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Originally published In Press as doi:10.1074/jbc.M400291200 on March 8, 2004

J. Biol. Chem., Vol. 279, Issue 20, 21478-21488, May 14, 2004
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Structural Studies of the Catalytic Reaction Pathway of a Hyperthermophilic Histidinol-phosphate Aminotransferase*

Francisco J. Fernandez{ddagger}§, M. Cristina Vega{ddagger}§, Frank Lehmann{ddagger}, Erika Sandmeier¶, Heinz Gehring¶, Philipp Christen¶, and Matthias Wilmanns{ddagger}||

From the {ddagger}EMBL incare Deutsches Elektronen-Synchrotron, Notkestrasse 85, Building 25A, D-22603 Hamburg, Germany and Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland

Received for publication, January 12, 2004 , and in revised form, February 24, 2004.


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 EXPERIMENTAL PROCEDURES
 RESULTS
 DISCUSSION
 REFERENCES
 
In histidine biosynthesis, histidinol-phosphate aminotransferase catalyzes the transfer of the amino group from glutamate to imidazole acetol-phosphate producing 2-oxoglutarate and histidinol phosphate. In some organisms such as the hyperthermophile Thermotoga maritima, specific tyrosine and aromatic amino acid transaminases have not been identified to date, suggesting an additional role for histidinol-phosphate aminotransferase in other transamination reactions generating aromatic amino acids. To gain insight into the specific function of this transaminase, we have determined its crystal structure in the absence of any ligand except phosphate, in the presence of covalently bound pyridoxal 5'-phosphate, of the coenzyme histidinol phosphate adduct, and of pyridoxamine 5'-phosphate. The enzyme accepts histidinol phosphate, tyrosine, tryptophan, and phenylalanine, but not histidine, as substrates. The structures provide a model of how these different substrates could be accommodated by histidinol-phosphate aminotransferase. Some of the structural features of the enzyme are more preserved between the T. maritima enzyme and a related threonine-phosphate decarboxylase from S. typhimurium than with histidinol-phosphate aminotransferases from different organisms.


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
EXPERIMENTAL PROCEDURES
 RESULTS
 DISCUSSION
 REFERENCES
 
Pyridoxal 5'-phosphate (PLP,1 vitamin B6) exhibits a unique property to form covalent adducts with many amino acids and, as such, is one of the most ubiquitously accepted cofactors. Depending on the local geometry of the active site and the orientation of the adduct, a proton, a carboxylate group, or a side chain may be eliminated, leading to racemization, transamination, decarboxylation, or to other more complex reactions (1-3). PLP-containing enzymes belong to at least four independent evolutionary families. The most widely occurring {alpha}-family consists of homodimeric enzyme units with a molecular mass of about 2 x 45 kDa, which may compose larger oligomeric assemblies. Each protomer consists of a large domain, comprising a seven-stranded {beta}-sheet core, and a small domain that includes a five-stranded {beta}-sheet. Topologically, the small domain is formed by two sequence segments N- and C-terminal to the large domain. This family can be further subdivided in classes Ia and Ib (2, 4). In aminotransferases belonging only to class Ia, large conformational shifts of the small domain are observed upon substrate binding. In class Ib aminotransferases, conformational shifts during catalysis are restricted to an N-terminal flexible segment referred to as "arm motif." The sequence and length of this motif vary highly among different members of class I PLP enzymes.

T. maritima L-histidinol-phosphate aminotransferase (tmHspAT, EC 2.6.1.9 [EC] ) belongs to class Ib of PLP-dependent aminotransferases. It catalyzes the seventh step in the histidine biosynthesis pathway, a transamination reaction in which the {alpha}-amino group of L-glutamate is transferred to 3-(imidazole-4-yl)-2-oxo-propyl phosphate, yielding L-histidinol phosphate (Hsp) and 2-oxoglutarate (Fig. 1). In addition, biochemical and genetic evidence supports the participation of HspAT in the final steps of tyrosine and phenylalanine biosynthesis by converting 4-hydroxyphenylpyruvate to tyrosine and phenylpyruvate to phenylalanine by transamination (5, 6). Under physiological conditions, these reactions may be catalyzed by three other enzymes, besides HspAT, tyrosine transaminase (EC 2.6.1.5 [EC] ), aromatic-amino-acid transaminase (EC 2.6.1.57 [EC] ), and aspartate transaminase (EC 2.6.1.1 [EC] ). Phylogenetic tree analysis revealed close sequence similarity of these transaminases as well as a more distant relation between these sequences and that of HspAT (2). The same analysis, however, has displayed a more closely related sequence similarity between HspAT and L-threonine-O-3-phosphate decarboxylase (CobD), despite the change in reaction specificity, than between that of HspAT and other transaminases. Indeed, current genome data bases contain sequences that are annotated as HspAT and CobD as exhibiting more than 90% identity (possibly because of annotation errors), indicating that it may be difficult to discriminate between HspAT and CobD activities based solely on sequence comparisons. Analysis of the presently available crystal structures of HspAT from Escherichia coli and of CobD from Salmonella typhimurium (sCobD) confirmed the close relation between these two enzymes (7-9). Small structural changes in the active site of sCobD, compared with that of tmHspAT, appear to be sufficient to force the carboxylate group of the substrate L-threonine-O-3-phosphate into an orientation that is orthogonal to the coenzyme imine {pi}-electron system, directing the overall reaction into decarboxylation rather than transamination (10).



