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J. Biol. Chem., Vol. 275, Issue 32, 24608-24612, August 11, 2000

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Crystal Structure of dTDP-4-keto-6-deoxy-D-hexulose 3,5-Epimerase from Methanobacterium thermoautotrophicum Complexed with dTDP^*

Dinesh Christendat^§¶, Vivian Saridakis^§, Akil Dharamsi^§**, Alexei Bochkarev, Emil F. Pai^§, Cheryl H. Arrowsmith^§§§, and Aled M. Edwards^§¶§§¶¶

From the  Division of Molecular and Structural Biology, Ontario Cancer Institute, Toronto, Ontario M5G 2M9, Canada, the ^§ Department of Medical Biophysics, ^¶ Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5W 1L6, Canada, ^** Integrated Proteomics Inc., Toronto, Ontario M5G 2M9, Canada, and the  Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, BRC-466, Oklahoma City, Oklahoma 73190

Received for publication, April 9, 2000, and in revised form, May 22, 2000

	ABSTRACT

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS AND DISCUSSION REFERENCES

Deoxythymidine diphosphate (dTDP)-4-keto-6-deoxy-D-hexulose 3,5-epimerase (RmlC) is involved in the biosynthesis of dTDP-L-rhamnose, which is an essential component of the bacterial cell wall. The crystal structure of RmlC from Methanobacterium thermoautotrophicum was determined in the presence and absence of dTDP, a substrate analogue. RmlC is a homodimer comprising a central jelly roll motif, which extends in two directions into longer -sheets. Binding of dTDP is stabilized by ionic interactions to the phosphate group and by a combination of ionic and hydrophobic interactions with the base. The active site, which is located in the center of the jelly roll, is formed by residues that are conserved in all known RmlC sequence homologues. The conservation of the active site residues suggests that the mechanism of action is also conserved and that the RmlC structure may be useful in guiding the design of antibacterial drugs.

	INTRODUCTION

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS AND DISCUSSION REFERENCES

Proteins whose expression and activity are restricted to prokaryotes are attractive antibiotic targets. The comparative analysis of comprehensive genome data bases has uncovered a large set of such proteins, which includes enzymes involved in bacterial-specific intermediary metabolism and those involved in the biosynthesis of the bacterial cell wall. The bacterial cell wall comprises a large number of carbohydrates that are not found in mammalian cells, one of which is the activated form of L-rhamnose, dTDP-L-rhamnose. dTDP-L-rhamnose is found in the O-antigen of many Gram-negative bacteria and is a common constituent of cell wall polysaccharides. dTDP-L-rhamnose is synthesized from -D-glucose 1-phosphate by a set of four bacterial-specific enzymes, called RmlA through D, whose sequences are highly conserved between different organisms. RmlA, glucose-1-phosphate thymidylyltransferase, catalyzes the synthesis of dTDP-D-glucose from dTTP and -D-glucose 1-phosphate. The next enzyme in the pathway, dTDP¹-D-glucose 4,6-dehydratase (RmlB) reduces dTDP-D-glucose to dTDP-4-keto-6-deoxy-D-glucose in an NADH-dependent reaction. RmlC, dTDP-4-keto-6-deoxy-D-hexulose 3,5-epimerase, then converts dTDP-4-keto-6-deoxy-D-glucose to dTDP-4-keto-L-rhamnose. Finally, RmlD, dTDP-4-keto-L-rhamnose reductase, reduces dTDP-4-keto-L-rhamnose to dTDP-L-rhamnose in an NADPH-dependent reaction (1, 2).

The enzymatic mechanism of dTDP-L-rhamnose biosynthesis began to be elucidated more than 30 years ago. More recent studies have focused on the molecular genetics and structural biology of the corresponding enzymes (1, 2). In this study, we report the crystal structures of the apo and a ligand-bound form of the RmlC homologue from Methanobacterium thermoautotrophicum, an organism that is one of the target organisms in our structural proteomics effort. Structural analysis of RmlC has uncovered significant structural homology to concanavalin A and has allowed us to hypothesize a mechanism for the dTDP-4-keto-6-deoxy-D-glucose epimerization reaction.

