Structure of Escherichia coli glutamate decarboxylase (GADalpha) in complex with glutarate at 2.05 angstroms resolution.

Glutamate decarboxylase (GAD) is a pyridoxal enzyme that catalyzes the conversion of L-glutamate into gamma-aminobutyric acid and carbon dioxide. The Escherichia coli enzyme exists as two isozymes, referred to as GADalpha and GADbeta. Crystals of the complex of the recombinant isozyme GADalpha with glutarate as a substrate analogue were grown in space group R3, with unit-cell parameters a = b = 117.1, c = 196.4 angstroms. The structure of the enzyme was solved by the molecular-replacement method and refined at 2.05 angstroms resolution to an R factor of 15.1% (R(free) = 19.9%). The asymmetric unit contains a dimer consisting of two subunits of the enzyme related by a noncrystallographic twofold axis which is perpendicular to and intersects a crystallographic threefold axis. The dimers are related by a crystallographic threefold axis to form a hexamer. The active site of each subunit is formed by residues of the large domains of both subunits of the dimer. The coenzyme pyridoxal phosphate (PLP) forms an aldimine bond with Lys276. The glutarate molecule bound in the active site of the enzyme adopts two conformations with equal occupancies. One of the two carboxy groups of the glutarate occupies the same position in both conformations and forms hydrogen bonds with the N atom of the main chain of Phe63 and the side chain of Thr62 of one subunit and the side chains of Asp86 and Asn83 of the adjacent subunit of the dimer. Apparently, it is in this position that the distal carboxy group of the substrate would be bound by the enzyme, thus providing recognition of glutamic acid by the enzyme.

Glutamate decarboxylase: computer studies of enzyme evolution.

The homology of subunit primary sequence of 40 glutamate decarboxylases (GAD) of different origin was analyzed by multiple alignment. A phylogenetic tree was designed on the basis of the resulting data. The following groups are distinguished in the consensus tree: archeans, bacteria, plant eukaryotes, and animal eukaryotes. The latter are clearly divided into two branches according to two enzyme isoforms. Borders of PLP domains in each enzyme were detected. The consensus phylogenetic tree for PLP domains is structurally rather similar to that obtained for subunits. Twenty homologous motifs of from 15 to 87 amino acid residues were revealed in all GAD studied. The results revealed the division of all of the enzymes into groups with characteristic sets of motifs in each and a fixed order of their arrangement along the sequence. Thus, we can show the divergent evolution of the enzyme. The results of multiple alignments during structural analysis of the 40 GAD confirmed and extended our previous data on conserved residues that arrange the position of the coenzyme (PLP) in the enzyme active center. The following residues should be noted: lysine forming a Schiff base with the PLP aldehyde group, an adjacent histidine, and aspartic acid that establishes a link with nitrogen of the PLP pyridine ring. The homology of the primary sequence fragments was also found in the residues in contact with the PLP phosphate group. Comparison of the GAD amino acid sequence with that of another PLP enzyme, aspartate aminotransferase, revealed a binding site for carboxylic group of the substrate--glutamic acid. The structures carrying out a particular catalytic function of all GAD studied were detected, i.e., convergent evolution of the enzyme was revealed.

Structure of glutamate decarboxylase and related PLP-enzymes: computer-graphical studies.

Amino acid sequences of E. coli glutamate decarboxylase (GADa) and those of 36 GAD of different origin were compared by pairwise alignment using computer program CLUSTAL. GADalpha and plant enzymes showed 59.8-67.8% subunit homology, GADalpha and other bacterial GAD--49.8-77.6%, whereas GADalpha and animal enzymes--13.9-58.8%. Two PLP domains exhibited higher homology comparing to that of the whole subunit in the case of GAD67, plant (68.4-73.9%), and bacterial (46.7-83.2%) enzymes. The alignment of PLP-domains of 37 GAD, three group II decarboxylases, and two pyridoxal enzymes with known 3D structures (bacterial ORD and mAAT from chicken heart) allowed us to reveal conserved residues of the active sites. Their functional role is discussed. Modelling of the PLP-binding sites in active centers for GADalpha and human brain GAD67 was done using the Swiss-PdbViewer homology modelling program. Although the homology between GADalpha and GAD67 is rather low, structural similarity of their active sites allows us to consider here a functional convergence. Thus, glutamate decarboxylation by GADalpha may be helpful for understanding general mechanism of this reaction.

