A new type of metal-binding site in cobalt- and zinc-containing adenylate kinases isolated from sulfate-reducers Desulfovibrio gigas and Desulfovibrio desulfuricans ATCC 27774

Gavel, Olga Yu.; Bursakov, Sergey A.; Rocco, Giulia Di; Trincão, José; Pickering, Ingrid J.; George, Graham N.; Calvete, Juan J.; Shnyrov, Valery L.; Brondino, Carlos D.; Pereira, Alice S.; Lampreia, Jorge; Tavares, Pedro; Moura, José J. G.; Moura, Isabel

doi:10.1016/j.jinorgbio.2008.01.023

Cited by 17 publications

(13 citation statements)

References 85 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This soluble sulphate enters into the immobilised beads via diffusion and later is carried into the inner membrane of the cells facilitated by sulphate permease. The sulphate is then reduced to sulphite by ATP sulphurylase and phosphoadenosine phosphosulphate reductase and this sulphite is further reduced sulphide by sulphite reductase [17,22]. The sulphide in turn reacts with O-acetylserine for the synthesis of cysteine via O-acetylserine thiolyase and then the cysteine produces sulphide by cysteine desulphydrase in the presence of zinc.…”

Section: Biosynthesis Using Sulphate Reducing Bacteriamentioning

confidence: 99%

Synthesis of zinc-based nanomaterials: a biological perspective

Abhilash

Pandey

2012

IET Nanobiotechnology

View full text Add to dashboard Cite

Nanoparticles are the materials characterised by dimensions of the order of 100 nm or less. They exhibit a high surface/volume ratio leading to different properties very different from those of the bulk materials. The development of uniform nanoparticles has been intensively pursued because of their technological and fundamental scientific importance. A number of chemical methods are available and are extensively used, but these are often energy intensive and use toxic chemicals. An alternative approach for the synthesis of uniform nanoparticles is the biological route that occurs at ambient temperature, pressure and at neutral pH. The main aim of this review is to enlist and compare various methods of synthesis of zinc-based nanoparticles with emphasis on the biological method.

show abstract

Section: Biosynthesis Using Sulphate Reducing Bacteriamentioning

confidence: 99%

Synthesis of zinc-based nanomaterials: a biological perspective

Abhilash

Pandey

2012

IET Nanobiotechnology

View full text Add to dashboard Cite

show abstract

“…The extract was used after centrifugation for the purification of AK. The native Co 2+ /Zn 2+ from D. gigas contains 0.4 ± 0.02 mol cobalt and 0.3 ± 0.03 mol zinc per mole of protein [12].…”

Section: Sample Preparation and Crystallizationmentioning

confidence: 99%

“…c-e The anomalous maps of the metal site in Zn-AK (contoured at 3r), Co-AK (contoured at 3.7r), and Fe-AK (contoured at 2.8r), respectively. Pictures were prepared using CCP4mg [45] counterweight loop [12], which is believed to control the movement of the LID domain during catalysis. This core domain mainly consists of a five-stranded b-sheet surrounded by five helices that keep the integrity of the tertiary structure of the enzyme.…”

Section: Core Domainmentioning

confidence: 99%

“…In AK from Gram-positive bacteria, zinc seems to stabilize the LID domain more readily than does the hydrogen-bond network present in Gram-negative bacteria and in all of the eukaryotic longform AK determined so far [4,13]. Several studies have shown that the presence of a metal ion in the LID domain causes considerable differences in the overall stability of AK and its removal leads to partial or complete loss of catalytic activity [7,12,14,[16][17][18].…”

Section: Introductionmentioning

confidence: 99%

“…The structural metal binding motif in Gram-positive bacteria is Cys-X 2 -Cys-X 16 -Cys-X 2 -Cys/Asp [12]. The sulfur positions of the four Cys side chains of Gram-positive bacteria are geometrically optimized to bind the metal ion [13].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

View full text Add to dashboard Cite

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.

show abstract

Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches

2011

View full text Add to dashboard Cite

Based on integrative computational hybrid approaches that combined statistical coupling analysis (SCA), molecular dynamics (MD), and normal mode analysis (NMA), evolutionarily coupled residues involved in functionally relevant motion in the adenylate kinase protein family were identified. The hybrids identified four top-ranking site pairs that belong to a conserved hydrogen bond network that is involved in the enzyme's flexibility. A second group of top-ranking site pairs was identified in critical regions for functional dynamics, such as those related to enzymatic turnover. The high consistency of the results obtained by SCA with NMA (SCA.NMA) and by SCA.MD hybrid analyses suggests that suitable replacement of the matrix of cross-correlation analysis of atomic fluctuations (derived by using NMA) with those based on MD contributes to the identification of such sites by means of a fast computational calculation. The analysis presented here strongly supports the hypothesis that evolutionary forces, such as coevolution at the sequence level, have promoted functional dynamic properties of the adenylate kinase protein family. Finally, these hybrid approaches can be used to identify, at the residue level, protein motion coordination patterns not previously observed, such as in hinge regions.

show abstract

A new type of metal-binding site in cobalt- and zinc-containing adenylate kinases isolated from sulfate-reducers Desulfovibrio gigas and Desulfovibrio desulfuricans ATCC 27774

Cited by 17 publications

References 85 publications

Synthesis of zinc-based nanomaterials: a biological perspective

Synthesis of zinc-based nanomaterials: a biological perspective

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

Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches

Contact Info

Product

Resources

About