Crystal structures of aconitase with trans-aconitate and nitrocitrate bound.

Crystal structures of mitochondrial aconitase with the inhibitors trans-aconitate and nitrocitrate bound to the [4Fe-4S] cluster have been solved and refined at 2.05 A resolution with R-factors of 0.168 and 0.172, respectively. Crystallization of aconitase with the substrates citrate and cis-aconitate has not been possible because the enzyme turns over and selects enzyme with isocitrate bound into the crystal lattice. Therefore we have analyzed crystal structures of the enzyme complexed with inhibitor analogs of these two substrates. The structure with nitrocitrate bound provides a model for citrate binding. The structure with trans-aconitate bound provides a model for cis-aconitate binding in two ways: Fe4 of the [4Fe-4S] cluster is five-coordinate and the carbon at the C beta position is trigonal. These results allow the model for the reaction mechanism to be extended to all three natural substrates of aconitase. The results support a model in which citrate and isocitrate form similar chelate structures related by 180 degrees rotation about the C alpha-C beta bond while the intermediate cis-aconitate binds in either of two ways (citrate mode or isocitrate mode). In both inhibitor complexes a H2O molecule is also bound to Fe4. In the structure with nitrocitrate bound, partial occupancy of sulfate in the active site is observed accompanied by hydroxyl binding to Fe4. Comparison of the structures with isocitrate, trans-aconitate, nitrocitrate and sulfate bound reveals preferred orientations for the three types of oxygens ligated to Fe4 (carboxyl, hydroxyl and H2O) supporting the proposed roles for His101, Asp165 and His167 in the catalytic mechanism.

Mechanistic aspects of cyanogenesis from active-site mutant Ser80Ala of hydroxynitrile lyase from Manihot esculenta in complex with acetone cyanohydrin.

The structure and function of hydroxynitrile lyase from Manihot esculenta (MeHNL) have been analyzed by X-ray crystallography and site-directed mutagenesis. The crystal structure of the MeHNL-S80A mutant enzyme has been refined to an R-factor of 18.0% against diffraction data to 2.1-A resolution. The three-dimensional structure of the MeHNL-S80A-acetone cyanohydrin complex was determined at 2.2-A resolution and refined to an R-factor of 18.7%. Thr11 and Cys81 involved in substrate binding have been substituted by Ala in site-directed mutagenesis. The kinetic measurements of these mutant enzymes are presented. Combined with structural data, the results support a mechanism for cyanogenesis in which His236 as a general base abstracts a proton from Ser80, thereby allowing proton transfer from the hydroxyl group of acetone cyanohydrin to Ser80. The His236 imidazolium cation then facilitates the leaving of the nitrile group by proton donating.

The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex.

The crystal structure of the S642A mutant of mitochondrial aconitase (mAc) with citrate bound has been determined at 1.8 A resolution and 100 K to capture this binding mode of substrates to the native enzyme. The 2.0 A resolution, 100 K crystal structure of the S642A mutant with isocitrate binding provides a control, showing that the Ser --> Ala replacement does not alter the binding of substrates in the active site. The aconitase mechanism requires that the intermediate product, cis-aconitate, flip over by 180 degrees about the C alpha-C beta double bond. Only one of these two alternative modes of binding, that of the isocitrate mode, has been previously visualized. Now, however, the structure revealing the citrate mode of binding provides direct support for the proposed enzyme mechanism.

Steric and conformational features of the aconitase mechanism.

Crystal structures of mitochondrial aconitase with alpha-methylisocitrate and with sulfate bound have been solved and refined at 2.0 A resolution with R factors of 18.2 and 16.8%, respectively. The steric factors and conformational effects observed in both new structures support the proposed mechanism for the overall reaction catalyzed by aconitase. The alternate substrate alpha-methylisocitrate is derived from alpha-methyl-cis-aconitate during crystallization and is observed to bind in the active site in a manner very similar to that observed for isocitrate. The methyl group is accommodated by favorable contact with Ile-425. However, the other potential hydration product of alpha-methyl-cis-aconitate, alpha-methylcitrate, cannot be accommodated in the active site due to steric conflict of the methyl group with Asp-165. The results are consistent with the requirement that cis-aconitate must bind in two ways, in the citrate mode and in the isocitrate mode. Crystals of aconitase with sulfate bound are isomorphous to those with isocitrate bound. However, the structure displays significant conformational changes, providing a model for the substrate-free state of enzyme. Three water molecules bind in place of the C alpha- and C beta-hydroxyl and carboxyl groups of isocitrate, while sulfate binds in place of the C gamma-carboxyl group. Side chains of Ser-642 and Arg-447 in the active site rotate to pair with other side chains in the absence of substrate. The new conformation of Arg-447 triggers a concerted set of shifts which transmits conformational change to the surface of the protein, 30 A from the active site. In the absence of substrate, a chain segment containing the [4Fe-4S] ligand Cys-358 also shifts, resulting in the net translation and reorientation of the Fe-S cluster.

