The structure of bovine mitochondrial adenylate kinase: Comparison with isoenzymes in other compartments

Schlauderer, G. J.; Schulz, Georg E.

doi:10.1002/pro.5560050304

Cited by 55 publications

(37 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The ␤-sheet is stabilized by hydrogen backbone interactions and attractive forces between few side chains inside the ␤-sheet. which is held by cysteine residues seems to substitute efficiently the hydrogen bond network (30). The crystal structure of adenylate kinase from B. stearothermophilus (entry 1.Zip in the Protein Data Bank) confirms this observation.…”

Section: Thermal Stability and Proteolysis By Trypsin Of Cys-modifiedmentioning

confidence: 56%

Genetically Engineered Zinc-chelating Adenylate Kinase fromEscherichia coli with Enhanced Thermal Stability

Perrier¹,

Burlacu-Miron²,

Bourgeois³

et al. 1998

Journal of Biological Chemistry

View full text Add to dashboard Cite

149(corresponding to Cys 130 , Cys 133 , Cys 150 , and Cys 153 in adenylate kinase from Bacillus stearothermophilus) in Escherichia coli adenylate kinase was undertaken for determining whether the presence of Cys residues is the only prerequisite to bind zinc or (possible) other cations. A number of variants of adenylate kinase from E. coli, containing 1-4 Cys residues were obtained, purified, and analyzed for metal content, structural integrity, activity, and thermodynamic stability. All mutants bearing 3 or 4 cysteine residues acquired zinc binding properties. Moreover, the quadruple mutant exhibited a remarkably high thermal stability as compared with the wild-type form with preservation of the kinetic parameters of the parent enzyme.Adenylate kinase (AK, 1 ATP:AMP phosphotransferase, EC 2.7.4.3) is a ubiquitous enzyme which contributes to homeostasis of adenine nucleotides in living cells (1). Three classes of AKs, differing in size, subcellular localization, and substrate specificity were identified in vertebrates, AK 1 in the cytosol, AK 2 in the mitochondrial intermembrane space, and AK 3 (called also GTP:AMP phosphotransferase) in the mitochondrial matrix. Only one form of AK was identified in bacteria. Mitochondrial adenylate kinases (AK 2 , AK 3 ) and the vast majority of bacterial adenylate kinases belong to the class of long forms. They differ from AK 1 and some bacterial AKs, the short variants, by a 28-residue long insertion organized into a small domain (2) called LID well exposed to the solvent (Fig. 1A) and undergoing a large movement during catalysis (3, 4).AKs from Gram-positive bacteria contain a structural zinc atom (5-7), a property which is due to the presence of 3 or 4 cysteine residues in the LID domain. Sequence alignment of AKs from Gram-positive and Gram-negative organisms, devoid of metal, showed that in the latter species the Cys residues are substituted with four other highly conserved amino acids, His, Ser, Asp, and Thr (Fig. 1B). This conservation suggests that these particular residues have some essential function, but different in the enzyme from the , and Thr 149 in Escherichia coli adenylate kinase with cysteine residues. Our aim was to know whether a motif composed of 3 or 4 Cys residues generates a metal-binding site in AK or whether other structural factors contribute to the specificity (zinc versus iron or any other metal) or to the strength of the protein/metal interaction. On the other hand, we wanted to know the relevance of the metal binding for catalysis or stability of AK. A number of variants of AK e containing one to four cysteine residues were thus obtained. In agreement with previous studies on zinc-binding AKs, we found that the 3 and 4 cysteine modified forms of AK e acquired zinc binding properties. Moreover, the 4 cysteine-containing AK e exhibited an increased stability against thermal denaturation as compared with the wild-type form, with full conservation of its catalytic properties. EXPERIMENTAL PROCEDURESMaterials-Adenine nucleotides, coupling enzymes, ...

show abstract

Section: Thermal Stability and Proteolysis By Trypsin Of Cys-modifiedmentioning

confidence: 56%

Genetically Engineered Zinc-chelating Adenylate Kinase fromEscherichia coli with Enhanced Thermal Stability

Perrier¹,

Burlacu-Miron²,

Bourgeois³

et al. 1998

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…References (73)(74)(75)(76)(77)(78)(79)(80)(81)(82)(83)(84)(85)(86)(87) appear in the Supporting Material.…”

Section: Acknowledgmentsmentioning

confidence: 99%

Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

Liu

2015

Biophysical Journal

View full text Add to dashboard Cite

Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems.

show abstract

“…They also play a structural role in AK, as confirmed in several crystallographic studies [6,12,13]. Mutations in the LID domain lead to considerable differences in the overall stability of AK [7,14,15].…”

mentioning

confidence: 70%

Zinc-, cobalt- and iron-chelated forms of adenylate kinase from the Gram-negative bacterium Desulfovibrio gigas

Kladova

Gavel

Zhadan

et al. 2009

International Journal of Biological Macromolecules

View full text Add to dashboard Cite

The structure of bovine mitochondrial adenylate kinase: Comparison with isoenzymes in other compartments

Cited by 55 publications

References 40 publications

Genetically Engineered Zinc-chelating Adenylate Kinase fromEscherichia coli with Enhanced Thermal Stability

Genetically Engineered Zinc-chelating Adenylate Kinase fromEscherichia coli with Enhanced Thermal Stability

Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

Zinc-, cobalt- and iron-chelated forms of adenylate kinase from the Gram-negative bacterium Desulfovibrio gigas

Contact Info

Product

Resources

About