Adenylate kinase structure

The first technique is very intuitive. Out of the few proteins that could be crystallized in a number of different conformations, adenylate kinase is probably the best-studied example. By combining nine observed crystal structures and interpolating between them, a movie was constructed that visualized a hypothetical path of its hinge-bending transition (jVonrhein et al. 1995]). 

To facilitate conformational transitions in the before-mentioned adenylate kinase, Elamrani and co-workers scaled all atomic masses by a large factor thus allowing the use of a high effective simulation temperature of 2000K ([Elamrani et al. 1996]). To prevent protein unfolding, elements of secondary structure had to be constrained. 

Figure 4.14 Examples of different types of open twisted a/p structures. Both schematic and topological diagrams are given. In the topological diagrams, arrows denote strands of p sheet and rectangles denote a helices, (a) The FMN-binding redox protein flavodoxln. (b) The enzyme adenylate kinase, which catalyzes the reaction AMP +...

The second structure, adenylate kinase (Figure 4.14b), has two such posi-I tions, one on each side of p strand 1. The connection from strand 1 to strand 12 goes to the right, whereas the connection from the flanking strands 3 and 4 both go to the left. Crevices are formed between p strands 1 and 3 and [between strands 1 and 4. One of these crevices forms part of an AMP-binding [site, and the other crevice forms part of an ATP-binding site that catalyzes the Iformation of ADP from AMP and ATP. 

Lahti CJ, d Oliveira CE, Johnson PJ (1992) Beta-succinyl-coenzyme A synthetase from Trichomonas vaginalis is a soluble hydrogenosomal protein with an amino-terminal sequence that resembles mitochondrial presequences. J Bacteriol 174 6822-6830 Lange S, Rozario C, Muller M (1994) Primary structure of the hydrogenosomal adenylate kinase of Trichomonas vaginalis and its phylogenetic relationships. Mol Biochem Parasitol 66 297-308... 

O Rorke, A. O Cuinn, G. Purification and some structural properties of adenylate kinase from Leuconostoc mesenteroides (Lactobacteriaceae). Int. 

Saint Girons, I. Gilles, A.-M. Margarita, D. Michelson, S. Monnot, M. Fermandjian, S. Danchin, A. Barzu, O. Structural and catalytic characteristics of Escherichia coli adenylate kinase. J. Biol. Ghent., 262, 622-629 (1987)... 

Glaser, P. Prescecan, E. Delepierre, M. Surewicz, W.K. Mantsch, H.H. Barzu, O. Gilles, A.-M. Zinc, a novel structural element found in the family of bacterial adenylate kinases. Biochemistry, 31, 3038-3043 (1992)... 

Wild, K. Grafmuller, R. Wagner, E. Schulz, G.E. Structure, catalysis and supramolecular assembly of adenylate kinase from maize. Eur. J. Biochem., 250, 326-331 (1997)... 

Schlauderer, G.J. Schulz, G.E. The structure of bovine mitochondrial adenylate kinase comparison with isoenzymes in other compartments. Protein Sci., 5, 434-441 (1996)... 

Lin, Y. Nageswara Rao, B.D. Structural characterization of adenine nucleotides bound to Escherichia coli adenylate kinase. 2. P and C Relaxation measurements in the presence of cobalt(II) and manganese(ll). Biochemistry, 39, 3647-3655 (2000)... 

Diederichs, K. Schulz, G.E. Three-dimensional structure of the complex between the mitochondrial matrix adenylate kinase and its substrate AMP. Biochemistry, 29, 8138-8144 (1990)... 

Adenylate kinase performs the essential function of recovering AMP formed by many enzymatic processes and converting it to ADP (Eq. 6-65) which can be reconverted to ATP by oxidative or substrate level phosphorylation. The enzyme is present in all organisms. In vertebrates different isoenzymes function in the cytosol, mitochondrial intermembrane space, and mitochondrial matrix.862 863 A group of other nucleotide and deoxynucleotide kinases convert nucleoside monophosphates into diphosphates.864 865 Some of them, e.g., uridylate kinase are similar in structure and properties to adenylate kinase.866 867 Another member of the adenylate kinase family is phosphoribulokinase, an important photosynthetic enzyme (see Fig. 17-14, step a).868... 