Studies on the domain structure of the Salmonella typhimurium AraC protein.

The Salmonella typhimurium araC gene product is known to be susceptible to proteolytic degradation. Limited cleavage by trypsin, kallikrein, elastase and pronase E yields stable fragments comprising approximately the N-terminal two thirds of the AraC protein. These fragments have in common the ability to dimerize in solution and to bind L-arabinose and D-fucose. Under appropriate conditions, hydrolysis of the AraC protein with Staphylococcus aureus V8 protease leads to a small C-terminal fragment which is able to bind specifically to a synthetic ara consensus sequence. These results indicate that, as with several other prokaryotic gene regulatory proteins, the basic functions of effector binding, subunit interaction and specific DNA binding are segregated into distinct domains of the AraC protein.

Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC).

Single crystals of the self-complementary octadeoxyribonucleotide d(GCCCGGGC) have been analysed by X-ray diffraction methods at a resolution of 1.8 A. The tetragonal unit cell of space group P4(3)2(1)2 has dimensions of a = 43.25 A and c = 24.61 A and contains eight strands of the oligonucleotide. The structure was refined by standard crystallographic techniques to an R factor of 17.1% using 1359 3 sigma structure factor observations. Two strands of the oligonucleotide are related by the crystallographic dyad axis to form a DNA helix in the A conformation. The d(GCCCGGGC) helix is characterized by a wide open major groove, a near perpendicular orientation of base pairs to the helix axis and an unusually small average helix twist angle of 31.3 degrees indicating a slightly underwound helix with 11.5 base pairs per turn. Extensive cross-strand stacking between guanine bases at the central cytosine-guanine step is made possible by a number of local conformational adjustments including a fully extended sugar-phosphate backbone of the central guanosine nucleotide.

Three-dimensional structure of d(GGGATCCC) in the crystalline state.

The structure of the self-complementary octamer d(GGGATCCC) has been analysed by single crystal X-ray diffraction methods at a nominal resolution of 2.5 A. With acceptable stereochemistry of the model the crystallographic R factor was 16.6% after restrained least-squares refinement. In the crystal, d(GGGATCCC) forms an A-DNA double helix with slightly varying conformation of the two strands. The average displacement of the base pairs from the helix axis is unusually large and is accompanied by pronounced sliding of the base pairs along their long axes at all dinucleotide steps except for the central AT. With 12 base pairs per complete turn the helix is considerably underwound. As observed with most oligodeoxyribonucleotides analysed by X-ray crystallography so far, the octamer displays reduced base pair tilt, increased rise per base pair and a more open major groove compared with canonical A-DNA. We propose that, based on these parameters, three A-helical sub-families may be defined; d(GGGATCCC) then is a representative of the class with intermediate tilt, rise, and major groove width.

Crystallization and preliminary X-ray diffraction studies of mandelonitrile lyase from almonds.

Single crystals of three different isoenzymes of (R)-(+) mandelonitrile lyase (hydroxynitrile lyase) from almonds (Prunus amygdalus) have been obtained by hanging drop vapor diffusion using polyethylene glycol 4000 and isopropanol as co-precipitants. The crystals belong to the monoclinic space group P2(1) with unit cell parameters a = 69.9, b = 95.1, c = 95.6 A, and beta = 118.5 degrees. A complete set of diffraction data has been collected to 2.6 A resolution on native crystals of isoenzyme III.

Crystallization and preliminary x-ray diffraction analysis of hydroxynitrile lyase from cassava (Manihot esculenta).