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  		FIG. 1.
Scheme of the proposed mechanism for the transamination reaction catalyzed by tmHspAT. Crystal structures of tmHspAT have been determined in the absence of any ligand except phosphate (tmHspAT), in the presence of PLP or internal aldimine 1a (tmHspAT·PLP), in the presence PLP and Hsp forming the Hsp-PLP adduct 5 (tmHspAT·Hsp-PLP), and in the presence of PMP 6a (tmHspAT·PMP). L-Histidinol phosphate 1b must be deprotonated to form the Michaelis-Menten complex with tmHspAT·PLP. The reversible scheme is shown opposite to the reaction catalyzed in histidine biosynthesis in accordance with conventions in recent reviews (2, 3). The absorption maximum for each of the intermediates is shown in parentheses, with the exception of the proposed gem-diamino intermediate 2, which does not have a pronounced absorption maximum between 300 and 600 nm (45).

 
We have determined the crystal structure of HspAT from the hyperthermophile Thermotoga maritima (tmHspAT) that is found in marine sediments at about 80 °C (11). In contrast to E. coli and S. typhimurium, the T. maritima genome neither contains a gene encoding a tyrosine transaminase (EC 2.6.1.5 [EC] ) nor an aromatic-amino-acid transaminase (EC 2.6.1.57 [EC] ) (12), raising the question of whether tmHspAT exhibits a broad substrate specificity. Our kinetic data on purified tmHspAT acting on aromatic amino acid substrates support this expectation. To monitor potential structural changes during catalysis, we have solved the tmHspAT crystal structure in four different states, including the apo form, the internal aldimine form, the ketimine intermediate, and the pyridoxamine 5'-phosphate form. The data demonstrate that in order for T. maritima to adapt to its specific living conditions, HspAT has retained its transamination function but has required extensive molecular alterations, in comparison to the structural requirements for changing its reaction specificity (from transamination to decarboxylation) within closely related organisms (E. coli and S. typhimurium).


   EXPERIMENTAL PROCEDURES
TOP
 ABSTRACT
 INTRODUCTION
 EXPERIMENTAL PROCEDURES
RESULTS
 DISCUSSION
 REFERENCES
 
Protein Expression and Purification—The tmHspAT gene (TM1040) encoding full-length tmHspAT (residues 1-335) was amplified by standard PCR techniques and subcloned into the pETM11 vector, which contains an N-terminal histidine tag and a TEV (tobacco etch virus) protease cleavage site (ENLYF(Q/G)A) between the NcoI and HindIII sites. The PCR oligonucleotides are as follows: sense primer for full-length tmHspAT, 5'-CATCCCCATGGGCCGTCGATTTGATTGCAAAGAG-3'; antisense primer, 5'-GACAAGCTTATGTCATTTGAACACCTCCAGTTCTC-3' (NcoI and HindIII sites in boldface type). Clones were confirmed by sequencing.

For native expression, cultures of E. coli BL21(DE3) containing the tmHspAT construct were grown in 1 liter of LB medium at 37 °C to A600 = 0.6, induced with 1.0 mM isopropyl-1-thio-{beta}-D-galactopyranoside at the same temperature, and harvested after 4-5 h. For SeMet incorporation, tmHspAT was expressed in the methionine auxotroph strain E. coli B834(DE3). Cultures of E. coli B834(DE3) were grown at 37 °C in 1 liter of minimal medium supplemented with 50 µg/ml L-methionine until A600 = 0.6-0.8, starved in 1 liter of mineral medium at 4 °C for 3 h, re-equilibrated at 37 °C for 30 min, and then induced with 1.0 mM isopropyl-1-thio-{beta}-D-galactopyranoside. The culture was harvested after 4-6 h. The yields of native and SeMet protein were in the range of ~25-30 mg/liter culture.

Native and SeMet tmHspAT were purified in a similar fashion. Wet cell pellets were washed once in phosphate-buffered saline buffer, resuspended in 20 ml of lysis buffer (50 mM Tris-HCl (pH 8.0), 300 mM NaCl, 5 mM imidazole, 10 mM {beta}-mercaptoethanol, and 0.2% (w/v) CHAPS) per liter of culture, and disrupted by heat shock (80 °C, 10 min). The supernatant was clarified by ultracentrifugation (Sorvall SS34 rotor, 23 krpm, 4 °C, 1 h) and filtered through a 0.22-µm membrane. tmHspAT was purified by nickel-chelating metal affinity chromatography, using a column volume of 3 ml of nickel-nitrilotriacetic acid resin (Novagen) per liter of expression culture in gravity-flow mode. Impurities were washed off the column by successively applying 20 volumes of lysis buffer, 5 volumes of lysis buffer plus 15 mM imidazole, and 5 volumes of lysis buffer plus 1 M NaCl. The protein was eluted in lysis buffer plus 250 mM imidazole. The N-terminal His tag introduced by the pETM11 vector was cleaved off with 1:50 (w/w) TEV protease in 20 mM Tris-HCl (pH 8.0), 50 mM NaCl, 10 mM {beta}-mercaptoethanol, and removed by loading the protease digest over 1 ml of freshly cast resin. The eluate, containing 95% pure tmHspAT as judged by SDS-PAGE, was further purified by anion exchange chromatography on a 10-ml Mono Q column (Amersham Biosciences). tmHspAT eluted with a 0.1-0.5 M NaCl gradient. Fractions containing tmHspAT were pooled, dialyzed against storage buffer (10 mM HEPES (pH 7.5), 10 mM dithiothreitol, 2 mM EDTA), and concentrated in Centricon 30 kDa devices (Millipore) to a final concentration of 35 mg/ml as determined by the Bradford method.

