Gunter Schneider

Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 Å resolution

The amino acid sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum has been fitted to the electron density maps. The resulting protein model has been refined to a nominal resolution of 1.7 A using the constrained-restrained least-squares refinement program of Sussman and the restrained least-squares refinement program of Hendrickson & Konnert. The crystallographic refinement, based on 76,452 reflections with F greater than sigma (F) in the resolution range 5.5 to 1.7 A resulted in a crystallographic R-factor of 18.0%. The asymmetric unit contains one dimeric ribulose-1,5-biphosphate carboxylase molecule, consisting of 869 amino acid residues and 736 water molecules. The geometry of the refined model is close to ideal, with root-mean-square deviations of 0.018 A in bond lengths and 2.7 degrees in bond angles. Two loop regions, comprising residues 54 to 63 and 324 to 335, and the last ten amino acid residues at the C terminus are disordered in our crystals. The expected trimodal distribution is obtained for the side-chain chi 1-angles with a marked preference for staggered conformation. The hydrogen-bonding pattern in the N-terminal beta-sheet and the parallel sheet in the beta/alpha-barrel is described. A number of hydrogen bonds and salt bridges are involved in domain-domain and subunit-subunit interactions. The subunit-subunit interface in the dimer covers an area of 2800 A2. Considerable deviations from the local 2-fold symmetry are found at both the N terminus (residues 2 to 5) and the C terminus (residues 422 to 457). Furthermore, loop 8 in the beta/alpha-barrel domain has a different conformation in the two subunits. A number of amino acid side-chains have different conformations in the two subunits. Most of these residues are located at the surface of the protein. An analysis of the individual temperature factors indicates a high mobility of the C-terminal region and for some of the loops at the active site. The positions and B-factors for 736 solvent sites have been refined (average B: 45.9 A2). Most of the solvent molecules are bound as clusters to the protein. The active site of the enzyme, especially the environment of the activator Lys191 in the non-activated enzyme is described. Crystallographic refinement at 1.7 A resolution clearly revealed the presence of a cis-proline at the active site. This residue is part of the highly conserved region Lys166-Pro167-Lys168.

Three-dimensional structure of apotransketolase : flexible loops at the active site enable cofactor binding

The structure determination of apotransketolase and the comparison of its three‐dimensional structure with that of the holoenzyme has revealed that no large conformational changes are associated with cofactor binding. Two loops at the active site are flexible in the apoenzyme which enables ThDP to reach its binding site. Binding of the cofactor induces defined conformations for these two loops at the active site. One of these loops is directly involving in binding of the cofactors, Ca2+ and ThDP. This loop acts like a flap which closes off the diphosphate binding site. After binding of the cofactor, residues of this loop form interactions to residues of loop 383–398 from the second subunit. These interactions stabilize the conformation of the two loops from a flexible to a ‘closed’ conformation.

Crystal structure of transketolase in complex with thiamine thiazolone diphosphate, an analogue of the reaction intermediate, at 2.3 A resolution.

The crystal structure of the complex of transketolase and thiamine thiazolone diphosphate has been determined at 2.3 Å resolution. The complex has a structure which closely resembles that of this enzyme with the cofactor ThDP. This is consistent with the observation that the binding of the analogue to transketolase involves ground state rather than transition state interactions. Since thiamine thiazolone diphosphate resembles an expected intermediate in the catalytic pathway, the structure of the intermediate was modelled from the crystal structure. Based on this model, enzymic groups responsible for binding of the intermediate and proton transfer during catalysis are suggested.

Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 å resolution

BACKGROUND In Escherichia coli, the enzymes of the biotin biosynthesis pathway are encoded by the bio operon. One of these enzymes, ATP-dependent dethiobiotin synthetase, catalyzes the carboxylation of 7,8-diaminopelargonic acid leading to the formation of the ureido ring of biotin. The enzyme belongs to the class of ATP-dependent carboxylases and we present here the first crystal structure determined for this class of enzyme. RESULTS We have determined the crystal structure of homodimeric dethiobiotin synthetase to 1.65 A resolution. The subunit consists of a seven-stranded parallel beta-sheet, surrounded by alpha-helices. The sheet contains the classical mononucleotide-binding motif with a fingerprint peptide Gly-X-X-X-X-X-Gly-Lys-Thr. The mononucleotide binding part of the structure is very similar to the GTP-binding protein H-ras-p21 and thus all GTP-binding proteins. A comparison reveals that some of the residues, which in H-ras-p21 interact with the nucleotide and the metal ion, are conserved in the synthetase. CONCLUSIONS The three-dimensional structure of dethiobiotin synthetase has revealed that ATP-dependent carboxylases contain the classical mononucleotide-binding fold. Considerable similarities to the structure of the GTP-binding protein H-ras-p21 were found, indicating that both proteins might have evolved from a common ancestral mononucleotide-binding fold.

