Giuseppina Gatti

Three-dimensional structure of the complex between pancreatic secretory trypsin inhibitor (Kazal type) and trypsinogen at 1.8 A resolution. Structure solution, crystallographic refinement and preliminary structural interpretation.

Abstract The three-dimensional structure of the proteic complex formed by bovine trypsinogen and the porcine pancreatic secretory trypsin inhibitor (Kazal type) has been solved by means of Patterson search techniques, using a predicted model of the trypsin-ovomucoid complex ( Papamokos et al., 1982 ). The structure of the complex, including 162 solvent molecules, has been refined at 1.8 A resolution (26,341 unique reflections) to a conventional crystallographic R factor of 0.195. The inhibitor molecule binds to trypsinogen via hydrogen bonds and/or apolar interactions at sites P9, P7, P6, P5, P3, P1, P1′, P2′ and P3′ of the contact area. The structure of the inhibitor itself resembles closely that of the third domain of Japanese quail ovomucoid inhibitor, recently reported by Weber et al. (1981) . The trypsinogen part of the complex resembles trypsin, as is the case in the trypsinogen-basic pancreatic trypsin inhibitor complex, but two segments of the activation domain adopt a different conformation. Most notably in the N-terminal region the Ile16-Gly19 loop, which is disordered in free trypsinogen and in the trypsinogen-basic pancreatic trypsin inhibitor complex ( Huber & Bode, 1978 ), assumes a regular structure and the polypeptide chain can be traced as far as residue Asp14. This new and fixed structure allows the formation of a buried salt link between the side-chains of Lys156 and Asp194. Conformations differing from those of trypsin are also found for residues 20 to 28 and residues 141 to 155. Some structural perturbation is observed in other parts of the molecule, including the calcium loop.

Aplysia limacina myoglobin. Crystallographic analysis at 1.6 Å resolution

The crystal structure of the ferric form of myoglobin from the mollusc Aplysia limacina has been refined at 1.6 A resolution, by restrained crystallographic refinement methods. The crystallographic R-factor is 0.19. The tertiary structure of the molecule conforms to the common globin fold, consisting of eight alpha-helices. The N-terminal helix A and helix G deviate significantly from linearity. The distal residue is recognized as Val63 (E7), which, however, does not contact the heme directly. Moreover the sixth (distal) co-ordination position of heme iron is not occupied by a water molecule at neutrality, i.e. below the acid-alkaline transition point of A. limacina myoglobin. The heme group sits in its crevice in the conventional orientation and no signs of heme isomerism are evident. The iron atom is 0.26 A out of the porphyrin plane, with a mean Fe-N (porphyrin) distance of 2.01 A. The co-ordination bond to the proximal histidine has a length of 2.05 A, and forms an angle of 4 degrees with the heme normal. A plane containing the imidazole ring of the proximal His intersects the heme at an angle of 29 degrees with the (porphyrin) 4N-2N direction. Inspection of the structure of pH 9.0 indicates that a hydroxyl ion is bound to the Fe sixth co-ordination position.

Crystal structure of yeast Cu,Zn superoxide dismutase: Crystallographic refinement at 2.5 Å resolution☆