Fructose 6-phosphate kinase (phosphofructo-kinase) has attracted much attention because of its regulatory properties (Chapter n).880-882 Prokaryotic forms are somewhat simpler.883 The related fructose 6-phosphate 2-kinase is a component of a bifunctional kinase-phosphatase (Fig. 11-2, steps d and e) and has a structure similar to that of adenylate kinase.884... 

In fact, kinetic studies of the GTP-dependent avian mitochondrial enzyme indicate two metal-binding sites, one on the polyphosphate group of the bound GTP and one on carboxylate side chains of the protein.252 255 The three-dimensional structure of the ATP-dependent E. coli enzyme reveals a nucleotide binding site similar to the ATP site of adenylate kinase (Fig. 12-30).256 A definite binding site for C02 is also present in the enzyme.257... 

Thiosulfate cyanide sulfurtransferase symmetry in 78 TTiiouridine 234 Three-dimensional structures of aconitase 689 adenylate kinase 655 aldehyde oxido-reductase 891 D-amino acid oxidase 791 a-amylase, pancreatic 607 aspartate aminotransferase 57,135 catalytic intermediates 752 aspartate carbamyltransferase 348 aspartate chemoreceptor 562 bacteriophage P22 66 cadherin 408 calmodulin 317 carbonic acid anhydrase I 679 carboxypeptidase A 64 catalase 853 cholera toxin 333, 546 chymotrypsin 611 citrate synthase 702, 703 cutinase 134 cyclosporin 488 cytochrome c 847 cytochrome c peroxidase 849 dihydrofolate reductase 807 DNA 214, 223,228,229, 241 DNA complex... 

Wernimont AK, Loppnau P, Crombet L et al. Crystal structure of PF10 0086, adenylate kinase from plasmodium falciparum. 

Amino acid sequence of adenylate kinase (Adk), ras protein and the fi subunit are aligned. The conserved glycine-rich sequence is shown (bottom). The secondary structures of adenylate kinase... 

Gly-Lys-Thr/ Ser) is found in many proteins capable of binding ATP or GTP including adenylate kinase66 671 and the ras p21 protein68-691 (Fig. 11.7). The sequence corresponds to a flexible loop structure between a helix and / sheet the sequence of adenylate kinase and ras protein are residues 15-23 (Gly-Gly-Pro-Gly-Ser-Gly-Lys-Gly-Thr) and 10-17 (Gly-Ala-Gly-Gly-Val-Gly-Lys Ser), respectively. 

Khoo JC, Russsel PJ Jr. Adenylate kinase from bakers yeast. IV. Substrate and inhibitor structural requirements. J. Biol. Chem. 1970 245 4163-4167. 

Figure 9.46. Structures of Adenylate Kinase and Guanylate Kinase. The nucleoside triphosphate-binding domain is a common feature in these and other homologous nucleotide kinases. The domain consists of a central P-pleated sheet surrounded on both sides by a helices (highlighted in purple) as well as a key loop (shown in green).

GJ. Schlauderer, K. Proba, and G.E. Schulz. 1996. Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP J. Mol. Biol. 256 223-221. (PubMed)... 

Phosphoryl transfer is a fundamental reaction in biochemistry and is one that was discussed in mechanistic and structural detail earlier (Section 9.4). Kinases are enzymes that catalyze the transfer of a phosphoryl group from ATP to an acceptor. Hexokinase, then, catalyzes the transfer of a phosphoryl group from ATP to a variety of six-carbon sugars (hexoses), such as glucose and mannose. Hexokinase, like adenylate kinase (Section 9.4.2) and all other kinases,... 

D.H. Harrison, J.A. Runquist, A. Holub, and H.M. Miziorko. 1998. The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase Biochemistry 37 5074-5085. (PubMed)... 

---