From the
Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 and the
Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712
Received for publication, February 24, 2003 , and in revised form, March 14, 2003.
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ABSTRACT |
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INTRODUCTION |
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Perhaps the best characterized member of the latter group, both kinetically and crystallographically, is UDP-galactose 4-epimerase (3, 4). This enzyme plays a key role in the Leloir pathway for galactose metabolism by interconverting UDP-galactose and UDP-glucose. The proposed catalytic mechanism of this epimerase involves several key features: 1) transfer of the hydride from C-4 of the sugar to NAD+ to form NADH and abstraction of the 4'-hydroxyl hydrogen of the sugar by an enzymatic base to yield a 4'-ketopyranose intermediate; 2) rotation of this intermediate by 180° about the phosphoryl-oxygen bond connecting the UDP and sugar moieties; and 3) transfer of the hydride from NADH back to the opposite face at C-4 of the keto-sugar intermediate and protonation of the resulting hydroxyl group. The enzymatic base in UDP-galactose 4-epimerase is thought to be a conserved tyrosine residue (4).
UDP-galactose 4-epimerase belongs to a subclass of NAD(P)-dependent enzymes referred to as the short-chain dehydrogenases/reductases (5). Members of this family contain a characteristic Tyr-XXX-Lys motif in which the conserved tyrosine is thought to play a key role in catalysis. Other proteins belonging to this subfamily include dTDP-D-glucose 4,6-dehydratase (6), GDP-mannose 4,6-dehydratase (7, 8), and ADP-L-glycero-D-manno-heptose 6-epimerase (9), among others. Alignments of the amino acid sequences for these enzymes with the Swiss-Prot data bank indicate that they share at least 20 and 40% sequence identity and similarity, respectively. On the basis of such amino acid sequence alignments another member of the superfamily has recently been identified, namely CDP-tyvelose 2-epimerase (10).
CDP-tyvelose 2-epimerase, hereafter referred to simply as tyvelose epimerase, is involved in the synthesis of tyvelose, a 3,6-dideoxyhexose that occurs in the O-antigens of some types of Gram-negative bacteria (11). Tyvelose is produced via a complex biochemical pathway that employs CDP-D-glucose as the starting ligand. The last step in the pathway, the conversion of CDP-D-paratose to CDP-D-tyvelose, is catalyzed by tyvelose epimerase as outlined in Scheme 1. Interestingly, tyvelose is found in the O-antigens of some pathogens such as Salmonella typhi and Yersinia pseudotuberculosis IVA. In that tyvelose is the major immunological determinant in these bacteria, screening for the tyvelose epimerase gene via PCR amplification is being considered for earlier identification and treatment of S. typhi infections (12).
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Here we describe the cloning, purification, and high-resolution x-ray crystallographic analysis of tyvelose epimerase from S. typhi. Crystals amenable for a high-resolution x-ray investigation of the enzyme were grown in the presence of CDP. The enzyme is a homotetramer displaying 222 symmetry. Each subunit contains 339 amino acid residues and one tightly bound NAD+ moiety. The subunit is distinctly bilobal with an N-terminal region responsible for dinucleotide binding, a C-terminal motif important for CDP positioning, and an active site wedged between these two lobes. Side chain functional groups directly involved in NAD+ binding include Asp-32, Asp-58, Ser-123, and Lys-169 whereas Ser-194, Asn-126, Lys-127, Gln-235, Arg-237, Arg-299, and Asp-302 function in anchoring the CDP moiety into the active site. The x-ray analysis described here defines both the quaternary structure of tyvelose epimerase and its active site geometry, and confirms that the enzyme belongs to the short-chain dehydrogenase/reductase superfamily.
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EXPERIMENTAL PROCEDURES |
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Protein ExpressionFor protein expression, E. coli Rosetta-(DE3)pLysS (Novagen) cells were transformed with the pET28a-tyv plasmid and plated onto LB media supplemented with 30 µg/ml kanamycin. After 16 h, the plates were scraped and the cells were resuspended in LB media to use for the inoculation of 6x 2-liter baffled flasks containing 500 ml of LB plus 30 µg/ml kanamycin and 30 µg/ml chloramphenicol. The cells were grown at 37 °C with aeration to an A600 of
0.4, at which time they were transferred to a 30 °C shaker for 30 min before inducing with 1 mM isopropyl-1-thio-
-D-galactopyranoside. The cells were allowed to grow for an additional 6 h at 30 °C before harvesting by centrifugation at 6000 x g for 8 min. The cell paste was frozen in liquid nitrogen and stored at 80 °C.