The structure of Cu,Zn yeast superoxide dismutase has been determined to 2.5 A resolution. The enzyme crystallizes in the P2(1)2(1)2 space group with two dimeric enzyme molecules per asymmetric unit. The structure has been solved by molecular replacement techniques using the dimer of the bovine enzyme as the search model, and refined by molecular dynamics with crystallographic pseudo-energy terms, followed by conventional crystallographic restrained refinement. The R-factor for 32,088 unique reflections in the 10.0 to 2.5 A resolution range (98.2% of all possible reflections) is 0.158 for a model comprising two protein dimers and 516 bound solvent molecules, with a root-mean-square deviation of 0.016 A from the ideal bond lengths, and an average B-factor value of 29.9 A2. A dimeric molecule of the enzyme is composed of two identical subunits related by a non-crystallographic 2-fold axis. Each subunit (153 amino acid residues) has as its structural scaffolding a flattened antiparallel eight-stranded beta-barrel, plus three external loops. The overall three-dimensional structure is quite similar to the phylogenetically distant bovine superoxide dismutase (55% amino acid homology), the largest deviations can be observed in the regions of amino acid insertions. The major insertion site hosting residues Ser25A and Gly25B, occurs in the 2,3 beta-turn between strands 2b and 3c, resulting in the structural perturbations of the two neighbouring strands. The second insertion site, at the end of the 3c beta-strand in the wide Greek-key loop, hosts the Asn35A residue, having an evident effect on the structure of the loop and possibly on the neighbouring 5,4 beta-turn. The salt bridge Arg77-Asp99 and the disulphide bridge Cys55-Cys144 stabilize the loop regions containing the metal ligands. The stereochemistry of the two metal centres is conserved, with respect to the bovine enzyme. The Cu2+ ligands show an uneven distortion from a square plane, while Zn2+ co-ordination geometry is distorted tetrahedral. The imidazole ring of the His61 residue forms a bridge between Cu and Zn ions. A solvent peak compatible with a fifth ligand is observed 2.0 A away from the copper in the active site channel, which is filled by ordered water molecules that possibly contribute to the stability and function of the enzyme. The charged residues responsible for the electrostatic guidance of the substrate to the active site (Glu130, Glu131, Lys134 and Arg141) are fairly conserved in their positions, some of them showing different interactions in the four chains due to the intermolecular contacts between the dimers.(ABSTRACT TRUNCATED AT 400 WORDS)

Interaction between serine (pro)enzymes, and kazal and kunitz inhibitors*

Equilibrium constants (Kd) for PSTI (porcine pancreatic secretory trypsin inhibitor: Kazal inhibitor) and BPTI (bovine basic pancreatic trypsin inhibitor: Kunitz inhibitor) binding to bovine β-trypsin, bovine trypsinogen, bovine α-chymotrypsin, human urinary kallikrein and porcine pancreatic kallikrein have been obtained at pH 8. Kd values have been determined by measuring the loss of the enzymatic activity and the spectral changes accompanying the formation of the PSTI: (pro)enzyme and BPTI: (pro)enzyme adducts. PSTI is characterized by systematically lower affinities than BPTI and does not inhibit either kallikrein up to inhibitor concentrations of 3 m m . As in the case of BPTI, the affinity of PSTI for bovine trypsinogen increases in the presence of 0·02 m -H-Ile-Val-OH, which mimics, in the proenzyme, the N-terminal segment of the activated bovine β-trypsin. BPTI: bovine trypsinogen: H-Ile-Val-OH and PSTI: bovine trypsinogen: H-Ile-Val-OH complexes show absorption spectra similar to those of BPTI: bovine β-trypsin and PSTI: bovine β-trypsin adducts. The pH dependence of the equilibrium constants for PSTI and BPTI binding to bovine β-trypsin, bovine trypsinogen and bovine α-chymotrypsin is roughly the same for both the inhibitors with the following scale of apparent affinities: β-trypsin ≫ α-chymotrypsin > trypsinogen. The simplest model that describes the experimental data, between pH 5 and 9·5, takes into account a single ionizable group with a pKUNL of approximately 7·2 in the free (pro)enzymes, which appears to decrease by about two units upon PSTI and BTPI binding. The most probable ionizing group to account for such a behaviour is His57, present at the active site of (pro)enzymes. Comparison of the three-dimensional structures of PSTI and BPTI adducts shows that the respective reactive sites, despite structural identity around the scissile peptide bond, differ in their geometry of subsites further away from it. In particular, the wider reactive site polypeptide loop of PSTI as compared to that of BPTI may be responsible, at least in part, for the different binding behaviour of the two inhibitors.