Removal of PLP—tmHspAT was purified as a mixture of the PLP- and PMP-containing forms, which are spectroscopically distinct. Pure tmHspAT·PLP was obtained by dialysis against storage buffer supplemented with 1 mM {alpha}-oxoglutaric acid at 35 °C overnight. The apo form of tmHspAT was prepared by incubating purified protein with a solution containing 10 mM L-glutamic acid, 1 M potassium phosphate (pH 7.0) at 50 °C overnight, followed by extensive buffer exchanges at 35 °C against 10 mM Tris-HCl, 5 mM dithiothreitol (pH 8.0) (8). The proportion of tmHspAT without PLP after this treatment was assessed by the ratio of absorbance at 327 and 427 nm.

X-ray Crystallography—Single crystals of tmHspAT·PLP suitable for x-ray diffraction analysis were obtained under a variety of conditions in the presence of low molecular weight polyethylene glycol and pH ranging from 5.0 to 6.0. Crystals were grown by the sitting-drop vapor diffusion method at 20 °C by assembling 1 µl of tmHspAT·PLP solution with 1 µl of reservoir solution, which also served as cryoprotectant. SeMet tmHspAT·PLP crystals grew optimally in 50% (v/v) ethylene glycol, 5% (w/v) PEG1000, sodium acetate (pH 5.1), developing plate-shaped crystals to a maximum size of 1.0 x 0.2 x 0.1 mm3 within 2-3 weeks. Native tmHspAT·PLP crystals grew in 40% (v/v) ethylene glycol, 0.1 M sodium acetate (pH 6.2), and exhibited a cubic shape with dimensions of 0.2 x 0.2 x 0.2 mm3. Crystals of the tmHspAT·PMP form were obtained under conditions identical to those for native tmHspAT·PLP crystals; their morphology and size were similar to those of native crystals. The covalent Hsp-PLP adduct was obtained by co-crystallizing native tmHspAT·PLP in the presence of 10 mM Hsp, under crystallization conditions identical to those for growing native tmHspAT·PLP crystals. Crystals of the apo form were obtained in 40% (v/v) ethylene glycol, 0.1 M sodium acetate (pH 6.2); these adopted a prismatic morphology with approximate dimensions of 0.3 x 0.2 x 0.1 mm3.

A three-wavelength anomalous dispersion data set was collected from a SeMet tmHspAT·PLP crystal at beamline BW7A (EMBL Hamburg, Germany, DESY), at wavelengths of 0.9778 Å (inflection), 0.9862 Å (peak), and 0.9184 Å (high energy remote), using a 165-mm Mar CCD detector. For each image, the crystal was rotated by 0.5°, and the crystal-detector distance was set to 240 mm. Data were processed and scaled with DENZO and SCALEPACK (13) and are summarized in Table I. The Matthews coefficient (14) for the tmHspAT crystals was 2.53 Å3 Da-1, corresponding to a solvent content of about 51%.


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  		TABLE I
X-ray data collection, processing, and phasing statistics

 
SOLVE version 2.02 (15) was used to determine the heavy atom substructure using the x-ray data covering the resolution range of 15.0-3.5 Å (Table I). The best solution comprehended 33 heavy atom positions per asymmetric unit and had a figure of merit (f.o.m.) of 0.53 prior to density modification. From the initial substructure, three sites were removed because their occupancies refined to values smaller than 0.2. The selenium positions of the N-terminal SeMet residues could not be located because of structural disorder. The map was improved by density modification (16) coupled with non-crystallographic symmetry averaging (17) using RESOLVE version 2.02 (18), with a final f.o.m. of 0.61 in the resolution range of 20-2.85 Å. About 50% of the model was automatically built by RESOLVE. Refinement was carried out with CNS_SOLVE version 1.1 (19), with all reflections within 20.0-2.85 Å. 9.3% of the data (3,343/36,087 reflections) were used for cross-validation. Refinement statistics are shown in Table II. Turbo-FRODO was used for map visualization and model building (20). The PLP coenzyme was identified in {sigma}A-weighted Fourier difference maps. Final R-free and R-factors were 27.2 and 22.0%, respectively.


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  		TABLE II
X-ray refinement statistics

 
X-ray data of an apo tmHspAT crystal were obtained at beamline BW7B (EMBL Hamburg, DESY), using a 345-mm Mar Image plate detector to a maximum resolution of 2.85 Å (Table I). They were collected at a wavelength of 0.8416 Å, in 0.2° rotation steps, and with a crystal-detector distance of 290 mm. An unambiguous molecular replacement solution was found with AMoRe (21) using one tmHspAT monomer as search model, resulting in an initial CC of 31.4 and an R-factor of 59.1%, which, after rigid body refinement, converged to a CC of 69.4 and R-factor of 43.2%. Further refinement was carried out with Cns_Solve version 1.1, converging to a final R-free and R-factor of 28.4 and 22.1%, respectively. Similar procedures were employed to solve the structures of the tmHspAT·Hsp-PLP and the tmHspAT-PMP complexes, using x-ray data sets that were collected at beamline X13 (EMBL Hamburg, DESY), which is equipped with a 165-mm Mar CCD detector. For these data sets, the wavelength was set to 0.8020 Å, and the crystal-detector distances were 180 and 260.6 mm, respectively. The correct molecular replacement solutions were obtained with AMoRe, yielding a CC and R-factor of 60.6 and 39.1% for tmHspAT·Hsp-PLP and 74.4 and 41.9% for tmHspAT·PMP. Refinement was carried out until convergence with Cns_Solve version 1.1, with final R-free and R-factor of 26.8 and 20.6%, respectively, for tmHspAT·Hsp-PLP, and 28.8 and 23.6%, respectively, for tmHspAT·PMP. Refinement statistics are summarized in Table II. An additional set of 1,183 reflections with <I>/{sigma}(<I>) of 1.8 was used during refinement of the tmHspATP·MP complex.