Expression of the Selenomethionine-labeled ProteinE. coli Rosetta-(DE3)pLysS (Novagen) cells were transformed with the pET28a-tyv plasmid and plated onto LB media supplemented with kanamycin. Approximately 24 h later, several large colonies were selected to inoculate 500 ml of M9 minimal media supplemented with 30 µg/ml kanamycin and 30 µg/ml chloramphenicol for growth overnight at 37 °C. Subsequently 10 ml of the overnight culture was used to inoculate 3x 2-liter baffled flasks containing 500 ml of M9 minimal media with 5 µg/ml thiamine, 30 µg/ml kanamycin, and 30 µg/ml chloramphenicol. Cultures were grown at 37 °C to an A600 of 0.2. At that point, the temperature of the incubator was adjusted to 30 °C for the remainder of the growth. Cultures were grown to an A600 of
0.75, before each flask was supplemented with 50 mg each of L-lysine, L-threonine, and L-phenylalanine, and 25 mg each of L-leucine, L-isoleucine, L-valine, and L-selenomethionine (13). After 20 additional minutes of growth, the cells were induced with 1 mM isopropyl-1-thio-
-D-galactopyranoside and allowed to grow for 6 h. Cultures were harvested by centrifugation at 6000 x g for 8 min, and the cell paste was frozen in liquid nitrogen for storage at 80 °C.
Protein PurificationAll protein purification steps were carried out on ice or at 4 °C. The cell paste was thawed in 100 ml of cold Ni-NTA1 lysis buffer containing 50 mM NaH2PO4, 300 mM NaCl, and 10 mM imidazole at pH 8.0. Cells were lysed on ice by four cycles of sonication (30 s) separated by 3 min of cooling. Cellular debris was removed by centrifugation at 4 °C for 25 min at 20,000 x g. The clarified lysate was loaded onto a 10-ml Ni-NTA-agarose (Qiagen Inc.) column pre-equilibrated with Ni-NTA lysis buffer. After loading, the column was washed with about 60 ml of Ni-NTA wash buffer (50 mM NaH2PO4, 300 mM NaCl, 20 mM imidazole, pH 8.0), followed by gradient elution of the protein from 20 to 300 mM imidazole in Ni-NTA lysis buffer. Protein-containing fractions were pooled based on SDS-PAGE, and dialyzed against 20 mM HEPPS (pH 8.0) with 200 mM NaCl. The dialyzed protein was concentrated to 23 mg/ml, based on an extinction coefficient of
1.3 ml/(mg cm) as calculated by the program Protean (DNAstar, Inc., Madison, WI).
Molecular Weight DeterminationAnalytical ultracentrifugation was performed by the University of Wisconsin, Madison Biochemistry Instrumentation Facility. Three samples of the purified native tyvelose epimerase at 0.25, 0.5, and 1.0 mg/ml in 10 mM HEPPS (pH 8.0) and 200 mM NaCl were provided for analysis. The experiments were performed with a Beckman Optima XL-A centrifuge and an An 60-Ti rotor at 20 °C using 12-mm double sector charcoal-filled Epson centerpieces. Rotor speeds of 3,000, 7,600, 11,000, and 13,500 rpm were utilized while monitoring the radial position of the sample by absorption of light at 280 nm. The molecular weight from a global fit of 9 data sets containing 1246 points was 154,000 indicating that the quaternary structure of tyvelose epimerase is tetrameric.
