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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The substrate binding sites of adenylate kinase (AK) proposed by X-ray crystallographic studies [Pai, E. F., Sachsenheimer, W., Schirmer, R. H., & Schulz, G. E. (1977) J. Mol. Biol. 114, 37-45, and subsequent revisions] were evaluated by site-specific mutagenesis in conjunction with structural analysis by NMR. The residues examined in this report include two near an adenosine site (threonine-39 and arginine-44) and two in the phosphate binding region (arginine-128 and arginine-149). The results and conclusions are summarized as follows: (a) Although Thr-39 is very close to an adenine site [Egner, U., Tomasselli, A. G., & Schulz, G. E. (1987) J. Mol. Biol. 195, 649-658], it is nonessential either structurally or functionally. (b) The R44M mutant enzyme showed significant increases in the Michaelis and dissociation constants of adenosine 5'-monophosphate (AMP) (36- and 22-fold, respectively) while all other kinetic parameters were relatively unperturbed. The proton NMR property of this mutant was unchanged in the free enzyme and only slightly perturbed in the binary complexes with AMP and with MgATP (adenosine 5'-triphosphate), and in the ternary complex with MgAP5A [P1,P5-bis(5'-adenosyl) pentaphosphate]. These results indicate that Arg-44 interacts specifically with AMP starting at the binary complex, and suggest that the MgATP site proposed by Pai et al. (1977) is likely to be the AMP site. (c) The kinetic parameters of R149M were dramatically perturbed: kcat decreased by a factor of 1540, Km increased to 130-fold, and kcat/Km decreased by a factor of 2 X 10(5).(ABSTRACT TRUNCATED AT 250 WORDS)
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PMID:Mechanism of adenylate kinase. Critical evaluation of the X-ray model and assignment of the AMP site. 212 96

Although X-ray crystallographic and NMR studies have been made on the adenylate kinases, the substrate-binding sites are not unequivocally established. In an attempt to shed light on the binding sites for MgATP2- and for AMP2- in human cytosolic adenylate kinase (EC 2.7.4.3, hAK1), we have investigated the enzymic effects of replacement of the arginine residues (R44, R132, R138, and R149), which had been assumed by Pai et al. [Pai, E. F., Sachsenheimer, W., Schirmer, R. H., & Schulz, G. E. (1977) J. Mol. Biol. 114, 37-45] to interact with the phosphoryl groups of AMP2- and MgATP2-. With use of the site-directed mutagenesis method, point mutations were made in the artificial gene for hAK1 [Kim, H. J., Nishikawa, S., Tanaka, T., Uesugi, S., Takenaka, H., Hamada, M., & Kuby, S. A. (1989) Protein Eng. 2, 379-386] to replace these arginine residues with alanyl residues and yield the mutants R44A hAK1, R132A hAK1, R138A hAK1, and R149A hAK1. The resulting large increases in the Km,app values for AMP2- of the mutant enzymes, the relatively small increases in the Km,app values for MgATP2-, and the fact that the R132A, R138A, and R149A mutant enzymes proved to be very poor catalysts are consistent with the idea that the assigned substrate binding sites of Pai et al. (1977) have been reversed and that their ATP-binding site may be assigned as the AMP site.
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PMID:In vitro mutagenesis studies at the arginine residues of adenylate kinase. A revised binding site for AMP in the X-ray-deduced model. 215 84

Human term placenta contains an ATP diphosphohydrolase activity which hydrolyses ATP to ADP and inorganic phosphate and ADP to AMP and a second mole of inorganic phosphate. The activity has a pH optimum between 8.0 and 8.5. Magnesium or calcium ions are required for maximum activity. Other nucleoside phosphates, p-nitrophenyl phosphate or sodium pyrophosphate, are not hydrolysed. The activity is not due to ATPases, or to myokinase, as determined by the use of inhibitors. NaF and NaN3 were found to inhibit strongly the activity thus identifying it as an ATP diphosphohydrolase. A sensitive enzymatic assay for measurement of AMP, one of the products of the reaction, was established, based on the strong inhibition of muscle fructose 1,6-biphosphatase by AMP. The range of the assay was 0.05-0.8 microM AMP. ATP diphosphohydrolase was found to have a rate of AMP production from ADP twice the rate from ATP. Under the same conditions, the assay for Pi release, on the other hand, gave velocities similar to each other for the two substrates. The activity appears to be identical to the ADP-hydrolysing activity in placenta reported by others.
Mol Cell Biochem 1990 Sep 03
PMID:Identification of ATP diphosphohydrolase activity in human term placenta using a novel assay for AMP. 217 97