	EXPERIMENTAL PROCEDURES

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS AND DISCUSSION REFERENCES

Protein Expression and Purification-- The RmlC gene from M. thermoautotrophicum genomic DNA was amplified by polymerase chain reaction and cloned into the pET15b expression vector (Novagen). Recombinant dTDP-4-keto-6-deoxy-D-hexulose epimerase (RmlC) was expressed in Escherichia coli BL21 Gold (DE3) cells (Stratagene) harboring a plasmid encoding three rare E. coli tRNA genes (AGG and AGA for Arg and ATA for Ile). Conditions for protein expression and purification were similar to those in the Qiagen protein purification handbook except that a heat step (55 °C for 10 min) and a centrifugation step were introduced after cell lysis to remove most contaminating E. coli proteins. Purified RmlC was dialyzed against 10 mM HEPES and 500 mM NaCl and concentrated to 10 mg/ml using BioMax concentrators (Millipore). For the preparation of selenomethionine (Se-Met) protein, RmlC was expressed in a methionine auxotroph strain B834(DE3) (Novagen) and purified under the same conditions as native RmlC with the addition of 5 mM -mercaptoethanol in all buffers.

Gel Filtration-- Gel filtration of RmlC was performed with a Superdex 200 prep 16/60 (Amersham Pharmacia Biotech) column equilibrated with 10 mM HEPES and 500 mM NaCl using high performance liquid chromatography (LKB-Wallac). Protein standards included aldolase, bovine serum albumin, ovalbumin, and cytochrome c. Chromatography was performed at 4 °C at a flow rate of 0.5 ml/min.

Crystallization-- An initial crystallization condition was obtained with a sparse crystallization matrix (Hampton Research Crystal Screen^TM I) using the hanging drop vapor diffusion technique. This condition was modified slightly by varying the pH and concentration of polyethylene glycol and yielded crystals suitable for native and MAD data collection. The best crystals grew in 10% polyethylene glycol 4000 and 100 mM sodium acetate at pH 4.6 in 2-4 days at 22 °C using hanging drops (3 µl:3 µl protein:precipitant ratio). They reached approximate dimensions of 600 × 200 × 200 microns³. These crystals belonged to space group C2 with unit cell dimensions 67.7 Å × 53.1 Å × 51.7 Å and  = 96.6°. There was a single molecule in the asymmetric unit and the Matthews coefficient was 2.3 Å³/dalton resulting in an estimated solvent content of 46%. Soaking of RmlC crystals was carried out in 10 mM dTDP with 10% polyethylene glycol 4000 and 100 mM sodium acetate at pH 4.6 for 4 h.

X-ray Diffraction and Structure Determination-- The structure of RmlC was determined by the MAD method using selenium as the anomalous scatterer. A three-wavelength MAD experiment was performed at the BioCARS 14BMD beamline at the Advanced Photon Source. The high resolution data of the native crystal were also collected with the BioCARS 14BMD beamline. The MAD and native data were processed and scaled with the DENZO/SCALEPACK (3) suite of programs. Three selenium sites were located using SOLVE (4) and refined using PHASES (5). Solvent flattening was done using PHASES. Model building was done with O (6). Crystallography and NMR system (7) was used for refinement with multiple rounds of minimization, simulated annealing, B-group, and individual B-factor refinement followed by manual rebuilding. Most of the water molecules were picked using crystallography and NMR system and additional ones were manually added after manual verification using O. The water molecules were picked using the following criteria in O: a peak of at least 2.5  on an F_o  F_c map, a peak of at least 1.0  on a 2F_o  F_c map, and reasonable intermolecular interactions. The crystallographic data collection and refinement statistics are given in Tables I and II, respectively.

View this table: [in this window] [in a new window]   Table I Summary of data collection statistics Numbers in parentheses represent values in the highest resolution shell (native 1.55-1.50 Å; SeMet 2.07-2.00 Å; dTDP 1.81-1.75 Å). Rsym = |I I|/I, where I is the observed integrated intensity, I is the average integrated intensity obtained from multiple measurements, and the summation is over all observed reflections.

View this table: [in this window] [in a new window]   Table II Summary of refinement statistics R and Rfree = | |Fo|  |Fc| |/|Fo|, where |Fo| is the observed structure factor amplitude and |Fc| is the calculated structure factor amplitude.

