Crystallographic studies of the catalytic mechanism of the neutral form of fructose-1,6-bisphosphatase

The crystal structures of fructose-1,6-bisphosphatase (EC 3.1.3.11) complexed with substrate alone or with substrate analogues in the presence of divalent metal ions have been determined. The substrate analogues, 2,5-anhydro-D-glucitol-1,6-bisphosphate (AhG-1,6-P2) and 2,5-anhydro-D-mannitol-1,6-bisphosphate (AhM-1,6-P2), differ from the alpha and beta anomers of fructose-1,6-bisphosphate (Fru-1,6-P2), respectively, in that the OH on C2 is replaced by a hydrogen atom. Structures have been refined at resolutions of 2.5 to 3.0 A to R factors of 0.172 to 0.195 with root-mean-square deviations of 0.012-0.018 A and 2.7-3.8 degrees from the ideal geometries of bond lengths and bond angles, respectively. In addition, the complex of substrate with the enzyme has been determined in the absence of metal. The electron density at 2.5-A resolution does not distinguish between alpha and beta anomers, which differ for the most part only in the position of the 1-phosphate group and the orientation of the C2-hydroxyl group. The positions of the 6-phosphate and the sugar ring of the substrate analogues are almost identical to those of the respective anomer of the substrate. In the presence of metal ions the positions of the 1-phosphate groups of both alpha and beta analogues differ significantly (0.8-1.0 A) from those of anomers of the substrate in the metal-free complex. Two metal ions (Mn2+ or Zn2+) are located at the enzyme active site of complexes of the alpha analogue AhG-1,6-P2. Metal site 1 is coordinated by the carboxylate groups of Glu-97, Asp-118, and Glu-280 and the 1-phosphate group of substrate analogue, while the metal site 2 is coordinated by the carboxylate groups of Glu-97, Asp-118, the 1-phosphate group of substrate analogue, and the carbonyl oxygen of Leu-120. Both metal sites have a distorted tetrahedral geometry. However, only one metal ion (Mg2+ or Mn2+) is found very near the metal site 1 in the enzyme's active site in complexes of the beta analogue AhM-1,6-P2 or for Mg2+ in the complex of the alpha analogue AhG-1,6-P2. This single metal ion is coordinated by the carboxylate groups of Glu-97, Asp-118, Asp-121, and Glu-280 and the 1-phosphate group of substrate analogue in a distorted square pyramidal geometry.(ABSTRACT TRUNCATED AT 400 WORDS)

Similarities and differences between human cyclophilin A and other beta-barrel structures. Structural refinement at 1.63 A resolution

The structure of the unligated recombinant human cyclophilin A (CyP A) has been refined to an R-factor of 0.18 at 1.63 A resolution. The root-mean-squared deviations of the refined structure are 0.013 A and 2.50 degrees from ideal geometries of bond length and bond angle, respectively. Eight antiparallel beta-strands of CyP A form a right-handed beta-barrel. The structure of CyP A is compared with other members in the antiparallel eight-stranded beta-barrel family and with the parallel eight-stranded alpha/beta barrels. Although all known eight-stranded barrels are right-handed, the tilted angle of the strands against the barrel axis varies from 45 degrees for retinol binding protein and 49 degrees for CyP A to 70 degrees for superoxide dismutase. As a result, the beta-barrel of CyP A is not completely superimposable with other members of beta-barrels. The structure of CyP A has a unique topology, distinct from other members in the beta-barrel family. In addition, CyP A is a closed beta-barrel so that neither the immunosuppressive drug cyclosporin A (CsA) nor the proline-containing substrate can bind to the hydrophobic core of the CyP A barrel, while the hydrophobic core of most other barrels is open for ligation. These observations probably indicate that CyP A is neither functionally nor evolutionally related to other beta-barrel structures. Details of interactions between solvent molecules and the active site residues of CyP A are illustrated. A water-co-operated mechanism, where the cis<-->trans isomerization might possibly consist of (1) transition of the prolyl bond and (2) release of N or C-terminal residues of substrate from CyP, is addressed. The refined structure reveals no disulfide bridges in CyP A. Cys115 is near the CsA site, but unlikely to be directly involved in CsA binding because of steric hindrance from Thr119 and Leu122. This geometry probably rules out any mechanisms involving a tetrahedral intermediate formed between cysteine and substrate during cis<-->trans isomerization.

