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2.7.4.3: adenylate kinase

This is an abbreviated version!
For detailed information about adenylate kinase, go to the full flat file.

Word Map on EC 2.7.4.3

Reaction

ATP
+
AMP
=
2 ADP

Synonyms

5'-AMP-kinase, ABC adenylate kinase, AD-004 like protein, adenosine 5'-triphosphate:adenosine 5'-monophosphate phosphotransferase, adenylate kinase, adenylate kinase 1, adenylate kinase 2, adenylate kinase 4, adenylate kinase 5, adenylate kinase 6, adenylate kinase 9, adenylate kinase isoenzyme 1, adenylate kinase isozyme 2, adenylate kinase-2, adenylate kinase-like protein 1, adenylic kinase, adenylokinase, ADK, ADK1, ADK2, ADLP, AK1, AK2, AK4, AK5, AK5p1, AK5p2, AK6, AK7, AK8, AK9, AKE, AKlse4, AKm, AKmeso, AKp, AKpsycrho, AKthermo, ATP:AMP phosphotransferase, CFTR, CINAP, coilin interacting nuclear ATPase protein, cystic fibrosis transmembrane conductance regulator, DAK2, Dak6, kinase, adenylate (phosphorylating), kinase, myo- (phosphorylating), MeADK1, MeADK2, MJ0458, myokinase, nonstructural protein 4B, NS4B, pfSMCnbd, phosphotransferase, Rv0733, Saci_0573, SpAdK, structural maintenance of chromosome protein

ECTree

     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.4 Phosphotransferases with a phosphate group as acceptor
                2.7.4.3 adenylate kinase