Crystallization of Native and Selenomethionine-labeled Tyvelose EpimerasePrior to crystallization, the protein was diluted to 13 mg/ml with 20 mM HEPPS (pH 8.0), and 200 mM NaCl and CDP were added to a final concentration of 5 mM. Potential crystallization conditions were examined with a sparse matrix screen composed of 144 conditions at both room temperature and 4 °C via the hanging drop method of vapor diffusion. Single crystals were observed at room temperature at pH 56 with 10% poly(ethylene glycol) 8000. Refinement of the crystallization conditions led to large single crystals grown at room temperature with precipitant solutions of 46% poly(ethylene glycol) 8000, 250 mM tetramethylammonium chloride, and 100 mM succinate (pH 5.5). Crystals achieved typical dimensions of 0.5 x 0.3 x 0.15 mm in 2 to 3 weeks and belonged to the space group P21 with unit cell dimensions of a = 47.9 Å, b = 167.3 Å, c = 89.4 Å, and
= 105.5°. The solvent content of the crystals was
50%, with one homotetramer in the asymmetric unit.
High Resolution X-ray Data CollectionBoth the native and selenomethionine-substituted protein crystals were flash-frozen in the same manner. Briefly, crystals were harvested from the hanging drop experiments and soaked for several hours to several days in a synthetic mother liquor composed of 1012% poly(ethylene glycol) 8000, 200 mM NaCl, 300 mM tetramethylammonium chloride, 5 mM CDP, and 100 mM succinate (pH 5.5). These crystals were then transferred to 4% ethylene glycol, 14% poly(ethylene glycol) 8000, 325 mM NaCl, 300 mM tetramethylammonium chloride, 5 mM CDP, and 100 mM succinate (pH 5.5) for 30 s, followed by a final transfer to 15% ethylene glycol, 20% poly(ethylene glycol) 8000, 400 mM NaCl, 300 mM tetramethylammonium chloride, 5 mM CDP, and 100 mM succinate (pH 5.5). Subsequently, the crystals were flash-cooled to 150 °C in a stream of nitrogen gas. Frozen crystals were stored under liquid nitrogen until synchrotron beam time became available. X-ray data sets from both the native protein and the selenomethionine-substituted enzyme crystals were collected on a 3 x 3 tiled "SBC3" CCD detector at the Structural Biology Center 19-BM beamline (Advanced Photon Source, Argonne National Laboratory, Argonne, IL). The x-ray data were processed with HKL2000 and scaled with SCALEPACK (14). Relevant x-ray data collection statistics are presented in Table I.
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X-ray Structural AnalysesThe structure of tyvelose epimerase was solved via multiwavelength anomalous dispersion phasing with x-ray data collected from the selenomethionine-substituted protein crystals. The software package SOLVE was utilized to determine and refine the positions of the selenium atoms (15). Visual inspection of the selenium sites with the graphics program TURBO revealed four clusters of atoms related by non-crystallographic 222 symmetry (16). Subsequent non-crystallographic symmetry averaging and solvent flattening with the software package DM resulted in a readily interpretable electron density map calculated to 2.6-Å resolution (17). The averaged map was used to build an initial model of one subunit of tyvelose epimerase, after which this subunit was rotated back into the unit cell to create the full tetramer. This tetramer served as a search model for molecular replacement with the program AMORE against the native x-ray data (18). Alternate cycles of least-squares refinement with the software package TNT (19) and manual model building reduced the R-factor to 17.9% for all measured x-ray data from 30- to 1.5-Å resolution. Relevant least-squares refinement statistics are summarized in Table II. A Ramachandran plot for all nonglycinyl main chain ,
values is displayed in Fig. 1a. In each monomer there are two residues that lie outside of the allowed regions: Ser-163 and Thr-269. The electron density for these residues is unambiguous. Ser-163 is located at the beginning of the sixth
-helix in the N-terminal region whereas Thr-269 lies within a Type III turn delineated by Thr-269 to Asn-272. Neither one of these residues is directly involved in ligand binding. The electron density corresponding to the bound ligands, CDP and NAD+ in Subunit I is shown in Fig. 1b.
