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First published online February 25, 2005; 10.1104/pp.104.048751 Plant Physiology 137:1009-1017 (2005) © 2005 American Society of Plant Biologists Crystal Structures of Alfalfa Caffeoyl Coenzyme A 3-O-Methyltransferase1Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale, 38027 Grenoble cedex 1, France (J.-L.F.); Jack Skirball Chemical Biology and Proteomics Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037 (C.Z., J.P.N.); Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92037 (C.Z., J.P.N.); and Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (R.A.D.)
Caffeoyl coenzyme A 3-O-methyltransferases (CCoAOMTs) are S-adenosyl-L-methionine-dependent O-methyltransferases (OMTs) involved in lignin biosynthesis. Plant CCoAOMTs belong to a distinct family of OMTs, more closely related to the mammalian catechol OMTs than to other plant OMTs. The crystal structure of alfalfa (Medicago sativa) CCoAOMT in complex with the reaction products S-adenosine-L-homocysteine and feruloyl/sinapoyl CoAs presented here belong to a structurally and mechanistically distinct family of plant small molecule OMTs. These structures provide a new understanding of the substrate preferences and the catalytic mechanism accompanying CCoAOMT-mediated O-methylation of CoA-linked phenylpropanoid substrates.
In plant cells, methylated hydroxycinnamic acid derivatives are important precursors in the biosynthesis of cell wall esterified phenolic compounds, soluble sinapate esters, dimeric lignans, and the extensively cross-linked polymer lignin. Lignin and esterified phenolic compounds provide structural support for the cell walls of conducting tissues and tracheary elements and were critical in the evolution of higher plants from their aquatic progenitors. Additionally, lignin serves as an inducible physical barrier against pathogen infections (Vance et al., 1980
Two S-adenosyl-L-Met (SAM)-dependent O-methyltransferases (OMTs) are involved in the methylation of monolignol precursors: caffeic acid 3-OMTs (COMTs; Zubieta et al., 2002
Transgenic experiments that down-regulated COMT activity severely reduced the syringyl monomer content of the resultant lignin but did not decrease the overall lignin content of the transgenic plants (Atanassova et al., 1995
Primary sequence analysis and structural comparison with other plant OMTs demonstrate that COMT and CCoAOMT belong to two distinct families of OMTs. The family to which COMT (Zubieta et al., 2002
Based on sequence identity, the closest non-CoA OMT to this CCoAOMT family is the group of animal catechol OMTs (Fig. 2). The soluble portion of catechol OMT from rat (19% sequence identity with CCoAOMT) has been structurally characterized (Vidgren et al., 1994
The crystal structures of alfalfa CCoAOMT in complex with the reaction products S-adenosyl-L-homocysteine (SAH) and feruloyl/sinapoyl CoAs presented here belong to a structurally and mechanistically distinct family of plant small molecule OMTs. These structures provide a new understanding of the substrate preferences and the catalytic mechanism accompanying CCoAOMT mediated O-methylation of CoA-linked substrates.
Structural Elucidation and Description
Alfalfa CCoAOMT is a 28-kD protein consisting of 247 amino acids (EC 2.1.1.104; Inoue et al., 1998
Each monomer (Fig. 3B) consists of a single catalytic domain. This domain exhibits a core / Rossmann fold that provides the binding site for SAM/SAH (Rossmann et al., 1974
Unlike previously characterized plant OMTs, which most likely utilize general base catalysis for activation of the methyl accepting hydroxyl group (Zubieta et al., 2001
By stripping the metal ion from CCoAOMT with EDTA and then replacing the putative Ca2+ ion with Mg2+, Mn2+, or Zn2+, the role of the divalent metal ion was examined. The EDTA-treated enzyme displayed a specific activity only 15% the level of untreated enzyme. Addition of Mg2+, Ca2+, and Zn2+ restored activity to 100% the level of untreated CCoAOMT. Curiously, the divalent cation Mn2+ only restored activity to 35% of untreated CCoAOMT, most likely due to the higher ligand-binding energy of Mn2+ versus the other divalent cations tested (Table I).