Single Turnover Kinetics—Single turnover experiments were carried out by monitoring the reaction using the absorbance maximum of PMP at 327 nm in 10 mM HEPES (pH 8.0). The experiments were conducted in a Kontron UVIKON 922 spectrophotometer at 20 °C using 1-cm quartz cuvettes. Protein concentration was measured by UV absorption at 280 nm using a molar extinction coefficient of 21,760 M-1 cm-1 (E280 = 0.554 mg-1 ml). Stock solutions of 60.7 mM phenylalanine, 30.0 mM tryptophan, 2.0 mM tyrosine, and 10.4 mM Hsp were used. Wavelength scans were recorded between 250 and 600 nm in duplicate. Reactions were started by adding tmHspAT to a final concentration of 6.7 µM (40 µM for phenylalanine) and increasing substrate concentrations.

The rate of transamination at 25, 30, 40, 50, 60, and 70 °C was measured by mixing 32 µl of 80 µM tmHspAT·PLP in 10 mM HEPES (pH 8.0) and 0.3 µl of 60.7 mM phenylalanine, after 1-min preincubation at the corresponding temperature. Heat inactivation studies were conducted by incubating the enzyme at each temperature for 5, 15, 30, and 60 min and following the single turnover kinetics at 25 °C. The final concentrations in the reaction vessel were 21.3 µM tmHspAT·PLP and 150 µM phenylalanine. Each measurement was carried out in duplicate in a PowerWave-X Select instrument (Bio-Tek Instruments).


   RESULTS
TOP
 ABSTRACT
 INTRODUCTION
 EXPERIMENTAL PROCEDURES
 RESULTS
DISCUSSION
 REFERENCES
 
Four tmHspAT Complex Structures from Three Different Crystal Forms
The crystal structure of the L-histidinol-phosphate aminotransferase (tmHspAT) from T. maritima has been determined in four different states as follows: (a) the apo form in the absence of any ligand except inorganic phosphate (tmHspAT); (b) the internal aldimine form in the presence of the covalently bound cofactor pyridoxal 5'-phosphate (tmHspAT·PLP); (c) the ketimine intermediate in the presence of the L-histidinol phosphate pyridoxal 5'-phosphate adduct (tmHspAT·Hsp-PLP); and (d) the pyridoxamine 5'-phosphate form (tmHspAT·PMP) (Tables I and II, Fig. 1, 2, 3). Both tmHspAT and tmHspAT·PLP crystallized in the same orthorhombic unit cell (P21212), comprising two tmHspAT dimers per asymmetric unit. However, the unit cell of the apo form (tmHspAT) is shrunk by about 9% compared with that of the tmHspAT·PLP form. The unit cell of the tmHspAT·Hsp-PLP complex is monoclinic, again comprising two tmHspAT dimers per asymmetric unit and displaying a packing arrangement that is similar to that of the orthorhombic crystal form. The two axes (a and b) of the monoclinic crystal are similar to the two axes (b and c) of the orthorhombic crystal form, and the c axis is equivalent to one-half of the a axis of the orthorhombic crystal form. Crystals of the orthorhombic tmHspAT·PLP form dissolve upon soaking with Hsp, and the structure of the tmHspAT·Hsp-PLP complex reveals that movements in the N-terminal arm region (see below) lead to modifications in the overall packing arrangement. The tmHspAT·PMP unit cell form is also orthorhombic (P212121), but it exhibits a distinct packing arrangement from other crystal forms. This form contains only one tmHspAT dimer per asymmetric unit. The diffraction limits of the monoclinic crystal form were superior to those of the other crystal forms, allowing the tmHspAT·Hsp-PLP complex structure to be determined at 2.35-Å resolution, whereas the other tmHspAT structures were determined at 2.80-2.85 Å. Experimental phases were computed from the selenium anomalous signal from L-selenomethionine (SeMet) incorporated crystals of the tmHspAT·PLP form. The other structures were determined by the molecular replacement method.



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  		FIG. 2.
Structure of tmHspAT from T. maritima. The residue ranges of the secondary structural elements, using chain B of tmHspAT·PLP (Protein Data Bank code 1H1C [PDB] ), are as follows: {beta}1, 21-25; {alpha}1, 35-44; {alpha}2, 46-49; {alpha}3, 59-66; {alpha}4, 67-69; {beta}2, 79-82; {alpha}5, 84-95; {beta}3, 98-101; {alpha}6, 108-116; {beta}4, 119-122; {beta}5, 140-145; {alpha}7, 157-165; {beta}6, 169-173; {alpha}8, 177-179; {alpha}9, 185-189; {beta}7, 194-199; {alpha}10, 207-209; {beta}8, 212-216; {alpha}11, 218-227; {alpha}12, 235-246; {alpha}13, 247-271; {beta}9, 275-276; {beta}10, 284-287; {alpha}14, 294-302; {beta}11, 306-309; {beta}12, 313-317; {alpha}15, 321-322. The figure has been generated with the software TOPS (46). B, ribbon representation of the tmHspAT·PLP dimer viewed along the 2-fold dimer axis. The color code of the first monomer is the same as that in A. The second monomer is depicted by orange and yellow colors. In addition, the N-terminal "arm" motif, which is visible only in one of the two chains in the tmHspAT·PLP form, is shown in green. The PLP cofactor is depicted by a ball- and-stick representation, using atom specific colors (carbon, gray; nitrogen, blue; oxygen, red; and phosphorus, pink). C, ribbon of the tmHspAT·PLP dimer rotated by 90°. In this orientation, the 2-fold dimer axis is horizontally oriented within the plane of the figure. The figure has been produced with the software Molscript (47).