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RESULTS AND DISCUSSION |
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Tertiary Structure of the Individual SubunitThe crystals employed in this investigation contained a complete tetramer in the asymmetric unit. The -carbon traces for all of the monomers are virtually identical, however, such that they superimpose with root mean square deviations of 0.4 Å or less. For the sake of simplicity the following discussion will only refer to Subunit I of the coordinate file. As depicted in Fig. 2b, the overall molecular architecture of the tyvelose epimerase subunit can be envisioned as two lobes: the N-terminal region formed by Ala-2 to Gln-200 and Ala-242 to Gly-268 and the C-terminal motif delineated by Phe-201 to His-241 and Thr-269 to Ile-339. The N-terminal motif is dominated by a seven stranded parallel
-sheet defined by Ala-2 to Thr-7, Asp-27 to Asp-32, Glu-53 to Gly-57, Ser-76 to Leu-80, Asn-119 to Ser-123, Asn-186 to Tyr-196, and Ala-263 to Ile-266. There are two additional anti-parallel
-strands formed by Lys-136 to Glu-139 and Tyr-144 to Cys-146 and connected by a Type I turn (Thr-140 to Arg-143). These secondary structural elements of the N-terminal region are connected by a total of seven
-helices (Phe-12 to Ala-21, Thr-40 to Leu-49, Lys-62 to Tyr-72, Met-86 to Asp-91, Pro-93 to Gln-113, Pro-164 to Phe-183, and Ala-242 to Ala-254) and numerous reverse turns. The C-terminal motif is less complicated with three strands of mixed
-sheet (Val-236 to Leu-240, Ser-273 to Ser-275, and Arg-304 to Phe-306), two strands of parallel
-sheet (Phe-227 to Gly-231 and Thr-294 to Leu-296), and four major
-helices (Trp-208 to Glu-218, Leu-276 to Tyr-286, Lys-311 to Ala-316, and Ala-325 to Ile-339). The overall dimensions of the subunit are
50 x 50 x 50 Å.
Binding Sites for NAD+ and CDPShown in Fig. 3 is a close-up view of the active site for the tyvelose epimerase subunit. There are 15 well ordered water molecules located within 3.2 Å of the CDP or NAD+ moieties. The cytosine ring of CDP is hydrogen bonded to the protein via the carbonyl oxygen of Tyr-204 and the peptidic NH of Ser-230. An ordered water molecule is located at 2.9 Å from the amino group of the pyrimidine ring. A strikingly aromatic patch of residues, composed of Tyr-204, Trp-208, Trp-211, and Phe-212, surrounds one side of the cytosine ring. The CDP ribose adopts the C2'-endo conformation and its 3-hydroxyl group is anchored to the protein via the side chains of Asp-302 and Gln-235. Both Arg-237 and Arg-299, through their side chain guanidinium groups, are involved in electrostatic interactions with the -phosphoryl oxygens. Additionally, N
of Arg-237 lies within 3 Å of one of the
-phosphoryl oxygens. Asn-126 and Ser-194 form hydrogen bonding interactions with the other two
-phosphoryl oxygens. The
-phosphoryl group of CDP is situated at
5 Å from the nicotinamide ring of NAD+.
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The nicotinamide ring of the dinucleotide adopts the syn-conformation as typically observed for B-side specific dehydrogenases. Both riboses of the dinucleotide adopt C2'-endo conformations. The adenine ring of NAD+ forms hydrogen bonding interactions with the carboxylate group of Asp-58 and the backbone peptidic NH group of Ile-59. Asp-32 bridges the 2- and 3-hydroxyl groups of the adenine ribose. The ribose 2-hydroxyl group also lies within hydrogen bonding distance to the peptidic NH group of Arg-36. There are four water molecules located within 3.2 Å of the phosphoryl oxygens of the NAD+ ligand. Additionally, the peptidic NH groups of Phe-12 and Leu-13 form hydrogen bonds with OP2 and OP5 of the NAD+, respectively. These residues reside in the first -helix of the Rossmann fold. The 3-hydroxyl group of the nicotinamide ribose lies with 3.2 Å of the backbone carbonyl oxygen of Leu-80, a water molecule, and N
of Lys-169. This interaction between Lys-169 and the dinucleotide is conserved among the members of the short-chain dehydrogenase/reductase family. The 2-hydroxyl group of the nicotinamide ribose is positioned near a water molecule that, in turn, lies within 3 Å of the nicotinamide ring nitrogen. In the short-chain dehydrogenase/reductase family, it has been postulated that Lys-169 activates Tyr-165 that is the ultimate base in the reaction mechanism. The distance between Lys-169 and Tyr-165 in tyvelose epimerase is 4.9 Å, a value that is comparable with that observed in other members of the superfamily. Interestingly, the distance between the nicotinamide ring nitrogen, which carries the positive charge in the oxidized form of the cofactor, and O
of Tyr-165 is 4.3 Å. It is possible that the chemical role of Lys-169 is in proper dinucleotide positioning and not in activation of the conserved tyrosine residue. Regarding the carboxamide moiety of the nicotinamide ring, there is an intramolecular hydrogen bond between its nitrogen and OP4 of the phosphate backbone (2.9 Å). The carbonyl oxygen of the carboxamide group hydrogen bonds with a water molecule and the backbone peptidic NH group of Met-195.