Crystallization

Crystallization on EC 2.7.4.3 - adenylate kinase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals of the mutant enzyme I26T are grown at 20°C by the hanging-drop method
purified recombinant enzyme mutants AKm1 and AKm2 in complex with inhibitor Ap5A, hanging drop vapour diffusion method, mixing of 30 mg/ml AKm1 or 18 mg/ml AKm2 in 10 mM HEPES pH 7.0, and 4 mM Ap5A, with an equal amount of a reservoir solution containing 18% w/v PEG 3350, 100 mM lithium sulfate, and 100 mM Bis-Tris, pH 5.5, for mutant AKm1 and containing 22% w/v PEG 3350, and 200 mM calcium chloride for mutant AKm2, 20°C, X-ray diffraction structure determination and analysis at 2.990 and 1.65 A resolution, respectively
muscle and liver
-
two crystal forms
-
space group P4122 or P4322
-
sitting-drop method
analysis of atomically detailed conformational transition pathway of adenylate kinase in the absence and presence of an inhibitor. In the ligand-free state, there is no significant barrier separating the open and closed conformations. The enzyme samples near closed conformations, even in the absence of its substrate. The ligand binding event occurs late, toward the closed state, and transforms the free energy landscape. In the ligand-bound state, the closed conformation is energetically most favored with a large barrier to opening
atomistic molecular dynamics simulation of the complete conformational transition. Starting from the closed conformation, half-opening of the AMP-binding domain precedes a partially correlated opening of the LID and AMP-binding domain, defining the second phase. A highly stable salt bridge D118-K136 at the LID-CORE interface, contributing substantially to the total nonbonded LID-CORE interactions, is a major factor that stabilizes the open conformation
-
characterization of both ATP and AMP conformations, conformations of ATP, AMP, and the ATP analogue adenylyl imidodiphosphate
-
coarse grained model for the interplay between protein structure, folding and function. High strain energy is correlated with localized unfolding during the functional transition. Competing native interactions from the open and closed form can account for the large conformational transitions. Local unfolding may be due, in part, to competing intra-protein interactions
coarse-grained models and nonlinear normal mode analysis. Intrinsic structural fluctuations dominate LID domain motion, whereas ligand-protein interactions and local unfolding are more important during NMP domain motion. LID-NMP domain interactions are indispensable for efficient catalysis. LID domain motion precedes NMP domain motion, during both opening and closing, providing mechanistic explanation for the observed 1:1:1 correspondence between LID domain closure, NMP domain closure, and substrate turnover
dynamics sampling simulations of the domain conformations of unliganded adenylate kinase. There is a bias towards the open-domain conformation for both domain pairs but no appreciable barrier. The interaction with the substrate enables the enzyme to adopt the closed-domain conformation. For the ATP-core domain pair, this interaction comes from a cation-pi interaction between Arg119 and the adenine moiety of ATP. For the AMP-core domain pair it is between Thr31 and the adenine moiety of AMP
-
in complex with inhibitor P1,P5-di(adenosine-5’)-pentaphosphate that simulates well the binding of substrates ATP and AMP. The alpha-phosphate of AMP is well positioned for a nucleophilic attack on the gamma-phosphate of ATP, giving a stabilized pentacoordinated transition state with nucleophile and leaving group in the apical positions of a trigonal bipyramide
-
single molecule conformational dynamics for prediction of open and closed kinetic rates at the whole temperature ranges from 10°C to 50°C. Identification of key residues and contacts responsible for the conformational transitions are identified by following the time evolution of the two-dimensional spatial contact maps and characterizing the transition state as well as intermediate structure ensembles
sitting drop vapor diffusion method, using 3% (w/v) PEG 2K with 1.8-2.3 M ammonium sulfate, pH 7.0-7.3
solution-state NMR approach to probe the native energy landscape of adenylate kinase in its free form, in complex with its natural substrates, and in the presence of a tight binding inhibitor. Binding of ATP induces a dynamic equilibrium in which the ATP binding motif populates both the open and the closed conformations with almost equal populations. A similar scenario is observed for AMP binding, which induces an equilibrium between open and closed conformations of the AMP binding motif. Simultaneous binding of AMP and ATP is required to force both substrate binding motifs to close cooperatively. Unidirectional energetic coupling between the ATP and AMP binding sites
x-ray diffraction analysis
-