The complete DNA sequence of the Micrococcus luteus spectinomycin (spc) operon and its adjacent regions has been determined. The sequence has revealed the presence of genes that are homologous to those of the Escherichia coli ribosomal and related proteins, L14, L24, L5, S8, L6, L18, S5, L30, L15, and secretion protein Y (sec Y), and the gene for adenylate kinase (adk). The gene arrangement in the spc operon is essentially the same as that of E. coli except for the absence in the M. luteus spc operon of the genes for S14 and X protein that exist in the E. coli spc operon. SecY and adk seem to be composed of another operon (adk operon) with at least an open reading frame. The deduced amino acid sequences for these ribosomal proteins are well conserved among the two species (40-65% identity). Reflecting the high genomic guanine and cytosine (GC) content of M. luteus (74%), the codon usage of the genes is extremely biased toward use of G and C, about 94% of the codon third positions being G or C. Seven codons, AUA, AAA, AGA, UUA, GUA, CUA, and CAA, all of which have A at the codon third positions, are completely absent in the M. luteus genes examined. Out of 11 genes in the M. luteus spc and adk operons, 5 (10) use GUG (UGA) and 6 (1) use AUG (UAA) as an initiation (termination) codon.
J Mol Evol 1989 Nov
PMID:Spectinomycin operon of Micrococcus luteus: evolutionary implications of organization and novel codon usage. 253 72

The adk genes from several thermosensitive (ts) mutants of Escherichia coli were cloned and sequenced. The mutations responsible for the thermolability of the gene product, the enzyme adenylate kinase, were established. From five independently isolated strains analysed, two contain a CCG to TCG transition changing proline 87 to serine (P87S), another two have a TCT to TTT transition that mutates serine 129 to phenylalanine (S129F), and the last one was found not to contain a mutation in the adk gene. Overproducing strains were constructed that contain ts genes in the genome as well as in the plasmids. These strains grow at high temperature, although much slower than wild-type. Most probably, the high rate of synthesis of adenylate kinase compensates for the destruction of the thermolabile protein by the elevated temperature. Mutated proteins were purified. The P87S but not the S129F mutation was found to cause thermosensitivity of the adenylate kinase reaction. Revertants of thermosensitivity were isolated and the nature of the mutation was determined by the RNase digestion method of RNA-DNA hybrids and by DNA sequencing. The revertants of the P87S mutation regained the wild-type sequence, whereas the revertants of the S129F strain retained the original mutation in the adenylate kinase gene. These results are discussed in the light of the three-dimensional structure of the enzyme and the possible role of adenylate kinase in phospholipid synthesis.
J Mol Biol 1989 May 05
PMID:Adenylate kinases from thermosensitive Escherichia coli strains. 254 33

The crystal structure of porcine cytosolic adenylate kinase has been established at 2.1 A resolution using a restrained least-squares refinement method. Based on 11,251 independent reflections of better than 10 A resolution, a final R-factor of 19.3% was obtained with a model obeying standard geometry within 0.026 A in bond lengths and 3.3 degrees in bond angles. In comparison with the previous structure at 3 A resolution, there is a significant improvement. The high resolution structure has been used to rationalize the strictly conserved residues in the adenylate kinase family. Among these is the glycine-rich loop, which forms a giant anion hole accommodating a sulfate ion which mimics a phosphoryl group of a substrate. Such a structure seems to occur in a large group of mononucleotide binding proteins. Moreover, a conserved cis-proline has been detected in the active center. A structural comparison with the complex between adenylate kinase from yeast and a substrate-analog at medium resolution indicates that this kinase performs appreciable mechanical movements during a catalytic cycle. The reported structure presumably represents an open form of the enzyme, similar to that in solution in the absence of substrates. However, since there are large intermolecular contacts in the crystal, some deviation from the solution structure has to be expected.
J Mol Biol 1988 Jan 20
PMID:Refined structure of porcine cytosolic adenylate kinase at 2.1 A resolution. 283 12