Comparison of Tyvelose Epimerase with UDP-galactose 4-EpimeraseTyvelose epimerase is highly homologous to both UDP-galactose 4-epimerase from E. coli (27% identity and 43% similarity), and human UDP-galactose 4-epimerase (23% identity and 41% similarity). In contrast to tyvelose epimerase, however, both the human and bacterial forms of UDP-galactose 4-epimerase are homodimers. Shown in Fig. 4a is a superposition of the polypeptide chain backbones for the human UDP-galactose 4-epimerase and the tyvelose epimerase subunits. There are only four major differences in conformations between these two enzymes as indicated by the letters AD in Fig. 4a. For example, there is a 7-residue deletion in tyvelose epimerase, relative to UDP-galactose 4-epimerase, starting at Arg-36 and extending to His-56. This particular region is involved in the A/C and B/D interfaces in tyvelose epimerase and thus may be one factor for the differing quaternary states between these two proteins. There is a 16-residue insertion in tyvelose epimerase, defined by Leu-132 to Tyr-153, which forms two anti-parallel -strands that are connected by a Type I turn (Thr-140 to Arg-143). Interestingly, this region in not involved in subunit:subunit contacts nor located near the NAD+ binding site. The functional significance of this insertion in tyvelose epimerase is unknown. The third region of difference occurs as a 6-residue deletion in tyvelose epimerase relative to UDP-galactose 4-epimerase from Gly-197 to Arg-199. This area is not located within the immediate vicinity of the NAD+ or CDP ligands. Finally, there is a 6-residue deletion in tyvelose epimerase from Gly-231 to Val-236, which corresponds to the region defined by Gly-227 to Val-238 in UDP galactose 4-epimerase. In both of these enzymes, this area of polypeptide chain is involved in binding the nucleotide portion of the substrate, either CDP or UDP, in tyvelose epimerase or UDP-galactose 4-epimerase, respectively. Indeed, while the positions of the NAD+ ligands in both enzymes are nearly identical, the locations of the CDP versus UDP moieties are somewhat different as can be seen in Fig. 4a. The
- and
-phosphorus atoms of the CDP versus UDP moieties are shifted by
2 Å. This shift may be a function of the need for the substrate, CDP-paratose, to position differently in the active site of tyvelose epimerase as compared with UDP-glucose (or UDP-galactose) in the active site of UDP-galactose 4-epimerase. Recall that in the reaction mechanism of UDP-galactose 4-epimerase, the inversion of stereochemistry occurs about C-4 of the hexose rather than C-2 as in tyvelose epimerase. Also, paratose is a 3,6-dideoxysugar. Strikingly, in the model of the human UDP-galactose 4-epimerase, the 2'-hydroxyl group of UDP-glucose is hydrogen bonded to Asn-207 whereas the 6'-hydroxyl group lies within 2.6 Å of O
1 of Asn-187. In tyvelose epimerase, these residues have been replaced by Gly-207 and Ser-194, respectively.