	RESULTS AND DISCUSSION

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS AND DISCUSSION REFERENCES

Structure Determination-- The structure of selenomethionine-enriched RmlC was determined by the MAD method and refined against 1.5 Å resolution data to a working R-factor of 0.183 and a free R-factor of 0.211. The refined apo model contains 183 amino acids (residues 3-185) and 127 water molecules (Fig. 1). The electron density of the apo form, which was used to build the model, is of excellent quality except for the loop between residues 140 and 144. The dTDP complex model was refined against 1.75-Å resolution data to a working R-factor of 0.195 and a free R-factor of 0.224. This model contains 183 amino acid residues, 119 water molecules, and one molecule of dTDP (Fig. 1). The first two amino acids at the N terminus are not visible in the electron density map in either model. PROCHECK (8) was used to evaluate the stereochemistry of both of the refined models, which showed that more than 90% of the residues are in the allowed region and only one amino acid (Glu-68) was in the disallowed regions, because it is present in a  turn between 6 and 7.

View larger version (40K): [in this window] [in a new window]   Fig. 1.   A, ribbon diagram of an RmlC subunit with a ball-and-stick model of complexed dTDP. The jelly roll structural motif is shown by the green and red -strands. The secondary structure elements are labeled as depicted in the text. This figure was prepared using Molscript (13) and Raster3D (14). B, stereo view of the Ca trace of a subunit of RmlC. The numbers refer to the amino acid residues.

Overview of the Structure-- RmlC is a homodimer; this was confirmed by gel filtration analysis (data not shown). The monomer comprises thirteen -strands and three short -helices (Fig. 1). Eight of the -strands are arranged in a central eight-stranded antiparallel -sheet (strands 5A to 12A) that resembles a jelly roll (Fig. 1). Four other strands 1A, 2A, 3B, and 4B (from subunits A and B) extend from strands 5A, 7A, 10A, and 11A from the jelly roll to form an eight-stranded anti-parallel -sheet. A second -sheet is formed by 13A aligned in an antiparallel manner with strands 6A, 8A, 9A, and 11A (Fig. 2). The helices are located on the periphery of the molecule. Helix 1 packs against strand 1 from the N-terminal -sheet. Helices 2 and 3 flank the carboxyl terminus of the subunit and are also involved in important crystal packing interactions. Helix 2 also contributes to the active site of the same subunit.

View larger version (65K): [in this window] [in a new window]   Fig. 2.   Overview of the dimeric structure of RmlC. Ribbon diagram of the RmlC dimer with a ball-and-stick model of complexed dTDP. Each subunit is colored differently. A, 2-fold axis of symmetry in the plane. B, rotation of A by 90° in the plane.

The dimer interface is formed by an extensive set of hydrophobic and electrostatic contacts between 3 and 5, 7 and 7, and 1 and 5. Some of these ionic interactions include Arg-61 to Asp-24 via a water molecule and the formation of two salt bridges (Glu-52 to Arg-76 and Asp-50 to Lys-134). Hydrophobic interactions occur between residues Phe-33 Ala-36, Tyr-28, Arg-26 (aliphatic side chain), Val-48, Val-59, Ile-78, and Leu-138 at the subunit interface. These interactions result in a total buried surface area of 3,042 Å² out of a total of 16,306 Å² for the dimer.

A search for structural homologues using the program DALI (9) revealed that RmlC is homologous to concanavalin A, phosphomannose isomerase, and arabinose operon regulatory protein (AraC). The nearest structural neighbor is concanavalin A, which has a Z-score of 6.4 and root mean square deviation (r.m.s.d.) of 1.8 Å over 87 out of 178 C atoms. The overall core topology of all these molecules is similar to the jelly roll structural motif.