Hydroxynitrile lyase from M. esculenta (cassava) was crystallized in two different crystal forms by the hanging-drop vapour-diffusion method. Crystals of form I were obtained from a mixture of polyethylene glycol 8000 and 2-methyl-2,4-pentanediol, and belong to the tetragonal space group P41212 or its enantiomorph P43212, with unit-cell parameters a = b = 105.9, c = 188.9 A and with two molecules in the asymmetric unit. These crystals diffract to 2.9 A with conventional X-ray sources and beyond 2.1 A resolution with synchrotron radiation. The crystals are relatively sensitive to radiation damage and conditions for flash-cooling the crystals have been established. A complete native data set has been collected up to 2.2 A resolution. Crystal form II has been obtained at pH 5.6 using lithium sulfate as a precipitant. The crystals apparently belong to the orthorhombic space group P21212, with unit-cell parameters a = 117.52, b = 127.09 and c = 78.08 A, have two molecules in the asymmetric unit and diffract to beyond 2.0 A resolution. A complete native data set has been collected to 2.2 A resolution.

The reaction of fluorocitrate with aconitase and the crystal structure of the enzyme-inhibitor complex.

It has been known for many years that fluoroacetate and fluorocitrate when metabolized are highly toxic, and that at least one effect of fluorocitrate is to inactivate aconitase. In this paper we present evidence supporting the hypothesis that the (-)-erythro diastereomer of 2-fluorocitrate acts as a mechanism based inhibitor of aconitase by first being converted to fluoro-cis-aconitate, followed by addition of hydroxide and with loss of fluoride to form 4-hydroxy-trans-aconitate (HTn), which binds very tightly, but not covalently, to the enzyme. Formation of HTn by these reactions is in accord with the working model for the enzyme mechanism. That HTn is the product of fluorocitrate inhibition is supported by the crystal structure of the enzyme-inhibitor complex at 2.05-A resolution, release of fluoride stoichiometric with total enzyme when (-)-erythro-2-fluorocitrate is added, HPLC analysis of the product, slow displacement of HTn by 10(6)-fold excess of isocitrate, and previously published Mössbauer experiments. When (+)-erythro-2-fluorocitrate is added to aconitase, the release of fluoride is stoichiometric with total substrate added, and HPLC analysis of the products indicates the formation of oxalosuccinate, and its derivative alpha-ketoglutarate. This is consistent with the proposed mechanism, as is the formation of HTn from (-)-erythro-2-fluorocitrate. The structure of the inhibited complex reveals that HTn binds like the inhibitor trans-aconitate while providing all the interactions of the natural substrate, isocitrate. The structure exhibits four hydrogen bonds < 2.7 A in length involving HTn, H2O bound to the [4Fe-4S] cluster, Asp-165 and His-167, as well as low temperature factors for these moieties, consistent with the observed very tight binding of the inhibitor.

Crystallographic studies and preliminary X-ray investigation of (S)-p-hydroxy-mandelonitrile lyase from Sorghum bicolor (L.).

(S)-p-Hydroxy-mandelonitrile lyase from Sorghum bicolor has been crystallized in three different forms using the hanging-drop vapor-diffusion technique. Crystal form I is obtained from 1.4 M (NH(4))(2)SO(4) in 100 mM Na-acetate, pH 4.6, and belongs to the orthorhombic space group P2(1)2(1)2(1). The cell dimensions are a = 71.4, b = 95.8, c = 149.1 A. A complete set of diffraction data has been collected to 2.6 A resolution. Form II crystals are grown from 500 mM Li(2)SO(4) in 13% polyethylene glycol 8000. These crystals appear as hexagonal plates and diffract to 2.98 A resolution but apparently are twinned. Cocrystallizing hydroxynitrile lyase with the inhibitor benzoic acid using 1.4 M (NH(4))(2)SO(4) in 100 mM Na citrate, pH 5.4 as precipitant yields crystal form III, which belongs to the monoclinic space group C2 with a = 150.7, b = 103.7, c = 90.6 A, beta = 101.3. X-ray diffraction data were collected to 2.3 A resolution.

Crystal structures of aconitase with isocitrate and nitroisocitrate bound.