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Previous detailed mechanistic investigations of tyvelose epimerase from Y. pseudotuberculosis IVA have suggested that its catalytic mechanism may be reminiscent to that proposed for UDP-galactose 4-epimerase (22). The reaction catalyzed by UDP-galactose epimerase is an epimerization about C-4 of UDP-glucose (or UDP-galactose) as indicated in Scheme 1. Extensive structural investigations in this laboratory have concluded that in the human UDP-galactose 4-epimerase, Tyr-157 functions to initiate the reaction by abstracting the 4'-hydroxyl hydrogen from UDP-glucose (or UDP-galactose) with the concomitant transfer of the hydride at C-4 to the nicotinamide ring of NAD+. Additionally, Ser-132 in the human epimerase is thought to facilitate proton transfer from the sugar 4'-hydroxyl group to O of Tyr-157 possibly via a low barrier hydrogen bond (4). Tyr-157 in human UDP-galactose 4-epimerase is conserved in tyvelose epimerase as Tyr-165 whereas Ser-132 in the human enzyme has been replaced with Thr-125. Both Tyr-165 and Thr-125 occupy similar positions within the active site of tyvelose epimerase as observed for Tyr-157 and Ser-132 in the UDP-galactose 4-epimerase active site region. Assuming that the reaction mechanisms are similar for these two epimerases as suggested by the mechanistic data, it is possible to speculate on the manner in which CDP-paratose or CDP-tyvelose might bind in the active site of the enzyme. Previous studies on the E. coli UDP-galactose 4-epimerase have demonstrated that the binding of the UDP moiety in the protein·NADH·UDP complex is virtually identical to that observed in the protein·NADH· UDP-glucose complex (20, 23). In light of this, a model of CDP-paratose was positioned into the tyvelose epimerase active site as indicated in Fig. 4b. This model was built by following the position of the CDP moiety as experimentally determined in this investigation and rotating the sugar portion to orient its C-2 near C-4 of the nicotinamide ring. In this model, C-2 of paratose is located at
3.7 Å of C-4 of NAD+ and its 2'-hydroxyl group is situated within
3.6 Å of O
of Tyr-165. In the model presented in Fig. 4b, the 4'-hydroxyl group of CDP-paratose lies within hydrogen bonding distance to Thr-125 and possibly to Asn-126. For the model depicted in Fig. 4b, Asn-126 had to be rotated in the active site to avoid overlap with the paratose 4'-hydroxyl group. Indeed, in support of this idea of rotation, Asn-126 demonstrates multiple conformations in the high resolution structure of the protein·NAD+·CDP complex determined here.
For the model of CDP-tyvelose presented in Fig. 4b, a series of rotations was made about the dihedral angles starting at the -phosphorus atom. Accordingly, this model places C-2 of the tyvelose moiety within 3.4 Å of C-4 of the nicotinamide ring and its hydroxyl group within 2.8 Å of O
of Tyr-165. The tyvelose 4'-hydroxyl group is now located within hydrogen bonding distance to Gln-206. In the models presented in Fig. 4b for the two sugar ligands, the positions of their
-phosphorus atoms differ by
1.0 Å. Support for this type of rotation in the active site is demonstrated by the high resolution structural analysis of the E. coli UDP-galactose 4-epimerase complexed with either UDP-glucose or UDP-galactose (24). In that study, significant changes were observed between the two bound substrates beginning at the
-phosphorus atoms where their positions differed relative to one another by 0.51 Å.
The putative binding mode depicted in Fig. 4b can be tested by preparing and crystallizing abortive complexes of tyvelose epimerase with NADH and either CDP-paratose or CDP-tyvelose. These studies are presently underway. Regardless of the outcome of these investigations, it can be concluded that rotation of a 2'-ketopyranose intermediate in the active site of tyvelose epimerase must be different from that proposed for UDP-galactose 4-epimerase because of the difference in its regioselectivity. In UDP-galactose 4-epimerase, the putative 4'-ketopyranose intermediate displays a pseudo-C2 axis, which is not present in a 2-ketose intermediate. As such, a more complicated set of rotations about the phosphoryl backbone of the CDP-2'-ketopyranose intermediate must occur to present the opposite side of the oxidized sugar back to the reduced NADH for subsequent hydride transfer.
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FOOTNOTES |
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* This work was supported in part by National Institutes of Health Grants DK47814 (to H. M. H.) and GM35906 (to H.-w. L.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
¶ To whom correspondence should be addressed. Tel.: 608-262-4988; Fax: 608-262-1319; E-mail: Hazel_Holden{at}biochem.wisc.edu.
1 The abbreviations used are: Ni-NTA, nickel-nitrilotriacetic acid; HEPPS, N-(2-hydroxyethyl)piperazine-N'-3-propanesulfonic acid.
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ACKNOWLEDGMENTS |
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REFERENCES |
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