Kinase transition state

Yousef, M.S. Fabiola, F. Gattis, J.L. Somasundaram, T. Chapman, M.S. Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution mechanistic insights. Acta Crystallogr. Sect. D, 58, 2009-2017 (2002)... 

GatCAB amidotransferase.This natural product mimics the charged 3 -terminus of aa-tRNA and has been used as a tool for the study of protein biosynthesis. The parent compound 22 is a very weak inhibitor of AdT. The amino acid chain is related to tyrosine and differs from the glutamic and aspartic side chains transformed in the kinase or the transamidase steps. Replacement of the methoxyphenyl moiety of puromycin by carboxylic acid derivatives (23-26) improved the ability to inhibit this AdT. Stable analogues of the transition state in the last step of the transamidation process (27-29) where the carbonyl to be attacked by NH3 is replaced by tetrahedral sulfur or phosphorus atom with a methyl group mimicking ammonia exhibited the highest activity. 

The substrate specificities of both mammalian and yeast hexo-kinases have been extensively studied (76,77). Nevertheless, work in this area continues both in the search for isoenzyme specific inhibitors and in increasingly detailed investigations of the catalytic mechanism. Recently potential transition state analogs PI-(adenosine-5 )-P3-glucose-6 triphosphate (Ap -glucose) and P1-(adenosine-5 )-P4-glucose-6 triphosphate (Ap.-giucose) were tested as inhibitors of four hexokinase isoenzymes. However, they were found to exhibit less affinity for the enzyme than either of the natural substrates alone (78). 

Figure 4.. Possible structure of the transition state for phos-phoryl transfer in the creatine kinase reaction. Adapted from Cook et al(95).

Gil-Ortiz, E Ramon-Maiques, S. Fita, L Rubio, V. The course of phosphorus in the reaction of N-acetyl-L-glutamate kinase, determined from the structures of crystalline complexes, including a complex with an AlF(4)(-) transition state mimic. J. Mol. Biol., 331, 231-244 (2003)... 

Brooks, S.P. Bennett, V.D. Suelter, C.H. Homogeneous chicken heart mitochondrial creatine kinase purified by dye-ligand and transition-state analog-affinity chromatography. Anal. Biochem., 164, 190-198 (1987)... 

K.N. The 2.1 A structure of Torpedo californica creatine kinase complexed with the ADP-Mg -NOj-creatine transition-state analogue complex. Biochemistry, 41, 13861-13867 (2002)... 

S.J. Ellington, W.R. Chapman, M.S. Expression, purification from inclusion bodies, and crystal characterization of a transition state analog complex of arginine kinase a model for studying phosphagen kinases. Protein Sci., 6, 444-449 (1997)... 

Purich, D.L. Fromm, H.J. Inhibition of rabbit skeletal muscle adenylate kinase by the transition state analogue, P P -di(adenosine-5 )tetraphos-phate. Biochim. Biophys. Acta, 276, 563-567 (1972)... 

Such studies on creatine kinase (Eq. 12-31) utilized both a bound Mn2+ ion and a nitroxide spin label to estimate distances of various protons from the nitroxide.683 Together with EPR measurements (Box 8-C), which gave the Mn2+-nitroxide distance, a model of the ATP Mn2 complex in the active site was constructed. Additional EPR experiments on Mn2+ complexes with ATP and ADP containing 170 in the a, (3, or y phospho groups showed that in the enzyme ATP creatine complex the metal ion is bound to all three phospho groups of ATP. It remained coordinated with the two phospho groups of ADP and also that of the phospho-creatine product in the enzyme ADP creatine-P complex as well as in the transition state, which is pictured occurring via a metaphosphate ion.684... 

Figure 12-19 Proposed transition state structure formed from Mn2+i ATP, and creatine bound in the active site of muscle creatine kinase. Based on EPR spectroscopy with regiospecifically 170-labeled substrates. The electrical charges have been added in one possible constellation. However, hydrogen atoms bound to phospho groups are not shown. After Leyh et al.68i...