Three-dimensional superposition of the CCoAOMT and catechol OMT structures (Fig. 5, A and B) shows a high level of similarity in the core of the enzyme, despite poor sequence similarity. Based on a structure alignment performed with the Dali server, the root mean square deviation between the 183 aligned alpha carbons is 2.4 Å. The Rossmann fold, encompassing the catalytic divalent cation and the SAM/SAH-binding sites, is highly conserved. The overall architectural similarity, the substrate-binding site, and the role of a divalent cation in the catalytic mechanism, structurally, functionally, and evolutionarily relate plant CCoAOMTs and mammalian catechol OMTs. However, the two taxonomically distinct enzyme families adopt different oligomerization states. While CCoAOMT is dimeric, the soluble portion of mammalian catechol OMT is monomeric, and no evidence of dimerization exists for the full-length rat catechol OMT. Unlike previously characterized plant OMTs (Zubieta et al., 2001
With regard to the mechanistically and structurally related catechol OMTs of mammalian origin, other differences between CCoAOMT and catechol OMT occur in the region lying near the CoA-binding site of CCoAOMT, including the N-terminal residues, a Pro-rich loop spanning residues 193 to 211 of CCoAOMT, as well as the loop between positions 237 and 239. This latter loop is shortened with respect to the structurally equivalent loop in catechol OMT that includes Glu-199 involved in substrate recognition in catechol OMT. Remarkably, when superimposing the structures, Glu-199 of catechol OMT resides at an equivalent spatial position to Lys-21 of CCoAOMT. In CCoAOMT, the N-terminal extension and the 193 to 211 and 237 to 239 loops form part of the substrate-binding pocket and likely determine the specificity of CCoAOMT for the CoA-linked substrates. Notably, the regiospecificity and kinetic activity of the recently described CCoAOMT family member characterized from ice plant appears to be influenced by the presence or absence of the amino terminal region, which clearly in CCoAOMT plays a role in recognition of the phenylpropanoid conjugate (Vogt, 2004
Considering the structure and its three-dimensional comparison with catechol OMT, we can suggest a catalytic mechanism based on the metal-mediated deprotonation of the caffeoyl 3-hydroxyl group followed by transmethylation due to the juxtapositioning of a reactive phenolic oxyanion near the reactive methyl group of SAM. The environment around the caffeoyl 3-hydroxyl moiety of the substrate is electropositive due to the positively charged sulfur of SAM and the Ca2+ ion. Most likely, the caffeoyl 3-hydroxyl exists as an oxyanion in order to balance charge in the active site region. Chelation to the metal ion further positions the 3-oxyanion moiety in close proximity to the reactive methyl group of SAM (approximately 3Å). This metal-dependent catalytic mechanism is also postulated for mammalian catechol OMT and related methyltransferases (Vidgren et al., 1994
The role of the residues in CCoAOMT, previously suggested to be important for enzyme activity (Hoffmann et al., 2001
More specifically, based upon a homology model computed based upon low sequence identity with mammalian catechol OMT, Asp-66 was hypothesized to make contact with the adenine moiety of CoA, whereas Gln-69 was hypothesized to bind either the adenine or the phosphate group. The experimental structure of CCoAOMT actually shows no evidence of such an interaction for Asp-66 and reveals that Gln-69 points in the opposite direction to the adenine and CoA phosphate, making any role of Gln-69 in CoA binding unlikely. The importance of these residues in the enzyme activity is most likely due to their proximity to Thr-63, which is involved in the divalent metal ion coordination, and to Met-61, which is involved in substrate binding. The loss of all activity previously observed upon mutating Arg-228 to Thr can be attributed only indirectly to catalysis through structural stabilization and not to a direct role in substrate recognition as previously suggested (Hoffmann et al., 2001 The comparison of the CCoAOMT structure with other known OMT structures (rat catechol OMT, alfalfa IOMT, alfalfa ChOMT, and alfalfa COMT; Fig. 5C) demonstrates, despite the differences related to substrate specificity, a high degree of structural similarity in the SAM-binding region of methyltransferases exists within and between kingdoms. This implies the fundamental conservation of the SAM-binding protein fold throughout evolution. The high degree of sequential divergence between plant OMTs, animal catechol OMTs, and bacterial OMTs does not impact the overall fold but does result in altered oligomerization states, altered modes of recognizing hydroxyl bearing substrates, and most notably, altered catalytic mechanisms accompanying catalytic transfer of a methyl moiety from SAM to a suitably placed methyl acceptor.
Materials Ni2+-nitrilotriacetic acid agarose (NTA) resin was purchased from Qiagen (Valencia, CA). Benzamidine-Sepharose and Superdex-200 FPLC columns were obtained from Amersham Biosciences (Piscataway, NJ). Cryoloops were purchased from Hampton Research (Laguna Niguel, CA).