The structure of a synthetic peptide corresponding to residues 1-45 of rabbit muscle adenylate kinase has been studied in aqueous solution by two-dimensional NMR, FTIR, and CD spectroscopy. This peptide, which binds MgATP and is believed to represent most of the MgATP-binding site of the enzyme [Fry, D.C., Kuby, S.A., & Mildvan, A.S. (1985) Biochemistry 24, 4680-4694], appears to maintain a conformation similar to that of residues 1-45 in the X-ray structure of intact porcine adenylate kinase [Sachsenheimer, W., & Schulz, G.E. (1977) J. Mol. Biol. 114, 23-26], with 42% of the residues of the peptide showing NOEs indicative of phi and psi angles corresponding to those found in the protein. The NMR studies suggest that the peptide is composed of two helical regions of residues 4-7 and 23-29, and three stretches of beta-strand at residues 8-15, 30-32, and 35-40, yielding an overall secondary structure consisting of 24% alpha-helix, 38% beta-structure, and 38% aperiodic. Although the resolution-enhanced amide I band of the peptide FTIR spectrum is broad and rather featureless, possibly due to disorder, it can be fit by using methods developed on well-characterized globular proteins. On this basis, the peptide consists of 35 +/- 10% beta-structure, 60 +/- 12% turns and aperiodic structure, and not more than 10% alpha-helix. The CD spectrum is best fit by assuming the presence of at most 13% alpha-helix in the peptide, 24 +/- 2% beta-structure, and 66 +/- 4% aperiodic. The inability of the high-frequency FTIR and CD methods to detect helices in the amount found by NMR may result from the short helical lengths as well as from static and dynamic disorder in the peptide. Upon binding of MgATP, numerous conformational changes in the backbone of the peptide are detected by NMR, with smaller alterations in the overall secondary structure as assessed by CD. Detailed assignments of resonances in the peptide spectrum and intermolecular NOEs between protons of bound MgATP and those of the peptide, as well as chemical shifts of peptide resonances induced by the binding of MgATP, are consistent with the previously proposed binding site for MgATP on adenylate kinase.
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PMID:Solution structure of the 45-residue MgATP-binding peptide of adenylate kinase as examined by 2-D NMR, FTIR, and CD spectroscopy. 284 70

Escherichia coli adenylate kinase has a very well resolved proton nuclear magnetic resonance spectrum in the region containing signals from aromatic amino acid side-chains. We found that the protein is structurally stable over a wide pH range and renatures spontaneously after acidic as well as basic denaturation. Only one out of the three histidyl imidazole rings titrates on changing the pH and has a pka value of 7.6. Two-dimensional nuclear magnetic resonance spectroscopy studies allowed use to identify most of the enzyme's aromatic spin systems, and by investigation of a mutant protein we were able to assign the aromatic part of the spin system of Tyr24 unambiguously.
J Mol Biol 1988 Apr 20
PMID:Proton-nuclear magnetic resonance studies of the aromatic spin systems of Escherichia coli adenylate kinase. 284 9

The enzyme adenylate kinase was isolated from Escherichia coli and crystallized together with a substrate-mimicking inhibitor. The crystal structure was solved using the multiple isomorphous replacement method at a resolution of 4.5 A (1 A = 0.1 nm). There are two enzyme-inhibitor complex molecules in the asymmetric unit, the relative positions of which are given. The resolution was extended to 2.3 A starting with the model of the homologous enzyme from yeast and using constrained-restrained and restrained refinements together with the known non-crystallographic symmetry. The final R-factor is 35.9%. The corresponding model is given as backbone tracing. The structure will be used for protein-engineering studies.
J Mol Biol 1988 Aug 20
PMID:Structure of the complex of adenylate kinase from Escherichia coli with the inhibitor P1,P5-di(adenosine-5'-)pentaphosphate. 284 3

A new kanamycin-resistance gene, detected in Acinetobacter baumannii and designated aphA-6, was sequenced. It specifies a 30319 Dalton 3'-aminoglycoside phosphotransferase (APH(3'] that mediates resistance to kanamycin and structurally related aminoglycosides, including amikacin. Pairwise comparisons of the six types of APH(3') so far detected in human pathogens (types I, II, III and VI) and in amino-glycoside-producing microorganisms (types IV and V), confirm that APH(3') enzymes have diverged from a common ancestor. Three highly retained motifs (1: V--HGD----N; 2: G--D-GR/K-G and 3: D--K/R--Y/F---LDE) located in the C-terminal part of the enzymes were defined. Screening of protein sequence data bases fore each of these motifs revealed that motifs 1 and 2 are both found in nucleotide-binding phosphotransferases associated with a variety of biological processes, namely adenylate kinase, viral oncogenic protein kinases, elongation factors, Na+/K+-transporting ATPase, myosin and antibiotic-modifying enzymes. Motif 2 probably corresponds to the MgATP binding site, while motifs 3 and 1 could be involved in the splitting of the phosphodiester bond and in the phosphate transfer, respectively. Moreover, an additional motif, almost invariably centrally located, was found in all aminoglycoside-modifying enzymes. The occurrence of this motif, possibly a recombination site which would have allowed the association of units of separate functions, is compatible with a modular concept for the structure of aminoglycoside-modifying enzymes.
Mol Microbiol 1988 Sep
PMID:Nucleotide sequence of Acinetobacter baumannii aphA-6 gene: evolutionary and functional implications of sequence homologies with nucleotide-binding proteins, kinases and other aminoglycoside-modifying enzymes. 284 86


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