Although inversion was not observed with the E. colt alkaline phosphatase, it has been observed for ribonucleases and many other hydrolytic enzymes and for most kinases transferring phospho groups from ATP. The difference lies in the existence of a phospho-enzyme intermediate in the action of alkaline phosphatase (see Eq. 12-38). Each of the two phosphotransferase steps in the phosphatase action apparently occurs with inversion. The simplest interpretation of all the experimental results is that phosphotransferases usually act by in-line -like mechanisms which may involve metaphosphate-ion-like transition states that are constrained to react with an incoming nucleophile to give inversion. An adjacent attack with pseudorotation would probably retain the original configuration and is therefore excluded. 

A simple procedure to prepare 5-aryl- and 5-pyridyl-2-furaldehydes from inexpensive, commercially available 2-furaldehyde diethyl acetal was reported. The reaction proceeded in a four-step, one-pot procedure and the yield of coupling step was usually between 58-91% <02OL375>. A facile route to 3,4-furandicarboxylic acids was developed. DDQ-oxidation of 2,5-dihydrofuran derivatives, which were produced from dimethyl maleic anhydride, furnished the desired esters of furan-3,4-dicarboxylic acid <02S1010>. The furan-fused tetracyclic core of halenaquinol and halenaquinone possessing antibiotic, cardiotonic, and protein tyrosine kinase inhibitory activities was synthesized. Intramolecular cycloaddition of an o-quinodimethane with furan gave the adduct as a single isomer via an enrfo-transition state, which was converted to trisubstituted furan by oxidation-elimination reactions <02T6097>. 

Peptide substrate then docJcs onto the protein kinase, in general presumably occupying a cleft along the C-terminal lobe, as exemplified by the peptide inhibitor in the PKA-AMPPNP-PKI and IRK-ATP structures. Catalysis appears to be via a dissociative transition state mecdianism and a planar phosphate intermediate [20, 22]. The incoming peptide hydroxyl is oriented via Asp-127, which is in turn further stabilized via a hydrogen bond to Asn-132. These latter two residues that... 

As was the case with other phosphotransfer reactions, the hydrolysis reaction catalyzed by PTPs lies along a mechanistic continuum between the limiting cases of associative and dissociative mechanisms. In the case of Yersina PTP, a crystal structure was solved with nitrate, a mimic of the transition state similar to the use of AIF3 with protein kinase A. In this case, analysis of the structure is proposed to be more consistent with a -1 charged metaphosphate, dissociative mechanism (11). 

Madhusudan, Akamine P, Xuong NH, Taylor SS. Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase. Nat. Struct. Biol. 2002 9 273-277. 

Figure 4 (a) Analogs of DNA that contain a dimethyl sulfone group have a distorted backbone compared with the natural biopolymer, which makes them useful as inhibitors of restriction enzymes, (b) A sulfonylbenzoyl nitrostyrene inhibitor of tyrosine protein kinase was designed based on a transition state model of the reaction of ATP with tyrosine residues and exhibits good activity, (c) Based on salicyl-AMP, a sulfamoyl-containing compound exhibits remarkable activity in the inhibition of siderophore biosynthesis. 

It seems that the syn selectivity in the nitroaldol reaction can best be explained as arising from steric hindrance in the bicyclic transition state it seems that the greater stereoselectivity obtained by use of catalysts 27 and 28 can be ascribed to increased catalyst stability, even in the presence of an excess of highly acidic nitroalkanes. The syn-selective asymmetric nitroaldol reaction was successfully applied to the catalytic asymmetric synthesis of t/zreo-dihydrosphingosine 45, which elicits a variety of cellular responses by inhibiting protein kinase C. An efficient synthesis of erythro-AHPA 42 from L-phenylalanine was, moreover, achieved by using LLB (Sch. 9) [59],... 

H.J. Muller-Dieckmann and G.E. Schulz. 1994. The structure of uridylate kinase with its substrates, showing the transition state geometry J. Mol. Biol. 236 361-367. (PubMed)... 

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