12474]. Additionally, we recently showed that mutations in histone deacetylase 8 identified in patients diagnosed with Cornelia de Lange Syndrome compromise catalytic activity by causing structural changes in the active site that perturb substrate binding and catalysis [Deardorff et al. (2012) Nature 489, 313; Decroos et al. (2014) ACS Chem. Biol., in press.]. In addition to our work with arginase, we are studying other metalloenzymes that adopt the arginase fold, such as polyamine deacetylase [Lombardi et al. (2011) Biochemistry 50, 1808].
In other metalloenzyme work, we have determined the crystal structure of A. aeolicus LpxC, a zinc-requiring enzyme that catalyzes the first step of lipid A biosynthesis in Gram-negative bacteria [Whittington et al. (2003) Proc. Natl. Acad. Sci. USA 100, 8146] (Figure 3). Subsequent structural studies have allowed us to pinpoint regions of the active site that interact with the fatty acid and diphosphate moieties of the substrate [Gennadios et al. (2006) Biochemistry 45, 7940; 15216], and these studies have guided the first steps in the structure-based design of new LpxC inhibitors that may ultimately be useful in the treatment of Gram-negative bacterial infections [Shin et al. (2007) Bioorg. Med. Chem. 15, 2617]. To date, we have broadened these structural studies to include LpxC enzymes from Gram-negative pathogens Y. pestis (bubonic plague) and F. tularensis (tularemia) [Cole et al. (2011) Biochemistry 50, 258.]
Figure 3: Structure and biological function of LpxC. This zinc enzyme catalyzes the first committed step of lipid A biosynthesis; lipid A is the hydrophobic anchor of lipopolysaccharide, which comprises the outer leaflet of the outer membrane of Gram-negative bacteria. The crystal structure of LpxC reveals a hydrophobic tunnel in the active site that accommodates the fatty acid moiety of the substrate, and this binding interaction is required for the active site to adopt a catalytically-active conformation.
Structural Basis of Terpenoid Biosynthesis
The family of terpenoid natural products currently numbers more than 70,000 members found in all forms of life. Terpenoids, are involved in diverse biological functions such as the mediation of plant-parasite interactions or the modulation of membrane fluidity. Since times of antiquity, terpenoid natural products have also been essential components of the pharmacopeia as analgesics, antibiotics, and anti-cancer compounds (e.g., Taxol). We are interested in the enzymes that catalyze the biosynthesis of different cyclic terpenoids [Christianson (2006) Chem. Rev. 106, 3412; Christianson (2008) Curr. Opin. Chem. Biol. 12, 141]. We have determined the three-dimensional crystal structures of terpenoid cyclases from various bacterial, fungal, and plant sources, such as epi-isozizaene synthase from S. colicolor [Aaron et al. (2010) Biochemistry 49, 1787], bornyl diphosphate synthase from culinary sage [Whittington et al. (2002), Proc. Natl. Acad. Sci. USA 99, 15375], aristolochene synthase from A. terreus [Shishova et al. (2007) Biochemistry 46, 1941], trichodiene synthase from F. sporotrichioides [Rynkiewicz et al. (2001) Proc. Natl. Acad. Sci. USA 98, 13543], δ-cadinene synthase from cotton [Gennadios et al. (2009) Biochemistry 48, 6175] and taxadiene synthase from the Pacific yew (which catalyzes the first committed step in the biosynthesis of Taxol, a potent cancer chemotherapeutic compound), [Köksal et al. (2011) Nature 469, 116]. To illustrate, structures of bornyl diphosphate synthase and taxadiene synthase are shown in Figures 4 and 5, respectively. These structures guide the study of site-specific mutants and alternative substrates as we explore the structural basis of diversity in terpenoid biosynthesis [e.g., see: Vedula et al. (2005) Biochemistry 44, 12719; Vedula et al. (2008) Arch. Biochem. Biophys. 469, 184; Christianson (2007) Science 316, 60], Köksal et al. (2012) Biochemistry 51, 3003, 301.
Figure 4: Reaction catalyzed by bornyl diphosphate synthase. Aza analogues of carbocation intermediates are shown in boxes; crystal structures of their complexes with the synthase reveal structural inferences on catalysis. The enzyme undergoes significant conformational changes upon the binding of 3 Mg2+ ions and pyrophosphate (or a substrate diphosphate group). These conformational changes sequester the active site from bulk solvent and trigger substrate ionization to initiate catalysis [Whittington et al. (2002) Proc. Natl. Acad. Sci. USA 99, 15375].