Alfalfa (Medicago sativa) CCoAOMT was cloned into the Escherichia coli expression vector pET-15b (Novagen, Madison, WI). The CCoAOMT construct was transformed into E. coli BL21(DE3). Transformed E. coli were grown at 37°C in terrific broth containing 100 µg/mL ampicillin until A600 = 1.0. After induction with 0.5 mM isopropyl-
Purified CCoAOMT was dialyzed against 25 mM HEPES, 100 mM NaCl, and 5 mM EDTA for 12 h. The protein was then concentrated to approximately 2 mg/mL. Typical reactions were run in 50-µL volumes containing 250 mM HEPES, pH 7.5; 50 mM NaCl; 0.1 mM adenosyl-L-Met-14C-methyl; 0.1 mM caffeoyl CoA; approximately 50 µg of CCoAOMT; and no added metal or 2 mM Ca2+, Mg2+, Zn2+, or Mn2+. CCoAOMT protein untreated with EDTA was assayed using 50 mM NaCl, 0.1 mM adenosyl-L-Met-14C-methyl, 0.1 mM caffeoyl CoA, approximately 50 µg of CCoAOMT, and 2 mM Mg2+. Reactions were allowed to proceed for 1 h at room temperature after which time 10 µL of 3 M NaOH was added to hydrolyze the thioester bond. After vortexing the solution, 40 µL of 1 M HCl was added to neutralize the NaOH and to protonate the liberated caffeic and ferulic acids. Finally, the 14C-labeled products were extracted with 200 µL of ethyl acetate and subjected to scintillation counting. Specific activity expressed as counts per microgram of CCoAOMT for untreated CCoAOMT assayed in the presence of 2 mM Mg2+ was set to 100% and all other reactions were then referenced to this value.
Crystals of CCoAOMT were grown by vapor diffusion in hanging drops consisting of a 1:1 mixture of protein and crystallization buffer (CCoAOMT: 12.5% [w/v] polyethylene glycol 8000; 0.05 M 3-{[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]amino}-1-propanesulfonic acid, pH 8.5; 0.20 M calcium acetate; and 2 mM DTT; at 15°C). Cryo protectants consisted of 20% (v/v) glycerol, 20% (w/v) polyethylene glycol 8000, 0.2 M calcium acetate, and 0.05 M 3-{[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]amino}-1-propanesulfonic acid, pH 8.5. Crystals were soaked in 1 mM of SAM prior to freezing.
The CCoAOMT structure was determined using x-ray diffraction data collected at 105 K on beamline FIP-BM30A (Roth et al., 2002
Accession Numbers The accession numbers for the sequences shown in Figure 2 are as follows: CCoAOMTs from alfalfa (AAC289731), Populus tremuloides (AAA806511), Vitis vinifera (CAA909691), Eucalyptus gunnii (CAA729111), tobacco (Nicotiana tabacum; AAC499131), parsley (Petroselinum crispum; CAA908941), and Populus kitakamiensis (BAA191021); Ma4OMT from Streptomyces mycarofaciens (Q00719); the soluble part of four animal catechol OMTs from Mus musculus (AAC333341), Rattus norvegicus (CAA782761), Sus scrofa (Q99028), Homo sapiens (AAH119351); and COMT (AAB466231), ChOMT (AAB480591), and IOMT (AAC499281) from alfalfa. The other genes referred to in the text are QOMT from Myxococcus xanthus (AAC441301) and Ma8OMT from Streptomyces glaucescens (P39896).
We thank the staff of the SSRL macromolecular crystallography team, members of the Noel laboratory for technical assistance, and Lynn Gregory at the Institut de Biologie Structurale for her careful proofreading. We also acknowledge the ESRF for provision of synchrotron radiation facilities. Finally, we thank Thomas Vogt of Leibniz-Institute of Plant Biochemistry (Halle) and Milton Stubbs of Martin-Luther-Universität Halle-Wittenberg for communicating their results prior to publication. Received June 25, 2004; returned for revision December 24, 2004; accepted December 28, 2004.
1 This work was supported by the National Science Foundation (grant no. 0236027 to J.P.N.).
2 Present address: European Molecular Biology Laboratory, 38042 Grenoble cedex 9, France. Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.104.048751. * Corresponding author; e-mail noel{at}salk.edu; fax 8584523683.
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Zubieta C, Kota P, Ferrer J-L, Dixon RA, Noel JP (2002) Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase. Plant Cell 14: 12651277 This article has been cited by other articles:
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