[Reactions of decarboxylated and side transamination during interaction of glutamate decarboxylase from Escherichia coli with substrate analogs, modified through C3 and C4 atoms]. / Reaktsii dekarboksilirovaniia i pobochnogo transaminirovaniia pri vzaimodeistvii glutamatdekarboksilazy iz Escherichia coli s analogami substrata, modifitsirovannymi po atomam C3 i C4.

The interaction of glutamate decarboxylase with the aspartate and glutamate analogues modified at C3 and C4 was studied. 3-Arsonoalanine, 3-phosphonoalanine, 2-amino-4-arsonobutyric acid, 2-amino-4-phosphonobutyric acid, a mixture of diastereoisomers of 4-(methylthio) glutamic acid and erythro-4-(methylthio) glutamic acid were shown to be poor substrates for the enzyme. Their decarboxylation was accompanied by transamination of the coenzyme (PLP) to pyridoxamine phosphate (PMP) which reversibly inactivated the enzyme. With arsonoalanine only part of PLP was converted into PMP and another part irreversibly formed a complex. 4-(Methylsulfonyl)-L-glutamic and 4-[(phenyl)(hydroxy)phosphoryl]-L-glutamic acids did not react with the glutamate decarboxylase.

The interaction of glutamate decarboxylase from Escherichia coli with substrate analogues modified at C-3 and C-4.

The interaction of glutamate decarboxylase with the aspartate analogues 3-arsonoalanine and 3-phosphonoalanine, with the glutamate analogues 2-amino-4-arsonobutyric acid and 2-amino-4-phosphonobutyric acid, and with 4-(methylthio)-L-glutamic acid, both as a mixture of diastereoisomers and as the (2S,4R)-form, was studied. All these analogues were poor substrates for the enzyme and only weak inhibitors. Their decarboxylation was accompanied by transamination of the enzyme-bound pyridoxal phosphate (PLP) to pyridoxamine phosphate (PMP), thus inactivating the decarboxylase. With arsonoalanine only part of the PLP was converted into PMP.

[Study of the quaternary structure of glutamate carboxylase from Escherichia coli]. / Issledovanie chetvertichnoi struktury glutamatdekarboksilazy iz Escherichia coli.

It was shown by electron microscopy, that the native molecule of glutamate decarboxylase is a hexamer with dihedral symmetry; the subunits are situated at the apices of an octahedron. Apoenzyme at pH 6.0 is dissociated form. It were found s20.w - 12.8 +/- 0.54S and 5.51 +/- 0.43S for the native hexamer and a dissociated form, respectively. By column gel-filtration the molecular mass of the dissociated form was estimated as 105-106 kDa, this value corresponds to a dimer. There were 10 buried SH-groups per subunit in the hexamer, after dimer formation 8 of them became accessible. The reversible hexamer-dimer dissociation depends on pH and PLP. The pH dependences of the enzyme dissociation and activity are very similar. In the result of adding of 6 PLP equivalents to the dimers the reactivation and hexamer assembly were reached, the SH-groups burying preceded both these reactions. Effect of pH and PLP on the quaternary structure is known for some other PLP-enzymes. It may be the additional proof for the idea of a common ancestor for PLP-enzymes.

[Reactivation and reconstitution of glutamate decarboxylase upon the interaction of its dimers with pyridoxal phosphate]. / Reaktivatsiia i rekonstruktsiia geksamera glutamatdekarboksilazy pri vzaimodeistvii ee dimerov s piridoksal'fosfatom.

The relationship between the reactivation and reconstitution of the hexameric form of glutamate decarboxylase during the interaction of inactive apoenzyme dimers with pyridoxal phosphate (PLP) has been studied. It was shown that the restoration of enzymatic activity, appearance of spectral maximum at 340 nm, and reconstitution of the hexamer depend on the amount of PLP added; this reaction is completed when the PLP concentration reaches that of the initial enzyme. This native hexamer of the holo- and apoenzyme does not practically contain exposed sulfhydryl groups. Ten cysteine residues become available after DS-Na denaturation. The dimer of the apoenzyme contains 8 exposed and 2 buried cysteine residues. The hexamer formation from the dimers is accompanied by the burying of the cysteine residues. When half of the required PLP was added, 7 cysteine residues became buried in experiments with DTNB and six in experiments with 4.4'-DTDP. Further addition of PLP led to the disappearance of the exposed sulfhydryl groups.