Thiamin diphosphate dependent enzymes: transketolase, pyruvate oxidase and pyruvate decarboxylase

Abstract The past few years have brought significant advances in our understanding of thiamin diphosphate dependent enzymes. The determination of the three-dimensional structures of transketolase, pyruvate oxidase and pyruvate decarboxylase has revealed a common thiamin-binding fold and provided the first structural insights into enzymatic thiamin catalysis.

Preliminary crystallographic data for stearoyl-acyl carrier protein desaturase from castor seed.

Recombinant stearoyl-acyl carrier protein desaturase (EC 1.14.99.6) from castor seed has been crystallized with polyethylene glycol 8000 as precipitant. The crystals are orthorhombic, space group P2(1)2(1)2(1) with cell dimensions a = 81.3, b = 146.4 and c = 197.7 A. The observed diffraction pattern extends to at least 2.5 A resolution. Rotation function calculations indicate a non-crystallographic 3-fold rotation axis parallel to the crystallographic a-axis. Perpendicular to this axis, 2-fold rotation axes were found at 30 degrees intervals, i.e. maxima at kappa = 180 degrees, phi = 90 degrees and omega = 30 degrees and 60 degrees, respectively. Together with the packing density of the crystals (Vm = 2.4 A3/Da for n = 6), these results suggest, that the crystal asymmetric unit most likely contains a hexamer of desaturase subunits.

Crystallization and preliminary crystallographic studies of the FAD domain of corn NADH : nitrate reductase

Crystals of the flavin domain of corn nitrate reductase expressed in Escherichia coli have been obtained at room temperature, using sodium citrate as precipitant. The crystals diffract to at least 2.5 A resolution at a synchrotron radiation source. Precession photographs show that they belong to the rhombohedral space group R3 with unit cell dimensions a = b = 145.4 A, c = 47.5 A, alpha = beta = 90 degrees and gamma = 120 degrees. There is one subunit per asymmetric unit which gives a packing density of 3.2 A3/Da, indicating a high solvent content in these crystals.

The Active Site of Ribulose Bisphosphate Carboxylase / Oxygenase

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) has attracted a lot of interest due to its central role in the carbon metabolism of plants and photosynthetic microorganisms (for a review see (1)). The dual function of this enzyme, catalyzing the primary steps in both photosynthetic carbon dioxide fixation and photorespiration, makes it a challenging target for attempts to improve the efficiency of photosynthesis. Recombinant DNA-techniques provide a promising tool to modify the carboxylase/oxygenase ratio by genetic engineering. However, the application of these techniques requires a detailed knowledge of the catalytic mechanism of the enzyme and the structure of its active site.

Structural and Functional Aspects of the Photosynthetic Fixation of Carbon Dioxide

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) has attracted a lot of interest due to its central role in the carbon metabolism of plants and photosynthetic microorganisms (for a review see (1)). The dual function of this enzyme, catalyzing the primary steps in both photosynthetic carbon dioxide fixation and photorespiration (Figure 1), makes it a challenging target for attempts to improve the efficiency of photosynthesis. Recombinant DNA-techniques provide a promising tool to modify the carboxylase/oxygenase ratio by genetic engineering. However, the application of these techniques requires a detailed knowledge of the catalytic mechanism of the enzyme and the structure of its active site.

Crystallization and structure of a recombinant ribulose-1,5-bisphosphate carboxylase

Abstract Ribulose-1,5-bisphosphate carboxylase/oxygenase is the key enzyme in photosynthetic carbon dioxide fixation and photorespiration. The dimeric carboxylase from the photosynthetic bacterium Rhodospirillum rubrum has been cloned and expressed in E. coli . The recombinant enzyme has been crystallized in a number of different crystal forms. The three-dimensional structure of the enzyme has been determined by X-ray crystallographic methods to 2.9Aresolution.