Location of the Active Site-- Residues involved in substrate binding and catalysis were identified by determining the structure of RmlC in the presence of a substrate analogue, dTDP. The electron density map of the complex revealed a well ordered dTDP with high occupancy (Fig. 3). The substrate-binding site is located in the center of a cavity formed by the jelly roll structural motif (which is at the middle of one face of one subunit) (Fig. 2). Residues from -strands 3 and 4 from one subunit combine with -strands 5, 6, 11, and 12 from the other subunit to form a complete active site. The active site is open at the center of each subunit to permit entry and exit of the ligand through the B-face (Fig. 2). The active site is lined with a number of charged residues (Gln-49, Asp-84, Asp-144, Asp-172, Glu-31, Lys-73, Lys-171, Glu-52, Arg-26, Arg-61, His-64, His-120, and Cys-135) and a number of residues with hydrogen-bonding potentials (Ser-53, Ser-55, Ser-169, Gln-49, Glu-3 and Asn-51), which together comprise a potential network for substrate binding and catalysis. The active site is also lined with aromatic residues (Trp-175, Phe-29, Phe-122, Tyr-133 and Tyr-139), which provide favorable environments for the base moiety of dTDP and potentially for the sugar moiety of the substrate (Fig. 4).

View larger version (98K): [in this window] [in a new window]   Fig. 3.   A, stereo representation of a sigmaA weighted 2Fo  Fc electron density map of the apo model after refinement at 1.5 Å. B, stereo representation of a sigmaA weighted 2Fo  Fc electron density map of the dTDP molecule as bound in the complex with RmlC after refinement at 1.75 Å. Both maps have been contoured at the 1 level.

View larger version (31K): [in this window] [in a new window]   Fig. 4.   A detailed view of the active site of RmlC. A, residues involved in binding dTDP and the location of the His-64-Asp-172 catalytic dyad are shown. Residues are color-coded based on whether they originate from subunit A (yellow) or B (blue), and the catalytic triad is colored green. B, a schematic two-dimensional structure of the active site of RmlC is shown. Residues and water molecules interacting with complexed dTDP are shown.

Comparison between Apo- and dTDP-bound dTDP-4-keto-6-deoxy-D-hexulose Epimerase-- The structure of a subunit of the apo form of RmlC is very similar to that of the dTDP-bound enzyme with an overall r.m.s.d. of 0.33 Å for 183 C atoms. There are, however, some notable differences between the apo- and dTDP-enzymes. The most prominent differences occur within residues 140-144, which are visible in the presence of dTDP. In the presence of the ligand, this loop becomes ordered, closing off a portion of the active site. This loop may be important in regulating the passage of the substrate/product into and out of the active site and may serve to keep the external solvent molecules away from the active site.

Substrate Binding-- The dTDP portion of dTDP-4-keto-6-deoxy-D-hexulose anchors the substrate in the active site of the enzyme. dTDP binds between strands 5, 6, 11, and 12 of one subunit and 3 and 4 of the other subunit. Aromatic stacking is observed between Tyr-139 and Phe-29 and the base of dTDP. In fact, the electron density of the side chains of Tyr-133, Tyr-139, and Lys-171 was observed only in the presence of dTDP. Tyr-139 stacks against the base moiety of dTDP and Lys-171 makes ionic interactions with an oxygen of the -phosphate of dTDP through a water molecule. The base of dTDP is bound in an anticonformation relative to the ribose ring (Fig. 4) by hydrogen bonding to Glu-31B and Gln-49A. The diphosphate portion of dTDP is securely anchored to the protein by ionic interactions between the oxygens of the phosphates with Arg-61A and Arg-26B. In addition to these interactions, there are also a number of interactions between the phosphate oxygens and the enzyme, which are mediated by water molecules (waters 1035, 1036, 1071, and 1095).

Model for Enzymatic Mechanism-- The use of three-dimensional structural information to generate hypotheses about reaction mechanisms and protein function is likely to be a common occurrence in structural genomics projects, which will provide structural information often in the absence of the corresponding biochemical information. In this instance, a possible reactive center(s) for the epimerization of hexulose by RmlC was determined by analyzing the three-dimensional structure and by applying distance constraints based on existing mechanisms of epimerization (10, 11). Sugar phosphate epimerization centers are commonly about 5-7 Å away from the phosphorous atom of the -phosphate (11). Within hydrogen-bonding distances from the epimerization centers, we identified a number of ionizable groups (His-64, His-120, Asp-172, Asp-84, and Lys-73) that are able to participate in acid/base chemistry. Both His-64 and His-120 are strategically placed in the active site such that they are proposed to be within hydrogen-bonding distance from the epimerization sites of the hexulose moiety of the substrate. Interestingly, the -imine of His-64 is hydrogen-bonded to one of the carboxylates of Asp-172 and similarly for His-120 with Asp-84. Interactions between His and Asp residues of this nature were observed in the active site of mandelate racemase (MR) where they functioned as catalytic dyads in the acid/base mechanism (12). There are also a number of well ordered water molecules occupying this region of the active site and they are within hydrogen-bonding distance to the hexulose moiety of the substrate. These water molecules could potentially be involved in proton exchange with acidic groups in the active site and may even participate in proton transfer to the enolate intermediate of hexulose.