[A model of enzymatic decarboxylation of glutamic acid]. / Model' fermentativnogo dekarboksilirovaniia glutaminovoi kisloty.

Interaction of glutamate decarboxylase with its adequate substrate and some quasi-substrates was studied by spectrokinetic, quantum-chemical and some other approaches. It was shown that in the course of decarboxylation an abortive transamination of pyridoxal-5'-phosphate leading to the enzyme inactivation does occur. Identification of intermediate coenzyme-substrate complexes allowed to formulate a model of enzymatic decarboxylation taking into account both the main and abortive reactions. The analysis of electronic structure of the intermediates revealed some of the factors determining the functional specificity of the reaction under study.

[Effects of pyridoxal-phosphate and its 4'- and 5'-substituted analogs on macromolecular structure of Escherichia coli glutamate decarboxylase]. / Vliianie pirodoksal'fosfata i ego 4'- i 5'-zameshchennykh analogov na makromolekuliarnuiu strukturu glutamatdekarboksilazy Escherichia coli.

Interactions of pyridoxal phosphate and its analogs (at pH 6.0) with dimeric glutamate apodecarboxylase (E. coli) were examined by spectrophotometric and CD-titration and by gel electrophoresis. It was shown that 5 equivalents of pyridoxal-phosphate fully restore the catalytic activity and optical properties of the enzyme, whereas 3 equivalents of the coenzyme suffice for reconstitution of the hexameric structure. Similar amounts of the 2 nor PLP adn 5'-methtyl PLP restore the hexameric macromolecule. 15 equivalents of pyridoxine phosphate or 54 -- of pyridoxamine phosphate are required for complete saturation of the apoenzymes binding sites and concomitant reconstitution of the hexameric structure. 5'-deoxy-5'-carboxymethyl pyridoxal, 5'-deoxy-5'-phosphonomethyl pyridoxal and cis-5'-deoxy-5'-phosphonomethylen pyridoxal were merely bound to the dimeric apoenzyme, but failed to restore the enzyme's quaternary structure. Pyridoxal, trans-5'-deoxy-5'-posphonomethylen pyridoxal and pyridoxine analogs substituted in position 5' with carboxyl or phosphonyl group did not interact with the apodecarboxylase.

[Simplified method of isolating glutamate decarboxylase from Escherichia coli]. / Uproshchennyi metod vydeleniia glutamatdekarboksilazy iz Escherichia coli.

A modified method for preparation of partially and highly purified glutamate decarboxylase from E. coli str. 600 was developed. Cell disruption was achieved by brief autolysis (6 hours at 37 degrees C). Residues of nucleic acids and acidic proteins were removed by means of streptomycin sulfate that replace protamine sulfate. The use of modified ion-exchange chromatography and improved monitoring of enzyme elution from DEAE-cellulose columns helped to prepare highly purified glutamate decarboxylase, the crystallization stage being omitted. Preparation of partially and highly purified enzyme with specific activities of 6,000-14,000 and 20,000-35,000 microliter CO2/10 min/mg protein, respectively were obtained.

[Substrate specificity of E. coli glutamate decarboxylase]. / Substratnaia spetsifichnost' glutamatdekarboksilazy E. coli.

Interaction of highly purified E. coli glutamate decarboxylase with a number substrate analogs was studied. Decarboxylation of the following amino acids was demonstrated: gamma-methylene glutamate, threo-beta-hydroxyglutamate, allo-gamma-hydroxyglutamate, threo-beta-methylglutamate, homocysteate, aminoadipate and cysteinesulfinate. The Km and either Ki or I50 values were determined for these compounds. The final products of the interaction of glutamate decarboxylase with these analogs have the same absorption spectra and capacity for reactivation by pyridoxal-P, as has the pyridoxamine-P form of the enzyme. Thus, decarboxylation of all the amino acids, mentioned above, was probably associated with the side reaction of transamination to coenzyme in the active center. Binding of aliphatic dicarboxylic acids or of valeric acid by glutamate decarboxylase leads to a slight shift of absorption spectra and of circular dichroism spectra from 420 to 423--425 nm. The following compounds fail to be bound and decarboxylated by the enzyme: gamma-aminobutyrate, D-glutamate, L-glutamine, 3,3-dimethylglutarate, methioninesulfone, methioninesulfoxide, norvaline, gamma-hydroxy-gamma-methylglutamate, erytro-beta-methylglutamate and erythro-beta-hydroxyglutamate.