Role of lysine-183 in D-glyceraldehyde-3-phosphate dehydrogenases. Properties of the N-acetylated yeast, sturgeon muscle and rabbit muscle enzymes

Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation

The emerging view of N^ε-lysine acetylation in eukaryotes is of a relatively abundant post-translational modification (PTM) that has a major impact on the function, structure, stability and/or location of thousands of proteins involved in diverse cellular processes. This PTM is typically considered to arise by the donation of the acetyl group from acetyl-coenzyme A (acCoA) to the ε-amino group of a lysine residue that is reversibly catalyzed by lysine acetyltransferases and deacetylases. Here, we provide genetic, mass spectrometric, biochemical and structural evidence that N^ε-lysine acetylation is an equally abundant and important PTM in bacteria. Applying a recently developed, label-free and global mass spectrometric approach to an isogenic set of mutants, we detected acetylation of thousands of lysine residues on hundreds of Escherichia coli proteins that participate in diverse and often essential cellular processes, including translation, transcription and central metabolism. Many of these acetylations were regulated in an acetyl phosphate (acP)-dependent manner, providing compelling evidence for a recently reported mechanism of bacterial N^ε-lysine acetylation. These mass spectrometric data, coupled with observations made by crystallography, biochemistry, and additional mass spectrometry showed that this acP-dependent acetylation is both non-enzymatic and specific, with specificity determined by the accessibility, reactivity and three-dimensional microenvironment of the target lysine. Crystallographic evidence shows acP can bind to proteins in active sites and cofactor binding sites, but also potentially anywhere molecules with a phosphate moiety could bind. Finally, we provide evidence that acP-dependent acetylation can impact the function of critical enzymes, including glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, and RNA polymerase.

[Comparative study on the chemical modification of sulfhydryl groups of glyceraldehyde-3-phosphate dehydrogenases from yeast and rabbit muscle. The relationship between structure and chemical reactivity]

Chemical modification of cystein 149 residues from yeast apo-glyceraldehyde-3-phosphate dehydrogenase either by iodoacetamidonaphtol or N-(4-dimethylamino-3,5-dinitrophenyl) maleimide results in the disappearance of free sulfhydryl groups according to "full sites reactivity", whereas loss of the dehydrogenase activity occurs following "half of the sites reactivity". Chemical modification of the same cystein residues of the rabbit muscle apoenzyme by N-(4-dimethylamino-3,5-dinitrophenyl) maleimid shows that both loss of activity and disappearance of the sulphydryl groups may be described as "full sites reactivity" phenomena. After chemical modification by iodoacetamidonaphtol both processes follow "half of the sites reactivity".

Structure and reactivity relationship in glyceraldehyde-3-phosphate dehydrogenase. Dinitrophenylation of cysteine residues of yeast and rabbit muscle enzymes

Dinitrophenylation of rabbit muscle and yeast glyceraldehyde-3-phosphate dehydrogenases modifies only SH groups. The rabbit muscle apoenzyme loses 75% of its original activity upon dinitrophenylation of two SH groups per tetramer whereas the yeast apoenzyme is totally inactivated under the same conditions. Dinitrophenylation of the active-site cysteine-149 of rabbit muscle and yeast holoenzymes results in an loss of activity corresponding to a 'half-of-the-sites' and a 'full-sites' reactivity, respectively. Determination of the sulphydryl content of the modified enzymes shows an unmasking of the cysteine residues of the dinitrophenylated rabbit muscle apoenzyme which is not observed for the yeast protein. However, conformational changes are revealed for both dinitrophenylated apoenzymes by differential absorption spectroscopy or by limited proteolysis. Sulphydryl group unmasking is not observed after modification of the cysteine residues of the rabbit muscle holoenzyme but it does occur when dinitrophenylation is performed in the presence of two moles NAD+/mole rabbit muscle enzyme. Although the apoenzyme is sensitive to an induced conformational change, our results favour symmetrical structures for both yeast apo and holo enzymes. The bis-dinitrophenylated rabbit muscle apoenzyme presents all the characteristics of an asymmetrical structure; however, it is not possible to deduce whether this symmetry is due to the chemical modification or whether it preexists in the native apoenzyme. The results of the dinitrophenylation of the rabbit holoenzyme, however, indicate that this enzyme possesses an asymmetrical structure.

Structural and functional consequences of subunit interactions in glyceraldehyde 3-phosphate dehydrogenase

A variety of species of GPDH undergo acylation at two of the four active cystein sites per mole of tetrameric enzyme. This reaction requires tightly bound NAD+, a situation restricted to two of the four NAD sites per tetramer. S leads to N acyl transfer from cysteins to lysine in the diacyl enzyme yields an inactive enzyme. The thiol ester bond of acyl enzyme is activated by NAD+ and NADH for the group transfer and reduction reactions, respectively. In furyl acryloyl-GPDH this activation is accompanied by large acyl-spectral shifts, a "blue shift" with NADH and a "red shift" with NAD+. The group transfer reaction as well as spectral shifts show biphasic kinetics. The amplitude of the fast phase of NAD+-induced spectral change in apo-enzyme is equal to that of the fast phase in phosphorolysis (or arsenolysis) at low [NAD+]. The kinetic pattern of spectral shifts by NAD+ and NADH are complementary; the amplitude of the fast phase in one is equal to that of the slow phase in the other. It has been proposed that the acyl enzyme exists in two conformational states. The relative proportion of these states varies with the extent of covalent (acyl group) or non-covalent (NAD+ or NADH) ligation in a manner consistent with the allosteric model of Monod, Wyman and Changeux. These conclusions apply equally to the true substrate acyl enzyme. With 1,3-diphosphoglycerate, a tetra-acylated enzyme is obtained. Two of these four acyl groups react very much faster than the remaining two. A comparison of their specific rates with the steady state turnover numbers indicates that only the less reactive two acyl groups govern the turnover number of the enzyme.