Conservation of Function-- To examine the generality of the proposed reaction mechanism, we examined if the residues proposed to be important for binding and catalysis were conserved. The sequences of 17 randomly selected members of the RmlC family were aligned. Thirty residues were conserved in all sequences (Fig. 5). Nine of these charged residues (Arg-26, Glu-31, Arg-61, His-64, Lys-73, Asp-84, His-120, Lys-171, and Asp-172) and are located in the active site. Another highly conserved region, which forms strand 6 (residues V⁵⁹XRGLHZQ⁶⁶, where X is hydrophobic and Z is aromatic), forms the base of the active site (where hexulose would be predicted to be positioned in the reaction). Two of the residues in strand 6, Arg-61 and His-64 are predicted to be involved in substrate binding and the hypothesized catalytic reaction of hexulose epimerization, respectively. Another conserved residue in this region is Gly-62 whose peptide bond is in the cis-conformation. Since this is an energetically unfavorable conformation it may indicate that Gly-62 is required to orient catalytic residues found on 6 in the active site. Notably, the set of invariant residues are found in the sequences of RmlC homologues from many pathogenic bacteria and others, suggesting that the architecture of the active site is also conserved and that this structure might be used to guide the development of antibacterial drugs.

View larger version (99K): [in this window] [in a new window]   Fig. 5.   Alignment of RmlC amino acid sequences indicating the location of conserved amino acids. Proposed substrate binding and catalytic residues are colored red. Alignment analysis was generated using ClustalW (15) at the European Bioinformatics Institute server.

	ACKNOWLEDGEMENTS

We thank the staff of BioCARS for their help during data collection at Sector 14 of the Advanced Photon Source. We thank Ashleigh Tuite for help during crystallization, Steven Beasley for help with protein purification, and Matthew Kimber for helpful discussions.

	Addendum

While this manuscript was under review, the structure of RmlC from Salmonella typhimurium was published (16).

	FOOTNOTES

^* Use of the Advanced Photon Source was supported by the United States Department of Energy, Basic Energy Sciences, Office of Science, under Contract W-31-109-Eng-38. Use of the BioCARS Sector 14 was supported by the National Institutes of Health, National Center for Research Resources, under Grant Number RR07707.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The atomic coordinates and stucture factors (1EP0 and 1EPZ, for the native protein and its complex with dTDP, respectively) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

Supported by the Banting and Best Institute fellowship.

^§§ Medical Research Council of Canada Scientists.

^¶¶ To whom correspondence should be addressed: Ontario Cancer Institute, 610 University Ave., Toronto, Ontario M5G 2M9, Canada. Tel.: 416-946-3435; Fax: 416-946-6529; E-mail: aled.edwards@ utoronto.ca.

Published, JBC Papers in Press, May 25, 2000, DOI 10.1074/jbc.C000238200

	ABBREVIATIONS

The abbreviations used are: dTDP, deoxythymidine diphosphate; RmlB, dTDP-D-glucose 4,6-dehydratase; RmlC, dTDP-4-keto-6-deoxy-D-hexulose 3,5-epimerase; RmlD, dTDP-4-keto-L-rhamnose reductase; MAD, multiwavelength anomalous dispersion.

	REFERENCES

TOP ABSTRACT INTRODUCTION EXPERIMENTAL PROCEDURES RESULTS AND DISCUSSION REFERENCES

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This Article Abstract Full Text (PDF) All Versions of this Article: 275/32/24608    most recent C000238200v1 Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Christendat, D. Articles by Edwards, A. M. Search for Related Content PubMed PubMed Citation Articles by Christendat, D. Articles by Edwards, A. M. Social Bookmarking                      What's this?