 



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  		FIG. 3.
Structure of active site ligands bound to tmHspAT. A, tmHspAT in the apo form, displaying an inorganic phosphate ion in the active site; B, tmHspAT·PLP, showing the internal aldimine PLP in the active site; C, tmHspAT· Hsp-PLP, displaying the Hsp-PLP adduct in the ketimine form; D, the tmHspAT· PMP complex. Each panel shows the ligand and specific hydrogen bonds or salt bridges. The atom type colors are the same as those in Fig. 2. In each panel, the final {sigma}A-weighted electron density map contoured at 1.0 {sigma} is also shown. The bond lengths quoted in A-C are averaged from four copies per asymmetric unit, and the bond lengths in D are from two copies per asymmetric unit. The average r.m.s deviations in protein-ligand bond lengths are as follows: A, tmHspAT, 0.27 Å (7 bonds); tmHspAT·PLP, 0.14 Å (13 bonds), tmHspAT·Hsp-PLP, 0.14 Å (16 bonds). Tyr-53' originates from the other tmH-spAT subunit. tmHspAT main chain interactions are labeled by an asterisk. The figure has been produced with DINO (www.dino3d.org).

 
Overall Structure of tmHspAT
The structure of tmHspAT resembles those of the class Ib fold of PLP enzymes. Each monomeric unit consists of two domains, of which the small domain is composed of residues 21-40 and 275-335, flanking the large domain (residues 41-274) (Fig. 2). Within the N-terminal segment of the small domain, strand {beta}1 and the loop preceding this strand (residues 23-27) are involved in shielding the tmHspAT active site. Like other members of the subclass Ib fold of PLP enzymes, tmHspAT comprises an N-terminal arm motif (residues 1-20). Only parts of this motif are visible in the apo structure as well as in the PLP and PMP complexes, whereas the complete motif is within defined electron density in the tmHspAT·Hsp-PLP complex structure. The structure reveals how the N-terminal arm motif interacts with helix {alpha}11 of the large domain of the adjacent subunit within each tmHspAT dimer. Of the four copies in the asymmetric unit, the N termini of two chains of the tmHspAT·Hsp-PLP complex form {alpha}-helices (residues 3-10), whereas no secondary structure forms within the same segment of the other two chains. However, it is not known whether the ordering transition of the N-terminal arm motif in the tmHspAT·Hsp-PLP complex originates from packing effects or whether it is triggered by conformational arrangements of the region C-terminal to the arm motif that contributes to the active site.

The presence of multiple tmHspAT copies of the differently liganded structures in the respective crystal forms (14 copies in total) has allowed 91 non-redundant structural superpositions of tmHspAT chains. The average r.m.s. deviation is 0.69 Å over all main chain atoms from about 300 matching residues, never exceeding 1 Å, thus demonstrating that there is no indication for major conformational changes in the overall tmHspAT structure during catalysis. Structural superposition of available tmHspAT dimers yields an average r.m.s. deviation of 0.80 Å over all main chain atoms from about 600 matching residues, based on 21 comparisons, ranging from 0.44 to 1.15 Å. These data support the categorization of tmHspAT as a member of the class Ib fold of PLP enzymes.

Active Site Organization in tmHspAT
We have crystallized tmHspAT in four different forms as follows: 1) the apo form prior to covalent binding of PLP; 2) the PLP-containing internal aldimine form; 3) the ketimine intermediate of the Hsp-PLP adduct; and 4) the PMP form. In this respect, we have been able to provide a structural framework for the molecular basis of a number of key steps of the catalytic mechanisms of tmHspAT (Figs. 1 and 3).

Apo-tmHspAT—The apo form of tmHspAT only contains an inorganic phosphate ion in the active site (Fig. 3A). This phosphate ion is bound in the active site pocket, which in the tmHspAT·PLP form is occupied by the phosphate group of the PLP cofactor (see below). The remaining active site is filled with one to two ordered solvent molecules.

tmHspAT·PLP—The tmHspAT crystals grew in the PLP form, without further treatment of the purified enzyme, as evidenced spectroscopically prior to crystallization (data not shown) and crystallographically (Fig. 3B). PLP exhibits several specific interactions with residues from the large domain (Asp-86, Asn-149, Asp-173, Tyr-176, Thr-199, Ser-201, Lys-202, and Arg-210) and with Tyr-53 from the adjacent subunit of the tmHspAT dimer. These residues are highly conserved among other class I PLP enzymes. The position and orientation of the PLP pyridine ring is constrained by stacking with the aromatic ring of Tyr-106 (Fig. 4), along with specific interactions with Asn-149, Asp-173, and Tyr-176. The bond angle connecting N{zeta}(Lys-202)-C4A-C4 has been refined to 121°, indicating sp2 hybridization of C4A prior to catalysis. The PLP phosphate group is bound by the same residues as the inorganic phosphate in the apo form (Fig. 3, A and B, and Fig. 4).