X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin at 2•0 Å resolution : stabilization of the fluoride ion by hydrogen bonding to Arg66 (E10)

The X-ray crystal structure of the fluoride derivative of Aplysia limacina ferric myoglobin has been solved and refined at 2.0 A resolution; the crystallographic R-factor is 13.6%. The fluoride ion binds to the sixth co-ordination position of the heme iron, 2.2 A from the metal. Binding of the negatively charged ligand on the distal side of the heme pocket of this myoglobin, which lacks the distal His, is associated with a network of hydrogen bonds that includes the fluoride ion, the residue Arg66 (E10), the heme propionate III, three ordered water molecules and backbone or side-chain atoms from the CD region. A comparison of fluoride and oxygen dissociation rate constants of A. limacina myoglobin, sperm whale (Physeter catodon) myoglobin and Glycera dibranchiata monomeric hemoglobin, suggests that the conformational readjustment of Arg66 (E10) in A. limacina myoglobin may represent the molecular basis for ligand stabilization, in the absence of a hydrogen-bond donor residue at the distal E7 position.

Crystal structure of ferric Aplysia limacina myoglobin at 2.0 Å resolution

The three-dimensional structure of ferric myoglobin from the mollusc Aplysia limacina has been refined at 2 X 0 A resolution. The crystallographic R factor, calculated at this stage, is 0 X 194. Despite its high content of apolar residues (both aromatic and aliphatic), Aplysia limacina myoglobin, which contains only one histidine residue (at the proximal position), has a structure that conforms to the common eight-helices globin fold observed in other phyla.

Reassessment of copper stoichiometry in ascorbate oxidase

A very pure ascorbate oxidase solution was obtained by dissolving a crystalline sample of the enzyme. The ratio between 280 and 610 nm absorbancies was 22.5. It contained 8.0 +/- 0.2 Cu ions, 50% EPR detectable, per dimeric molecule (140,000 M.W.) with a molar extinction coefficient of 10,000 cm-1 at 610 nm. Two Cu ions were removed by treatment with N,N-diethyldithiocarbamate. The optical blue absorption band was unaffected, while two EPR detectable Cu ions were lost, with disappearance of the type 2 Cu signal. It is concluded that native ascorbate oxidase contains two type 1, two type 2, and four type 3 Cu ions.

Selective crystallization of horse isoferritins.

Various precipitating agents were examined in order to crystallize horse heart and spleen ferritins. Cadmium sulfate induced the crystallization of the spleen ferritin, while 2-methyl-2,4-pentanediol and poly(ethylene glycol) only induced that of the heart ferritin. Isoelectric focusing analysis showed that the crystals grown from cadmium sulfate contained only the more acidic isoferritins, and those grown from methyl pentanediol only the less acidic isoferritins. Heart ferritin crystallizes in a cubic space group, as previously reported for spleen ferritin crystals grown from cadmium sulfate.

Crystallographic characterization and three-dimensional model of yeast Cu,Zn superoxide dismutase

The Cu,Zn superoxide dismutase from yeast was crystallized in the orthorhombic space group P21212 with unit cell dimension a = 105.1 A,b = 142.2 A, c = 62.1 A. The crystals grow in 25 mM citrate, 10 mM phosphate buffer pH 6.5, and 6% (W/V) polyethylene glycol, with a Vm of 3,4 A3/dalton, for two dimers/asymmetric unit. The crystals were unstable in the mother liquor, but were stabilized by transfer to a 35% polyethylene glycol solution. This crystalline form diffracts at high resolution and is suitable for determination of the atomic structure. The three dimensional structure of the yeast enzyme could be model-built by computer graphics techniques using the bovine enzyme atomic coordinates as template. The proposed model requires removal of some salt bridges and non equivalence of the metal-binding sites in the subunits, in line with reported functional properties of the yeast enzyme.

Single crystal absorption spectra of ascorbate oxidase from green zucchini squash

Single crystal polarized absorption spectra of the dimeric multicopper enzyme ascorbate oxidase from green zucchini squash indicate that its most relevant functional and structural properties are maintained in the crystalline state. Since the polarized absorption spectra of crystalline ascorbate oxidase are very similar, in the visible region, to those of crystalline plastocyanin, we expect that structural data will show similar orientation of the type 1 Cu2+ center with respect to the crystal axes. The selective removal of type 2 Cu2+ from the crystal has been realized and has a potential value for the identification of the copper centers in the crystallographic analysis of the enzyme. Evidence is presented for an azide binding site formed by type 2 and type 3 Cu3+, similar to the trinuclear copper center suggested to be present in laccase.