Conformation of MgATP bound to nucleotidyl and phosphoryl transfer enzymes 1H-transferred NOE measurements on complexes of methionyl tRNA synthetase and pyruvate kinase

Yeast hexokinase PII--bound nucleotide conformation at the active site

The structure of adenine nucleotide bound at the active site of yeast hexokinase PII (PII) was studied in the complexes PII x ADPMg(II), PII x ADPMg(II) x Glc and PII x ADPMg(II) x NO3- x Glc using two-dimensional transferred NOE spectroscopy. Binding of the nucleotide ligand to the enzyme resulted in downfield shift of several ligand resonances. Changes in the chemical shift as a function of ligand concentration indicate that various resonances in the bound and free form of the ligand appear to be in fast exchange. The largest chemical shift change between the bound and the free states (delta vM = 88 +/- 9 Hz) at an NMR frequency of 500 MHz was observed for the H2 resonance of the adenine ring. A lower limit for the rate of ligand dissociation from the complex derived from these results is k(off) >> 550 s(-1). Interproton NOEs for various ligand protons in PII x ADPMg(II), PII x ADPMg(II) x Glc and PII x ADPMg(II) x NO3- x Glc complexes were measured at 500 MHz at 10 degrees C. The NOE buildup curves constructed from such measurements made at various mixing times (40, 80, 120, 160 and 200 ms) were analyzed using complete relaxation matrix calculations and various interproton distances were determined. These distances were used in restrained molecular dynamics calculations to derive the conformation of the nucleotide bound at the active site of the enzyme. The results of these calculations indicate that the nucleotide binds in an anti conformation. The glycosidic torsion angle chi (O4'-C1'-N9-C8) determined for the nucleotide in PII x ADPMg(II), PII x ADPMg(II) x Glc and PII x ADPMg(II) x NO3- x Glc complexes are 68 +/- 4 degrees, 52 +/- 4 degrees and 49 +/- 4 degrees respectively. In all these complexes, the ribose pucker is best represented by the unsymmetrical O4'-endo-C1'-exo twist ((o)T1). The observed decrease in the glycosidic torsion angle of the bound nucleotide is attributed to the glucose-induced conformational changes in the enzyme. The structure of the nucleotide derived here is at variance from the one proposed on the basis of X-ray crystallography and model building [Shoham, M. & Steitz, T. A. (1980) J. Mol. Biol. 140, 1-14].

Adenosine conformations of nucleotides bound to methionyl tRNA synthetase by transferred nuclear Overhauser effect spectroscopy

The conformations of MgATP and AMP bound to a monomeric tryptic fragment of methionyl tRNA synthetase have been investigated by two-dimensional proton transferred nuclear Overhauser effect spectroscopy (TRNOESY). The sample protocol was chosen to minimize contributions from adventitious binding of the nucleotides to the observed NOE. The experiments were performed at 500 MHz on three different complexes, E.MgATP, E.MgATP.L-methioninol, and E.AMP.L-methioninol. A starter set of distances obtained by fitting NOE build-up curves (not involving H5' and H5") were used to determine a CHARMm energy-minimized structure. The positioning of the H5' and H5" protons was determined on the basis of a conformational search of the torsion angle to obtain the best fit with the observed NOEs for their superposed resonance. Using this structure, a relaxation matrix was set up to calculate theoretical build-up curves for all of the NOEs and compare them with the observed curves. The final structures deduced for the adenosine moieties in the three complexes are very similar, and are described by a glycosidic torsion angle (chi) of 56 degrees +/- 5 degrees and a phase angle of pseudorotation (P) in the range of 47 degrees to 52 degrees, describing a 3(4)T-4E sugar pucker. The glycosidic torsion angle, chi, deduced here for this adenylyl transfer enzyme and those determined previously for three phosphoryl transfer enzymes (creatine kinase, arginine kinase, and pyruvate kinase), and one pyrophosphoryl enzyme (PRibPP synthetase), are all in the range 52 degrees +/- 8 degrees. The narrow range of values suggests a possible common motif for the recognition and binding of the adenosine moiety at the active sites of ATP-utilizing enzymes, irrespective of the point of cleavage on the phosphate chain.

Two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY) studies of nucleotide conformations in arginine kinase complexes

Two-dimensional proton transfer nuclear Overhauser spectroscopy (TRNOESY) studies of the conformations of the adenosine moieties in the nucleotides bound at the active site of the lobster (Homarus americanus) muscle arginine kinase are reported. TRNOESY measurements were made using a sample protocol chosen to minimize contributions from weak non-specific binding of the nucleotides to the observed NOE's. This was done by making the measurements as a function of ligand concentration while keeping the ligand to enzyme concentration ratio fixed at 10:1. The experiments were performed at 500 MHz and 10 degrees C for six different mixing times in the range 40-300 ms. The measurements were made on three complexes of the enzyme: E.MgATP, E.MgADP, and the long-lived transition-state-analog complex (E.MgADP.NO-3.arginine). All the complexes, including the transition-state-analog complex with an estimated lifetime of about 50 ms, satisfy the fast-exchange condition. The TRNOE buildup curves for all the nucleotide-proton pairs in each complex were analyzed using a complete relaxation matrix appropriate for fast exchange. The interproton distances obtained from the NOE analysis were used as constraints in obtaining an energy-minimized conformation on the basis of the program CHARMm. The glycosidic torsion angle (chi) for the adenosine moiety in all three complexes is about 50 degrees +/- 5 degrees. The glycosidic orientation agrees well with that determined for MgATP and MgADP complexes of creatine kinase (Murali et al., 1993), MgATP bound at the active and ancillary sites of pyruvate kinase (Jarori et al., 1994a), and PRPP synthetase (Jarori et al., 1994b).(ABSTRACT TRUNCATED AT 250 WORDS)

Two-dimensional transferred nuclear Overhauser effect spectroscopy study of the confirmation of MgATP bound at the active and ancillary sites of rabbit muscle pyruvate kinase

Pyruvate kinase binds one adenosine 5'-triphosphate (ATP) molecule at its active site and another at an ancillary site on each subunit. In order to determine the conformation of ATP bound at these sites, proton transferred two-dimensional nuclear Overhauser effect spectroscopy (TRNOESY) measurements were made at 500 MHz and 10 degrees C for several mixing times in the range 40-200 ms. The NOE values for the proton pair H1'-H2' of ribose (which are 2.9 +/- 0.2 A apart, irrespective of nucleotide conformation) as a function of ligand concentration (1-10 mM ATP), with the ratio of ligand to enzyme being kept constant, indicate that at higher ligand concentrations adventitious binding of ATP at nonspecific site(s) makes a major contribution to the observed NOEs. When the ligand concentration is < 2 mM, site-specific NOEs can be measured. Furthermore, addition of phosphoenolpyruvate (PEP) to the enzyme-MgATP sample results in competitive displacement of MgATP from the active site and reduces the observed NOE to that arising exclusively at the ancillary site, thus allowing the measurement of site-specific NOEs. The interproton distances determined from such site-specific NOE buildup curves were used as constraints in CHARMm to obtain the structure of MgATP. At the active site, MgATP has a glycosidic torsion chi = 44 +/- 5 degrees and the phase angle of pseudorotation for ribose P = 42.4 degrees. At the ancillary site chi = 46 +/- 5 degrees and P = 127.6 degrees. Thus the orientation of the adenine with respect to the sugar moiety is the same at both sites.(ABSTRACT TRUNCATED AT 250 WORDS)