The crystal structures of mitochondrial aconitase with isocitrate and nitroisocitrate bound have been solved and refined to R factors of 0.179 and 0.161, respectively, for all observed data in the range 8.0-2.1 A. Porcine heart enzyme was used for determining the structure with isocitrate bound. The presence of isocitrate in the crystals was corroborated by Mössbauer spectroscopy. Bovine heart enzyme was used for determining the structure with the reaction intermediate analogue nitroisocitrate bound. The inhibitor binds to the enzyme in a manner virtually identical to that of isocitrate. Both compounds bind to the unique Fe atom of the [4Fe-4S] cluster via a hydroxyl oxygen and one carboxyl oxygen. A H2O molecule is also bound, making Fe six-coordinate. The unique Fe is pulled away approximately 0.2 A from the corner of the cubane compared to the position it would occupy in a symmetrically ligated [4Fe-4S] cluster. At least 23 residues from all four domains of aconitase contribute to the active site. These residues participate in substrate recognition (Arg447, Arg452, Arg580, Arg644, Gln72, Ser166, Ser643), cluster ligation and interaction (Cys358, Cys421, Cys424, Asn258, Asn446), and hydrogen bonds supporting active site side chains (Ala74, Asp568, Ser571, Thr567). Residues implicated in catalysis are Ser642 and three histidine-carboxylate pairs (Asp100-His101, Asp165-His147, Glu262-His167). The base necessary for proton abstraction from C beta of isocitrate appears to be Ser642; the O gamma atom is proximal to the calculated hydrogen position, while the environment of O gamma suggests stabilization of an alkoxide (an oxyanion hole formed by the amide and side chain of Arg644). The histidine-carboxylate pairs appear to be required for proton transfer reactions involving two oxygens bound to Fe, one derived from solvent (bound H2O) and one derived from substrate hydroxyl. Each oxygen is in contact with a histidine, and both are in contact with the side chain of Asp165, which bridges the two sites on the six-coordinate Fe.

Automated docking in crystallography: analysis of the substrates of aconitase.

Automated docking of substrates to proteins of known structure aids the process of crystallographic analysis in two ways. First, automated docking can be used to generate a small number of starting models for substrates using only protein coordinates from an early stage of refinement. Second, automated docking provides a method for exploring aspects of catalysis that are inaccessible to crystallography by postulating binding modes of catalytic intermediates. This paper describes the use of automated docking to explore the binding of substrates to aconitase. The technique starts with a substrate molecule in an arbitrary configuration and position and finds favorable docked configurations in a (static) protein active site based on a molecular mechanics type force field. Using protein coordinates from an early stage of refinement of an aconitase-isocitrate complex, we successfully predicted the binding configuration of isocitrate. Four configurations were found, the energetically most favorable of which fit the observed electron density well and was used as a starting model for further refinement. Two configurations were found in citrate docking experiments, the second of which approximates the mode of substrate binding in an aconitase-nitrocitrate complex. We were also able to propose two binding modes of the catalytic intermediate cis-aconitate. These correspond closely to the isocitrate and the citrate binding modes. The relation of these new results to the proposed reaction mechanism is discussed.

A two-dimensional NMR study of the solution structure of a DNA dodecamer comprising the concensus sequence for the specific DNA-binding sites of the glucocorticoid receptor protein.

A two-dimensional 500-MHz 1H-NMR study on the non-self-complementary double-stranded DNA dodecamer 5'd(C-C-A-G-A-A-C-A-G-T-G-G)5'd(C-C-A-C-T-G-T-T-C-T-G-G), is presented. This oligonucleotide contains the consensus octanucleotide sequence 5'd(A-G-A-A-C-A-G-T) for the specific DNA-binding sites of the glucocorticoid receptor protein [Payvar, F. et al. (1984) Cell 35, 381-392]. Using a combination of two-dimensional pure phase absorption nuclear Overhauser enhancement (NOESY) and homonuclear J-correlated (COSY) spectroscopy all non-exchangeable base (with the exception fo the adenine H2 protons), methyl and deoxyribose H1', H2', H2", H3' and H4' resonances are assigned unambiguously using a sequential resonance assignment strategy. From the relative intensities of the cross peaks in the pure phase absorption NOESY spectra at two mixing times it is shown that the dodecamer adopts a B-type conformation in solution.