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  		FIG. 4.
Superposition of the active sites of the four tmHspAT ligand complexes. The structures of the active sites of the four tmHspAT complexes were superimposed with an r.m.s. deviation of 0.37 Å over all main chain atoms using the program Align (35). Active site residues shown are as follows: Y23, L24, L26, N27, Y53', Y106, N149, A175, T199, S201, K202, F231, V307, and V314 (nomenclature based on tmHspA). The color codes are as follows: tmHspAT, yellow; tmHspAT·PLP, black; tmHspAT·Hsp-PLP, red; tmHspAT·PMP, cyan. The figure was produced with DINO.

 
tmHspAT·Hsp-PLP—Although there is no evidence that tmHspAT undergoes large conformational changes during catalysis (see above), it was not possible to form the tmHspAT· Hsp-PLP complex by soaking L-histidinol phosphate (Hsp) in tmHspAT·PLP crystals, providing indirect evidence for geometrical adjustments in the active site of the enzyme upon transamination. Instead, the structure of the Hsp-PLP adduct in tmHspAT was determined from a separate crystal form (Tables I and II) displaying the complete adduct within electron density (Fig. 3C). In the refined model of the adduct, the angle N-4-C{alpha}-C{beta} is 122.0 ± 0.6°, suggesting sp2 hybridization. The final electron density map did not indicate the presence of a hydroxyl group in the C{alpha} position of the adduct. Based on the colorless appearance of the tmHspAT·Hsp-PLP crystals (Fig. 1), the adduct has been interpreted as being the ketimine intermediate form. Comparison of the structures of tmHspAT· PLP and tmHspAT·Hsp-PLP reveals that the PLP pyridine ring is tilted by 11 ± 1° (Fig. 4). This movement is accompanied by a similar tilt of the phenol ring of Tyr-106 to maintain stacking interactions with the pyridine ring, observed in the tmHspAT·PLP complex. Binding of the PLP phosphate group is maintained as in the tmHspAT·PLP form, indicating its function as coenzyme anchor. The Hsp imidazole ring specifically interacts with Asp-86 and Tyr-106, and the Hsp phosphate group is bound by Ser-107 and Arg-315. Residues 23-27 from the small domain shield the Hsp-binding site, however, without being involved in direct specific interactions.

tmHspAT-PMP—The active site arrangement in the tmHspAT·PMP complex is basically identical to that of the tmHspAT·Hsp-PLP complex. The tilt between the pyridine rings in these two complexes is 3.4 ± 0.3°, whereas the tilt with respect to the pyridine ring of the tmHspAT·PLP form is 12 ± 1°.


   DISCUSSION
TOP
 ABSTRACT
 INTRODUCTION
 EXPERIMENTAL PROCEDURES
 RESULTS
 DISCUSSION
REFERENCES
 
Close Relationship between tmHspAT, eHspAT, and sCobD—When the structure of L-threonine-O-3-phosphate decarboxylase (sCobD) from S. typhimurium became available, its comparison with the crystal structures of HspAT from E. coli (eHspAT) (8, 9) confirmed previous findings on the close relationship between these enzymes, suggesting a common evolutionary ancestry (2, 7, 10). In support of this observation, a comparison of the coordinates of tmHspAT against the available structures in the Protein Data Bank revealed a similar degree of structural similarity between tmHspAT and sCobD as those noted for HspAT homologues from different organisms (E. coli and T. maritima). This finding was true regardless of whether the entire structure or only the active site region was compared (Table III). Although the evolution of tmHspAT and sCobD has led to enzymes with separate, albeit mechanistically related (3), catalytic activities, we postulate that adaptation to specific environmental conditions was the main cause for the evolutionary divergence of the HspAT structures from T. maritima and E. coli. To identify the molecular origins of this divergence, we have analyzed the overall structures of these two enzymes, their active sites, as well as some well established molecular parameters potentially indicative of thermal stabilization (Table IV). In parallel, we have compared the properties of the eHspAT structures (8, 9) with those of the structures of CobD from S. typhimurium (7, 10). Given the close similarity between the S. typhimurium and E. coli genomes and similar living conditions of the two organisms (22), it can be expected that the requirements for structural adaptations have been less than those observed for T. maritima (12).


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  		TABLE III
Structural similarities in tmHspAT, eHspAT, and sCobD

The r.m.s. deviations have been calculated with the software Align (35), using all C{alpha}[p] atoms (All) or using active site residues only (AS) (Tyr-23, Leu-24, Leu-26, Asn-27, Tyr-53', Tyr-106, Asn-149, Ala-175, Thr-199, Ser-201, Lys-202, Phe-231, Val-307, and Val-314). When applicable, standard deviations are shown in parentheses. The following coordinates were used: 1UU0 (tmHspAT), 1FG7 [PDB] (sCobD), 1H1C [PDB] (tmHspAT·PLP), 1GEW [PDB] (eHspAT·PLP), 1LKC [PDB] (sCobD·PLP), 1UU1 [PDB] (tmHspAT·Hsp-PLP), 1GEX [PDB] (eHspAT·Hsp-PLP), 1LC8 [PDB] (sCobD·threonine-phosphate-PLP), 1UU2 [PDB] (tmHspAT·Hsp-PMP), and 1FG7 [PDB] (eHspAT·PMP).

 


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  		TABLE IV
Molecular parameters in tmHspAT, eHspAT, and sCobD

The numbers are averages over the available structures. The following coordinate sets were used: tmHspAT, 1H1C [PDB] , 1UU0, 1UU1 [PDB] , and 1UU2 [PDB] ; eHspAT, 1GEX [PDB] , 1GEW [PDB] , 1GEY [PDB] , 1FG3 [PDB] , 1FG7 [PDB] , and 1IJI [PDB] ; sCobD, 1LKC [PDB] . The numbers in parentheses refer to standard uncertainties where applicable.

 
Overall Structure—Although the overall structures of the eHspAT and tmHspAT dimers are similar (r.m.s. deviation of 1.3 Å, Table III), the region connecting the N-terminal segment of the small domain and the large domain (residues 25-58) is folded differently (Fig. 5). In the tmHspAT dimer, this region forms a two-helical bundle (residues 36-44) across the 2-fold dimer axis, whereas in the eHspAT structure, the same region forms an intermolecular antiparallel {beta}-sheet across the 2-fold dimer axis. The molecular rationale for this type of secondary structure swapping originates from a seven-residue deletion in the eHspAT sequence (7) that prevents an {alpha}-helical arrangement. A tmHspAT-like {alpha}-helical segment is also found in the structure of sCobD (Fig. 5B), but it is two residues shorter. Given its postulated functional in shielding the active site and in positioning the N-terminal arm, it is remarkable that its structure is more conserved in two representative enzymes of different reaction specificity (tmHspAT, sCobD) rather than in HspAT homologues, thus supporting the close evolutionary relations between HspAT and sCobD.



