Cobalt-, zinc- and iron-bound forms of adenylate kinase (AK) from the sulfate-reducing bacterium<i>Desulfovibrio gigas</i>: purification, crystallization and preliminary X-ray diffraction analysis

Kladova, Anna V.; Gavel, Olga Yu.; Mukhopaadhyay, A.; Boer, Roeland; Teixeira, Susana; Shnyrov, Valery L.; Moura, Isabel; Moura, José J. G.; Romão, Maria João; Trincão, José; Bursakov, Sergey A.

doi:10.1107/s1744309109029157

Cited by 4 publications

(5 citation statements)

References 20 publications

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“…The position of the cobalt atom derived from anomalous signal collected with the X-ray source at the Co 2+ edge together with the electron density, was confirmed to be identical to that of Mg 2+ (AAdk11, Fig. 1d ) 31 . Based on these structures, we propose that the metal cofactor helps anchor the flexible donor phosphoryl group for a more favorable attack by the oxygen nucleophile of the acceptor nucleotide.…”

Section: Resultsmentioning

confidence: 73%

The energy landscape of adenylate kinase during catalysis

Kerns

Agafonov

Cho

et al. 2015

Nat Struct Mol Biol

165

244

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Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, MD simulations, and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events, phosphoryl transfer (>105-fold) and lid-opening (103-fold). In contrast, mutation of an essential active-site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid-opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a pre-organized active site.

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Section: Resultsmentioning

confidence: 73%

The energy landscape of adenylate kinase during catalysis

Kerns

Agafonov

Cho

et al. 2015

Nat Struct Mol Biol

165

244

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“…The second is cobalt- and zinc-containing adenylate kinases (AKs) 60 . A novel type of metal-binding site for three metal ions: cobalt, zinc and iron (II) is reported to be present in AKs 61 . Anaeromyxobacter is an arsenate-respiring bacterium isolated from arsenic-contaminated soil that contains three distinct arsenic resistance gene clusters (ars operons) 62 .…”

Section: Discussionmentioning

confidence: 99%

Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident

Zhang

Huang

Wang

et al. 2017

Sci Rep

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A shocking Longjiang River cadmium pollution accident occurred in 2012, the effects of which on microbial communities remain unclear. Alkaline precipitation technology was applied for remediation, but concerns rose about the stability of this technology. To understand the geographic distribution of cadmium and its correlation with microbes, in this study, 39 water samples and 39 sludge samples from this river and 2 soil samples from the nearby farmland were collected for chemical and microbial analyses. The Cd concentrations of all water samples were lower than 0.005 mg/L and reached the quality standards for Chinese surface water. A ranking of sludge samples based on Cd contents showed sewage outfall > dosing sites > farmland, all of which were higher than the quality standard for soil. Alkaline precipitation technology was effective for Cd precipitation. Cd was unstable; it was constantly dissolving and being released from the sludge. The Cd content of each phase was mainly influenced by the total Cd content. Over 40,000 effective sequences were detected in each sample, and a total of 59,833 OTUs and 1,273 genera were found using Illumina MiSeq sequencing. Two phyla and 39 genera were notably positively correlated with the Cd distribution, while the cases of 10 phyla and 6 genera were the opposite.

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“…Protein cloning, bacterial growth, and homogeneous protein production with a unique metal ion were reported in our earlier work [21,22].…”

Section: Sample Preparation and Crystallizationmentioning

confidence: 94%

“…The best crystallization conditions were 0.2 M sodium/potassium tartrate, 0.1 M 2-(N-morpholino)ethanesulfonic acid (pH 6.5), and 20% PEG 200 or PEG 800 (the protein to well solution ratio in the drop was 1:1, 1:2, or 1:3, with the final drop volume of 4, 6, or 8 ll) using a protein stock concentration of approximately 10 mg/ml [22]. The crystals were cryoprotected by soaking them at 277 K in mother liquor containing 15-30% glycerol.…”

Section: Sample Preparation and Crystallizationmentioning

confidence: 99%

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Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria

et al. 2010

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Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, zinc, cobalt, and iron, have been found in AK from Gram-negative bacteria. Crystal structures of substrate-free AK from Desulfovibrio gigas with three different metal ions (Zn 2? , Zn-AK; Co 2? , Co-AK; and Fe 2? , Fe-AK) bound in its LID domain have been determined by X-ray crystallography to resolutions 1.8, 2.0, and 3.0 Å , respectively. The zinc and iron forms of the enzyme were crystallized in space group I222, whereas the cobalt-form crystals were C2. The presence of the metals was confirmed by calculation of anomalous difference maps and by X-ray fluorescence scans. The work presented here is the first report of a structure of a metal-containing AK from a Gram-negative bacterium. The native enzyme was crystallized, and only zinc was detected in the LID domain. Co-AK and Fe-AK were obtained by overexpressing the protein in Escherichia coli. Zn-AK and Fe-AK crystallized as monomers in the asymmetric unit, whereas Co-AK crystallized as a dimer. Nevertheless, all three crystal structures are very similar to each other, with the same LID domain topology, the only change being the presence of the different metal atoms. In the absence of any substrate, the LID domain of all holoforms of AK was present in a fully open conformational state. Normal mode analysis was performed to predict fluctuations of the LID domain along the catalytic pathway.

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Cobalt-, zinc- and iron-bound forms of adenylate kinase (AK) from the sulfate-reducing bacteriumDesulfovibrio gigas: purification, crystallization and preliminary X-ray diffraction analysis

Abstract: -AK form. The structures of the three metal-bound forms of AK will provide new insights into the role and selectivity of the metal in these enzymes.

Cited by 4 publications

References 20 publications

The energy landscape of adenylate kinase during catalysis

The energy landscape of adenylate kinase during catalysis

Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident

Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria

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