purified recombinant enzyme mutants AKm1 and AKm2 in complex with inhibitor Ap5A, hanging drop vapour diffusion method, mixing of 30 mg/ml AKm1 or 18 mg/ml AKm2 in 10 mM HEPES pH 7.0, and 4 mM Ap5A, with an equal amount of a reservoir solution containing 18% w/v PEG 3350, 100 mM lithium sulfate, and 100 mM Bis-Tris, pH 5.5, for mutant AKm1 and containing 22% w/v PEG 3350, and 200 mM calcium chloride for mutant AKm2, 20°C, X-ray diffraction structure determination and analysis at 2.990 and 1.65 A resolution, respectively
cocrystallized with bis(adenosine)-5'-tetraphosphate
crystal structure is established in complex with bis(adenosine)-5'-tetraphosphate and malonate ion or in complex with P1,P5-di(adenosine-5')pentaphosphate
crystallized in two conformations, in closed conformation with adenosine monophosphate and in open conformation without substrate
in complex with ADP, dADP, and Mg2+ADP-PO43-, hanging drop vapor diffusion method, using 0.1 M HEPES pH 7.5, 1.5 M Li2SO4, 0.2 M NaCl, 0.5 mM dithiothreitol, and 25 mM MgCl2
mutant enzyme L171P, hanging drop vapor diffusion method, 4°C under conditions of 1.22-1.28 M (NH4)2SO4 and 0.1 M Tris-HCl, pH 8.5
with the inhibitor P1,P5-di(adenosine-5')-pentaphosphate bound to the active site, sitting drop vapor diffusion method, using 1.5 M sodium citrate pH 6.5, 150 mM sodium chloride, 0.5% n-dodecyl-N,N-dimethylamine-N-oxide, at 10°C
adenylate kinase bound to Zn2+, Co2+ or Fe2+, hanging drop vapor diffusion method, using 0.2 M sodium/potassium tartrate, 0.1 M 2-(N-morpholino)ethanesulfonic acid (pH 6.5), and 20% (w/v) PEG 200 or PEG 800
Megalodesulfovibrio gigas
native enzyme in complex with Zn2+, recombinant enzymes in complex with Fe2+ or Co2+, hanging drop vapor diffusion method, using 0.2 M sodium/potassium tartrate, 0.1 M MES pH 6.5 and 20% (w/v) PEG 8K
Megalodesulfovibrio gigas
hanging-drop vapour-diffusion method, X-ray diffraction data to 2.70 A resolution is collected, the crystal belong to space group P4(1)2(1)2 or P4(3)2(1)2. The unit-cell parameters were a = b = 76.18, c = 238.70 Å, alpha = beta = gamma = 90°
sitting drop vapor diffusion method, using in 3.4 M ammonium chloride, 0.1 M sodium acetate (pH 4.7), and 3% ethylene glycol (v/v), at 22°C
hanging-drop method
in complex with two molecules of ADP and Mg2+. Structure reveals significant conformational changes of the LID and NMP-binding domain upon substrate binding. The ternary complex represents the enzyme at the start of ATP synthesis reaction, is consistent with nucleophilic attack of a terminal oxygen from the acceptor ADP on the beta-phosphate from the donor substrate, and hints to an associative mechanism for phosphoryl transfer
-
sitting-drop method
crystal structure of the nucleotide-binding domain of the Pyrococcus furiosus structural maintenance of chromosome protein (pfSMCnbd) in complex with the adenylate kinase inhibitor P1,P5-di(adenosine-5')pentaphosphate
apo isoform ADK1, hanging drop vapor diffusion method, using 100 mM Tris-HCl (pH 8.5) and 2.4 M dibasic ammonium phosphate
-
purified recombinant enzyme mutants AKm1 and AKm2 in complex with inhibitor Ap5A, hanging drop vapour diffusion method, mixing of 30 mg/ml AKm1 or 18 mg/ml AKm2 in 10 mM HEPES pH 7.0, and 4 mM Ap5A, with an equal amount of a reservoir solution containing 18% w/v PEG 3350, 100 mM lithium sulfate, and 100 mM Bis-Tris, pH 5.5, for mutant AKm1 and containing 22% w/v PEG 3350, and 200 mM calcium chloride for mutant AKm2, 20°C, X-ray diffraction structure determination and analysis at 2.990 and 1.65 A resolution, respectively
small-scale batch method at 20°C
purified detagged recombinant enzyme free or in complex with inhibitor Ap5A, hanging drop vapour diffusion method, mixing of 0.0025 ml of 18 mg/ml protein in 50 mM Tris-HCl, pH 7.5, 150 mM NaCl, and 1 mM MgCl2, with 0.0025 ml of reservoir solution containing 2.0 M (NH4)2SO4, 0.1 M CHES, pH 9.5, 0.2 M Li2SO4, and 0.1 M CsCl2 for the ligand-free enzyme, and 0.1 M sodium acetate, 0.1 M sodium acetate, pH 4.6, 30% PEG 8000, and 50 mM NaF for the inhibitor-bound enzyme, 22°C, X-ray diffraction structure determination and analysis at 1.7 and 1.48 A resolution, respectively, molecular replacement using structures Marinibacillus marinus PDB ID 3FB4 and Burkholderia pseudomallei PDB ID 3GMT as search models
purified recombinant enzyme in ligand-free and inhibitor Ap5A-bound states, hanging drop vapour diffusion method, mixing of 0.0025 ml of 10 mg/ml protein in 50 mM Tris-HCl, pH 7.5, 50-150 mM NaCl, 5 mM MgCl2, with 0.0025 ml reservoir solution containing 1.0 M sodium citrate, 0.1 M HEPES, pH 7.5 for the ligand-free crystals and 0.2 M sodium acetate, pH 7.2, 30% PEG 8000 for the inhibitor-bound crystals, 22°C, X-ray diffraction structure determination and analysis at 1.96 and 1.65 A resolution, respectively. SpAdK can crystallize promiscuously in different forms, and the open structure is flexible in conformation
3 interconvertible crystal forms
-