Figure 5: Structural relationships among terpenoid cyclases.The class I terpenoid cyclase fold of pentalenene synthase (blue) contains metal-binding motifs DDXXD and (N,D)DXX(S,T)XXXE (red and orange, respectively); in 5-epi-aristolochene synthase, this domain is linked to a smaller, vestigial domain (green). A related domain is found in the class II terpenoid cyclase fold of squalene-hopene cyclase, where it contains the general acid motif DXDD (brown) and a second domain (yellow) inserted between the first and second helices; a hydrophobic plateau flanking helix 8 (gray stripes) enables membrane insertion. Taxadiene synthase contains both class I and class II terpenoid cyclase folds, but only the class I domain is catalytically active. The role of N-termini (purple) in class I plant cyclases is to "cap" the active site, as shown for 5-epi-aristolochene synthase.
- A.B. Harvard College (1983)
- A.M. Harvard University (1985)
- Ph.D. Harvard University (1987)
- Searle Scholar Award (1989–1992)
- Young Investigator Award, Office of Naval Research (1989–1992)
- Alfred P. Sloan Foundation Research Fellow (1992–1994)
- Camille and Henry Dreyfus Teacher-Scholar Award (1993–1994)
- Pfizer Award in Enzyme Chemistry, American Chemical Society (1999)
- Fellow in Natural Sciences (Chemistry), Sidney Sussex College, University of Cambridge (2006)
- Underwood Fellowship, Department of Biochemistry, University of Cambridge (2006–2007)
- Senior Fellow, American Asthma Foundation (2006)
- Fellow of the John Simon Guggenheim Memorial Foundation (2006–2007)
- National Academies Board on Chemical Sciences and Technology (2011–2017)
- The Repligen Award in Chemistry of Biological Processes, American Chemical Society (2013)
- Fellow of the Royal Society of Chemistry (London) (2013)
Köksal, M., Jin, Y., Coates, R.M., Croteau, R., Christianson, D.W. (2011) Taxadiene Synthase Structure and Evolution of Modular Architecture in Terpene Biosynthesis. Nature 469, 116-120.
Cole, K.E., Gattis, S.G., Angell, H.D., Fierke, C.A., Christianson, D.W. (2011) Structure of the Metal-Dependent Deacetylase LpxC from Yersinia enterocolitica Complexed with the Potent Inhibitor CHIR-090. Biochemistry 50, 258-265.
Lombardi, P.M., Angell, H.D., Whittington, D.A., Flynn, E.F., Rajashankar, K.R., Christianson, D.W. (2011) Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases. Biochemistry 50, 1808-1817.
Köksal, M., Hu, H., Coates, R.M., Peters, R.J., Christianson, D.W. (2011) Structure and Mechanism of the Diterpene Cyclase ent-Copalyl Diphosphate Synthase. Nature Chem. Biol. 7, 431-433.
Cole, K.E., Dowling, D.P., Boone, M.A., Phillips, A.J., Christianson, D.W. (2011) Structural Basis of the Antiproliferative Activity of Largazole, a Depsipeptide Inhibitor of the Histone Deacetylases. J. Am. Chem. Soc. 133, 12474-12477 (Communication to the Editor).
Ilies, M., Di Costanzo, L., Dowling, D.P., Thorn, K.J., Christianson, D.W. (2011) Binding of α, α-Disubstituted Amino Acids to Arginase Suggests New Avenues for Inhibitor Design. J. Med. Chem. 54, 5432-5443.
Lombardi, P.M., Cole, K.A., Dowling, D.P., Christianson, D.W. (2011) Structure, Mechanism, and Inhibition of Histone Deacetylases and Related Metalloenzymes. Curr. Op. Struct. Biol. 21, 735-743 (invited review).
Köksal, M., Chou, W.K.W., Cane, D.E., Christianson, D.W. (2012) Structure of 2-Methylisoborneol Synthase from Streptomyces coelicolor and Implications for the Cyclization of a Noncanonical C-Methylated Monoterpenoid Substrate. Biochemistry 51, 3011-3020.
Deardorff, M.A., Bando, M., Nakato, R., Watrin, E., Itoh, T., Minamino, M., Saitoh, K., Komata, M., Katou, Y., Clark, D., Cole, K.E., De Baere, E., Decroos, C., Di Donato, N., Ernst, S., Francey, L.J., Gyftodimou, Y., Hirashima, K., Hullings, M., Ishikawa, Y., Jaulin, C., Kaur, M., Kiyono, T., Lombardi, P.M., Magnaghi-Jaulin, L., Mortier, G.R., Nozaki, N., Petersen, M.B., Seimiya, H., Siu, V.M., Suzuki, Y., Takagaki, K., Wilde, J.J., Willems, P.J., Prigent, C., Gillessen-Kaesbach, G., Christianson, D.W., Kaiser, F.J., Jackson, L.G., Hirota, T., Krantz, I.D., Shirahige, K. (2012) HDAC8 Mutations in Cornelia de Lange Syndrome Affect the Cohesin Acetylation Cycle. Nature 489, 313-317.