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  		FIG. 5.
Dimer formation by a helical bundle in tmHspAT and sCobD versus a {beta}-sheet in eHspAT. A, ribbons of the structures of tmHspAT (left), sCobD (center), and eHspAT (right), with the N termini highlighted in red (residues 6-60 and 21-60), yellow (residues 8-63), and orange (residues 5-62), respectively. B, structure based sequence alignment of the N-terminal regions that match with residues 21-60 of tmHspAT. The locations of the secondary structural elements are indicated.

 
Active Site Structure—CobD and HspAT exhibit different active site requirements associated with their specific reaction mechanisms, transamination for HspAT versus decarboxylation for CobD. First, only HspAT needs to be capable of dual substrate recognition (Hsp, glutamate). Second, in CobD, the orientation of the leaving group at the substrate C{alpha} position and the catalytic residues promoting its elimination need to be appropriately positioned to direct catalysis toward decarboxylation rather than transamination (7). Previous comparison of the eHspAT and sCobD structures revealed that the differences within the active sites are limited to the respective substrate-binding sites, whereas the PLP-binding sites are virtually identical (7). Comparison of the active sites of eHspAT (8, 9) and tmHspAT indicates that they are basically identical with respect to binding of the PLP group and the Hsp substrate. The r.m.s. deviations for the active site residues are in the order of 0.4 Å (Table III), which is within the range of the estimated experimental coordinate error. In particular, those residues that are involved in dual substrate recognition (8) are invariant within the eHspAT and tmHspAT sequences, suggesting an identical dual substrate-binding mechanism. The equivalent residues of the active site from sCobD superimpose with r.m.s. deviations in the range of 0.6-0.7 Å with those of either of tmHspAT or eHspAT (Table III).

Thermal Stabilization—Structures of several enzymes of the histidine biosynthesis pathway from the hyperthermophile T. maritima have already been determined, including tmHisA (23), tmHisF (23), tmHisH (24), the binary tmHisH-tmHisF complex (24), and the hetero-octameric tmHisG-tmHisZ complex,2 thereby allowing comparisons with the respective enzyme structures from mesophilic organisms (25-28). Previous statistical analyses of large structural data sets revealed that the frequency of salt bridges, surface polarity, and structural compactness may be important criteria that affect the structural parameters for thermal stabilization, in general (29, 30), and in T. maritima, in particular (31, 32). These trends are preserved across the available structures from the histidine biosynthesis pathway from T. maritima, whereas we have noted that the salt bridges are not highly conserved, suggesting that adaptation of T. maritima to its living conditions is a late event during evolution.3

As expected, purified tmHspAT displays maximum catalytic activity at temperatures higher than 60 °C (Fig. 6A). In order to gain insight into the molecular origins of thermostability of tmHspAT, we compared some of the general properties of the available tmHspAT, eHspAT, and sCobD structures (Table IV). Our analysis reveals that some parameters, known to be indicative of thermostability, are similar in the eHspAT and sCobD structures but differ in tmHspAT. (i) The tmHspAT structure contains about 50% more salt bridges than the eHspAT structure, and their number is even about 2-fold higher than in the sCobD structure. (ii) Whereas the proportion of polar surface is similar (42%) in the eHspAT and sCobD structures, it is 6% higher in tmHspAT. (iii) The tmHspAT structure is about 3% more compact than the eHspAT and sCobD structures, corresponding to a volume difference of 500-1000 Å3. (iv) The gap volume (33) in the tmHspAT dimer interface is only 15% that found in the eHspAT and sCobD structures, indicating a much tighter surface complementarity in the tmHspAT interface. We have also noted that the amino acid composition in tmHspAT is quite different from that found in the other two enzymes. For instance, whereas tmHspAT comprises two glutamines only, eHspAT and sCobD contain 21 and 16 glutamines, respectively. Taken together, these data clearly support the notion that the tmHspAT enzyme exhibits hyperthermophilic properties.



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  		FIG. 6.
Catalytic activity of tmHspAT by single turnover kinetics. A, relative catalytic activities, using Hsp as substrate, measured within a temperature range of 25-70 °C. The highest activity was observed at 60 °C and was used as reference to determine the relative activities at other temperatures. At 70 °C or higher, tmHspAT starts to become inactivated after a 10-min preincubation. B, single turnover kinetics of tmHspAT upon addition of phenylalanine (circle), tryptophan (square), L-histidinol phosphate (triangle) (left), and tyrosine (diamond) (right). Maximum concentration attainable for any of the substrates was limited by solubility in the reaction buffer. Initial velocity values were normalized by the maximum velocity of the corresponding substrate used for comparison. The kinetic parameters derived from these data are given in Table V.