Crystal structure of the neutral form of fructose 1,6-bisphosphatase complexed with regulatory inhibitor fructose 2,6-bisphosphate at 2.6-A resolution

The three-dimensional structure of the complex between fructose 1,6-bisphosphatase (EC 3.1.3.11) and the physiological inhibitor beta-D-fructose 2,6-bisphosphate (Fru-2,6-P2), an analogue of the substrate (fructose 1,6-bisphosphate), has been refined at 2.6-A resolution to a residual error (R) factor of 0.171. The rms deviations are 0.012 A and 2.88 degrees from ideal geometries of bond lengths and angles, respectively. The Fru-2,6-P2 occupies the active sites of both polypeptides C1 and C2 in the crystallographic asymmetric unit in the space group P3(2)21. The furanose and 6-phosphate of Fru-2,6-P2 are located at the fructose 6-phosphate site established earlier, and the 2-phosphate binds to the OH of Ser-124, the NH3+ of Lys-274, and the backbone NH of Gly-122 and Ser-123. Backbone displacements of 1 A occur for residues from Asp-121 to Asn-125. Model building of substrate alpha-D-Fru-1,6-P2 based on the binding structure of Fru-2,6-P2 in the active site shows interactions of the 1-phosphate with the backbone NH of Ser-123 and Ser-124. In the AMP sites, density peaks attributed to Fru-2,6-P2 are seen in C1 (and C4) but not in C2 (and C3). This minor binding of Fru-2,6-P2 to AMP sites partially explains the synergistic interaction between AMP and Fru-2,6-P2 and the protection of the AMP site from acetylation in the presence of Fru-2,6-P2. In the synergistic interaction between AMP and Fru-2,6-P2, inhibition of catalytic metal binding by the presence of Fru-2,6-P2 at the active site, and propagation of structural changes over some 28 A along beta-strand B3 from residues 121 to 125 in the active site to Lys-112 and Tyr-113 in the AMP site, as well as movement of helices across the interdimeric interfaces, may affect AMP binding and the subsequent R-to-T transition. In addition, occupancy of Fru-2,6-P2 at the AMP sites of C1 and C4 may favor binding of AMP to the remaining unoccupied AMP sites and thus promote the accompanying quaternary conformational changes.

Molecular structure of fructose-1,6-bisphosphatase at 2.8-A resolution

Fructose-1,6-bisphosphatase (D-fructose-1,6-bisphosphate 1-phosphohydrolase, EC 3.1.3.11) from the cortex of pig kidney and its complexes with either fructose 2,6-bisphosphate (Fru-2,6-P2) or adenosine monophosphate (AMP) have been crystallized in the space group P3(2)21. The three-dimensional structure of the native enzyme has been solved at 3.0-A resolution by the multiple isomorphous replacement method and refined at 2.8-A resolution to a crystallographic R factor of 0.194. A total of 316 of 335 residues, omitting disordered regions 1-5 and 54-67, have been built into the monomer, which has average dimensions of about 30 A by 50 A by 35 A. Four monomeric units aggregate into a molecular tetramer with D2 symmetry, which approximates a disk about 35 A thick. Each monomer consists of about 33% alpha-helix, 23% beta-strand, and 6% beta-turn. Four sites for Fru-2,6-P2 and two major sites for AMP binding per tetramer have been identified by difference Fourier techniques. The binding site for Fru-2,6-P2 is shared by two neighboring monomers and consists of side-chain atoms of Asn-212, Tyr-244, Tyr-264, and Lys-274; backbone atoms of Gly-246 through Met-248; and only Arg-243 from the adjacent subunit. In addition, Asn-125, Tyr-215, and Lys-269 are located within a distance of about 5 A of Fru-2,6-P2. A negatively charged pocket near this binding site includes Asp-118, Asp-121, Glu-280, Glu-97, and Glu-98. The AMP binding site is located near Val-17, Gln-20, Gly-21, Ala-24 through Met-30, Lys-112, Tyr-113, Arg-140, and Met-177.