D'Antonio, E.L., Hai, Y., Christianson, D.W. (2012) Structure and Function of Non-Native Metal Clusters in Human Arginase I. Biochemistry 51, 8399-8409.
D'Antonio, E.L., Ullman, B., Roberts, S.C., Gaur Dixit, U., Wilson, M.E., Hai, Y., Christianson, D.W. (2013) Crystal Structure of Arginase from Leishmania mexicana and Implications for the Inhibition of Polyamine Biosynthesis in Parasitic Infections. Arch. Biochem. Biophys. 535, 163-176.
Genshaft, A., Moser, J.-A.S., D'Antonio, E.L., Bowman, C.M., Christianson, D.W. (2013) Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures. Proteins: Struct., Funct., Bioinf. 81, 1051–1057
Köksal, M., Chou, W.K.W., Cane, D.E., Christianson, D.W. (2013) Unexpected Reactivity of 2-Fluorolinalyl Diphosphate in the Active Site of Crystalline 2-Methylisoborneol Synthase. Biochemistry 52, 5247-5255.
Chen, M., Al-lami, N., Janvier, M., D'Antonio, E.L., Faraldos, J.A., Cane, D.E., Allemann, R.K., Christianson, D.W. (2013) Mechanistic Insights from the Binding of Substrate and Carbocation Intermediate Analogues to Aristolochene Synthase. Biochemistry 52, 5441-5453.
Hai, Y., Dugery, R.J., Healy, D., Christianson, D.W. (2013) Formiminoglutamase from Trypanosoma cruzi is an Arginase-Like Manganese Metalloenzyme. Biochemistry 52, 9294-9309.
Li, R., Chou, W.K.W., Himmelberger, J.A., Litwin, K.M., Harris, G.G., Cane, D.E., Christianson, D.W. (2014) Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase. Biochemistry 53, 1155-1168.
Kaiser, F.J., Ansari, M., Braunholz, D., Gil-Rodríguez, M.C., Decroos, C., Wilde, J.J., Fincher, C.T., Kaur, M., Bando, M., Bowman, C.M., Bradley, J., Clark, D., del Campo-Casanelles, M., Di Donato, N., Dubbs, H., Eckhold, J., Ernst, S., Ferreira, J.C., Francey, L., Gehlken, U., Guillén-Navarro, E., Gyftodimou, Y., Hall, B.D., Hennekam, R., Hullings, M., Hunter, J., Kline, A.D., Krumina, Z., Leppig, K., Lynch, S.A., Mallozzi, M.B., Mannini, L., McKee, S., Mehta, S., Micule, L., Mohammed, S., Moran, E., Mortier, G.R., Moser, J.-A.S., Nozaki, N., Nunes, L., Pappas, J., Pérez-Aytés, A., Petersen, M.B., Poffyn, A., Puisac, B., Revencu, N., Roeder, E., Saitta, S., Scheuerle, A., Siu, V.M., Thiese, H., Vater, I., Willems, P., Williamson, K., Wilson, L., Hakonarson, H., Wierzba, J., Musio, A., Gillessen-Kaesbach, G., Ramos, F.J., Jackson, L.G., Shirahige, K., Pié, J., Christianson, D.W., Krantz, I.D., FitzPatrick, D.R., Deardorff, M.A. (2014) HDAC8 Mutations Cause an X-Linked Clinically Recognizable Cornelia de Lange Syndrome-Like Disorder. Hum. Mol. Genet. 23, 2888-2900 (cover article).
Hai, Y., Edwards, J.E., Van Zandt, M.C., Hoffmann, K.F., Christianson, D.W. (2014) Crystal Structure of Schistosoma mansoni Arginase, a Potential Drug Target for the Treatment of Schistosomiasis. Biochemistry, in press.
Decroos, C., Bowman, C.M., Moser, J.-A.S., Christianson, K.E., Deardorff, M.A., Christianson, D.W. (2014) Compromised Structure and Function of HDAC8 Mutants in Cornelia de Lange Syndrome Spectrum Disorders. ACS Chem. Biol., in press.