 
Is tmHspAT a Broad Specificity Transaminase?—Comparison of the tmHspAT coordinates against the presently available structures of the Protein Data Bank, using the software Dali (34), revealed that aspartate aminotransferases (AspAT) and tyrosine aminotransferases exhibit the highest structural similarity with tmHspAT. For instance, aspartate aminotransferase from T. thermophilus (1BJW [PDB] ) superimposes onto tmHspAT with an r.m.s. deviation of 2.8 Å, and a structure-based sequence alignment reveals that 34% of the residues are identical. The respective numbers for tyrosine transaminase from Trypanosoma cruzi (1BWO [PDB] ) are 3.1 Å and 34%. Given the close structural similarity of AspAT and AroAT (2), we expect that these relations are maintained between all members of this family and the HspAT/CobD cluster. Indeed, although not ranking among the top 10 scoring structures in the Dali search, the available AroAT structures from Paracoccus denitrificans (2AY1 [PDB] , residues 13-405), E. coli (3TAT [PDB] , residues 13-407), and Pyrococcus horikoshii (1DJU [PDB] , residues 10-383) can also be superimposed onto tmHspAT (residues 12-334) with r.m.s. deviations of 2.4, 2.5, and 2.7 Å over 1196, 1199, and 1154 main chain atoms, respectively, using the software Align (35).

However, close examination of the T. maritima genome provides no evidence for an AroAT activity (12). The TIGR microbial genome data base (www.tigr.org) lists a total of 10 amino-transferase genes in T. maritima, four of which remain functionally putative. Of these four genes, TM1131 belongs to a paralogous family of genes, including the gene encoding tmHspAT (hisC), and its sequence is similar to that of a hyperthermophilic, archaeal broad specificity aminotransferase (SPTREMBL entry Q9V2W5). Therefore, we suspected that HspAT may display a broadened specificity, and we measured its catalytic constants for several amino acids. Indeed, under the conditions used for the measurements (20 °C), HspAT displays an approximate 30, 10, and 5% transamination activity for tyrosine, tryptophan, and phenylalanine, using its reactivity toward Hsp as reference (Table V and Fig. 6B). In contrast, it does not show any measurable transamination activity for L-histidine (data not shown). Modeling the different substrates into the tmHspAT·Hsp-PLP active site shows that the aromatic side chains can fit into the same region of Hsp that is occupied by the imidazole group, within interaction distance with key residues. The enhanced reactivity of tyrosine compared with that of tryptophan or phenylalanine may be due to one additional hydrogen bond possibly donated by its hydroxyl group. Our findings are in accordance with earlier comparative kinetic data on HspAT and AroAT from B. subtilis, indicating that HspAT, due to of its superior catalytic properties, plays a central role in aromatic amino acid biosynthesis (5, 6). On the other hand, broad substrate specificities have been measured for several AroATs (36-40). Structure-based engineering experiments have revealed that a few residue replacements are sufficient to induce the swapping of substrate specificities (41). However, to our knowledge, the converse experiment of measuring the potential catalytic activity of an AroAT toward Hsp has not yet been published.


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  		TABLE V
Catalytic efficiencies of tmHspAT with different substrates

 
In summary, current sequence and structural data of family {alpha} transaminases/decarboxylases demonstrate that there are two closely related enzyme clusters, where one comprises AspAT and AroAT, and the other includes HspAT and CobD. Members from both clusters exhibit overlapping substrate specificity and partially overlapping reaction specificity. Recent sequence data indicate that bacterial genomes often contain an incomplete set of genes coding for known aminotransferases. For instance, the T. maritima genome, according to current annotation data, lacks an AroAT, providing a rationale for overlapping substrate specificities, a phenomenon initially recognized 40 years ago (6, 42, 43).

Accession Codes—The atomic coordinates for T. maritima tmHspAT in complex with PLP, in the apo form, in complex with the Hsp adduct, and in complex with PMP have been deposited with the Protein Data Bank (44) under accession codes 1H1C [PDB] , 1UU0, 1UU1 [PDB] , and 1UU2 [PDB] , respectively.


   FOOTNOTES
 
The atomic coordinates and structure factors (codes 1H1C [PDB] , 1UU0, 1UU1 [PDB] , and 1UU2 [PDB] ) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

* This work was supported by Deutsche Forschungsgemeinschaft Grants WI 1058/5-3 and WI 1058/5-4 (to M. W.). 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. Back

§ Both authors contributed equally to this work. Back

|| To whom correspondence should be addressed: EMBL incare DESY, Notkestrasse 85, Bldg. 25A, D-22603 Hamburg, Germany. Tel.: 49-40-89902-126; Fax: 49-40-89902-149; E-mail: wilmanns{at}embl-hamburg.de.

1 The abbreviations used are: PLP, pyridoxal-5'-phosphate; PMP, pyridoxamine-5'-phosphate; Hsp, L-histidinol phosphate; Hsp-PLP, L-histidinol phosphate pyridoxal-5'-phosphate adduct; tmHspAT, T. maritima L-histidinol-phosphate aminotransferase; eHspAT, E. coli L-histidinol-phosphate aminotransferase; sCobD, S. typhimurium L-threonine-O-3-phosphate decarboxylase; AspAT, aspartate aminotransferase; AroAT, aromatic aminotransferase; IAP, imidazole acetol phosphate or 3-(imidazole-4-yl)-2-oxo-propyl phosphate; CC, correlation coefficient; r.m.s., root-mean-square; SeMet, L-selenomethionine; CHAPS, 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonic acid; f.o.m., figure of merit. Back

2 M. C. Vega, F. J. Fernandez, G. E. Murphy, A. Popov, R. Sterner, P. Zou, and M. Wilmanns, unpublished data. Back

3 F. J. Fernandez, M. C. Vega, and M. Wilmanns, unpublished data. Back


   ACKNOWLEDGMENTS
 
We thank Allan Matte for kindly providing the L-histidinol phosphate used in this work, Andrea Schmidt for assistance during x-ray data collection, and Antonio Romero for helpful discussions on cryoprotectants. Areti Malapetsas is thanked for proofreading the manuscript.



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 RESULTS
 DISCUSSION
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