ABSTRACT
The endochitinase from Coccidioides immitis (CiX1) is a member of the class 18 chitinase family. Here we show the enzyme functions by a retaining catalytic mechanism; that is, the beta-conformation of the chitin substrate linkages is preserved after hydrolysis. The pattern of cleavage of N-acetyglucosamine (GlcNAc) oligosaccharide substrates has been determined. (GlcNAc)6 is predominantly cleaved into (GlcNAc)2 and (GlcNAc)4, where the (GlcNAc)2 group arises from the nonreducing end of the substrate and is formed as the beta-anomer. With time, transglycosylation occurs, generating (GlcNAc)8 from the product dimer and fresh hexamer. Similar patterns are seen for the cleavage of (GlcNAc)5 and (GlcNAc)4 where dimers cleaved from the nonreducing end reflect the most common binding and hydrolysis pattern. Intrinsic fluorescence measurements suggest the dissociation constant for (GlcNAc)4 is 50 microM. Synthetic substrates with fluorescent leaving groups exhibit complicated profiles in the relationship between initial velocity and substrate concentration, making it difficult to obtain the values of kinetic constants. An improved theoretical analysis of the time-course of (GlcNAc)6 degradation allows the unitary free energy of binding of the individual subsites of the enzyme to be estimated. The free energy values obtained are consistent with the dissociation constant obtained by fluorescence measurements, and generate a model of substrate interaction that can be tested against the crystal structure of the enzyme.
Subject(s)
Chitinases/metabolism , Coccidioides/enzymology , Fungal Proteins/metabolism , Saccharomyces cerevisiae Proteins , Acetylglucosamine/metabolism , Binding Sites , Coccidioides/pathogenicity , Hydrogen-Ion Concentration , Hydrolysis , Kinetics , Oligosaccharides/metabolism , Substrate Specificity , Time FactorsABSTRACT
Histidine decarboxylase (HDC) from Lactobacillus 30a produces histamine that is essential to counter waste acids, and to optimize cell growth. The HDC trimer is active at low pH and inactive at neutral to alkaline pH. We have solved the X-ray structure of HDC at pH 8 and revealed the novel mechanism of pH regulation. At high pH helix B is unwound, destroying the substrate binding pocket. At acid pH the helix is stabilized, partly through protonation of Asp198 and Asp53 on either side of the molecular interface, acting as a proton trap. In contrast to hemoglobin regulation, pH has a large effect on the tertiary structure of HDC monomers and relatively little or no effect on quaternary structure.
Subject(s)
Histidine Decarboxylase/chemistry , Histidine Decarboxylase/metabolism , Lactobacillus/enzymology , Binding Sites , Crystallography, X-Ray , Hydrogen-Ion Concentration , Models, Molecular , Protein Structure, Quaternary , Protein Structure, Tertiary , ProtonsABSTRACT
Ricin A-chain is an N-glucosidase that attacks ribosomal RNA at a highly conserved adenine residue. Our recent crystallographic studies show that not only adenine and formycin, but also pterin-based rings can bind in the active site of ricin. For a better understanding of the means by which ricin recognizes adenine rings, the geometries and interaction energies were calculated for a number of complexes between ricin and tautomeric modifications of formycin, adenine, pterin, and guanine. These were studied by molecular mechanics, semi-empirical quantum mechanics, and ab initio quantum mechanical methods. The calculations indicate that the formycin ring binds better than adenine and pterin better than formycin, a result that is consistent with the crystallographic data. A tautomer of pterin that is not in the low energy form in either the gas phase or in aqueous solution has the best interaction with the enzyme. The net interaction energy, defined as the interaction energy calculated in vacuo between the receptor and an inhibitor minus the solvation energy of the inhibitor, provides a good prediction of the ability of the inhibitor to bind to the receptor. The results from experimental and molecular modeling work suggest that the ricin binding site is not flexible and may only recognize a limited range of adenine-like rings.
Subject(s)
Ricin/chemistry , Ricin/metabolism , Adenine/chemistry , Adenine/metabolism , Binding Sites , Enzyme Inhibitors , Formycins/chemistry , Formycins/metabolism , Glucosidases/antagonists & inhibitors , Glucosidases/chemistry , Glucosidases/metabolism , Guanine/chemistry , Guanine/metabolism , Hydrogen Bonding , Ligands , Models, Chemical , Protein Binding , Pterins/chemistry , Pterins/metabolism , Substrate SpecificityABSTRACT
Chitinase is necessary for fungal growth and cell division and, therefore, is an ideal target for the design of inhibitors which may act as antifungal agents. A chitinase from the fungal pathogen Coccidioides immitis has been expressed as a fusion protein with gluathione-S-transferase (GST), which aids in purification. After cleavage from GST, chitinase was crystallized from 30% PEG 4000 in 0. 1 M sodium acetate pH 4.6. The crystals have a tetragonal crystal lattice and belong to space group P41212 or P43212 and diffract to 2. 2 A resolution. The unit-cell parameters are a = b = 91.2, c = 95.4 A; there is only one chitinase molecule in the asymmetric unit.
Subject(s)
Chitinases/chemistry , Coccidioides/enzymology , Fungal Proteins/chemistry , Chitinases/isolation & purification , Crystallization , Crystallography, X-Ray , Fungal Proteins/isolation & purification , Metals, Heavy/chemistry , Protein ConformationABSTRACT
Saccharomyces cerevisiae possesses three isozymes of 5,10-methylenetetrahydrofolate dehydrogenase (MTD). The NAD-dependent enzyme is the first monofunctional form found in eukaryotes. Here we report its crystallization in a form suitable for high-resolution structure. The space group is P4(2)2(1)2 with cell constants a = b = 75.9, c = 160.0 A, and there is one 36 kDa molecule in the asymmetric unit. Crystals diffract to 2.9 A resolution.
