YodA from Escherichia coli Is a Metal-binding, Lipocalin-like Protein

David, Gabriel; Blondeau, Karine; Schiltz, M.; Penel, Simon; Lewit-Bentley, Anita

doi:10.1074/jbc.m304484200

Cited by 57 publications

(65 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…1) and likewise possesses one high affinity Zn(II) binding site, located at the end of the hydrophobic cavity formed between the calyx and the helical domain. In SeZinT, Zn(II) is bound in the same position as Cd(II) and Ni(II) in EcZinT [16]. However, the Zn(II) coordination differs.…”

Section: Discussionmentioning

confidence: 99%

“…It consists of the calyx domain -an antiparallel updown β-barrel -and a smaller helical domain. Specifically, the Cα traces of SeZinT and EcZinT with Ni(II) bound to the Zn(II) binding site (PDB code: 1OEJ) [16] are almost super-imposable. The root-mean square deviation (rmsd) is 0.375Å (Fig.…”

Section: Sezint: Structural Analysismentioning

confidence: 99%

“…2D). In the EcZinT structure, two Zn(II) are placed in the canonical binding pocket as just described, most likely because the crystals were obtained at 200 mM [16], a very high concentration as compared to 5 mM Zn(II) used to grow the Zn(II)-SeZinT crystals and to the sub-millimolar concentrations typical of physiological conditions. As shown below, fluorescence titrations of SeZinT with Zn(II) provide evidence that the protein binds only one Zn(II) with high affinity.…”

Section: Sezint: Structural Analysismentioning

confidence: 99%

“…The only ZinT structure known pertains to metal-bound E. coli ZinT (EcZinT, indicated originally as YodA) [16]. EcZinT is composed of two domains: a major one related structurally to the lipocalin/calycin protein family and a smaller helical domain.…”

Section: Introductionmentioning

confidence: 99%

“…EcZinT is composed of two domains: a major one related structurally to the lipocalin/calycin protein family and a smaller helical domain. The metal-binding site, formed by histidine side chains, is buried at the domain interface, along the side of the calycin domain [16]. It was not established whether the binding of Zn(II) gives rise to protein conformational changes.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc

Ilari

Alaleona

Tria

et al. 2014

Biochimica et Biophysica Acta (BBA) - General Subjects

View full text Add to dashboard Cite

This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues.Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. Background: In Gram-negative bacteria the ZnuABC transporter ensures adequate zinc import in Zn(II)-poor environments, like those encountered by pathogens within the infected host. Recently, the metal-binding protein ZinT was suggested to operate as an accessory component of ZnuABC in periplasmic zinc recruitment. Since ZinT is known to form a ZinT-ZnuA complex in the presence of Zn(II) it was proposed to transfer Zn(II) to ZnuA. The present work was undertaken to test this claim. Methods: ZinT and its structural relationship with ZnuA have been characterized by multiple biophysical techniques (X-ray crystallography, SAXS, analytical ultracentrifugation, fluorescence spectroscopy). Results: The metal-free and metal-bound crystal structures of Salmonella enterica ZinT show one Zn(II) binding site and limited structural changes upon metal removal. Spectroscopic titrations with Zn(II) yield a K D value of 22 ± 2 nM for ZinT, while those with ZnuA point to one high affinity (K D b 20 nM) and one low affinity Zn(II) binding site (K D in the micromolar range). Sedimentation velocity experiments established that Zn(II)-bound ZinT interacts with ZnuA, whereas apo-ZinT does not. The model of the ZinT-ZnuA complex derived from small angle X-ray scattering experiments points to a disposition that favors metal transfer as the metal binding cavities of the two proteins face each other. Conclusions: ZinT acts as a Zn(II)-buffering protein that delivers Zn(II) to ZnuA. General significance: Knowledge of the ZinT-ZnuA relationship is crucial for understanding bacterial Zn(II) uptake.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Sezint: Structural Analysismentioning

confidence: 99%

Section: Sezint: Structural Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc

Ilari

Alaleona

Tria

et al. 2014

Biochimica et Biophysica Acta (BBA) - General Subjects

View full text Add to dashboard Cite

show abstract

Comparative analysis of proteomic changes in contrasting flax cultivars upon cadmium exposure

et al. 2010

View full text Add to dashboard Cite

Cadmium (Cd) is classified as a serious pollutant due to its high toxicity, high carcinogenicity, and widespread presence in the environment. Phytoremediation represents an effective low-cost approach for removing pollutants from contaminated soils, and a crop with significant phytoremediation potential is flax. However, significant differences in Cd accumulation and tolerance were previously found among commercial flax cultivars. Notably, cv. Jitka showed substantially higher tolerance to elevated Cd levels in soil and plant tissues than cv. Tábor. Here, significant changes in the expression of 14 proteins (related to disease/defense, metabolism, protein destination and storage, signal transduction, energy and cell structure) were detected by image and mass spectrometric analysis of two-dimensionally separated proteins extracted from Cd-treated cell suspension cultures derived from these contrasting cultivars. Further, two proteins, ferritin and glutamine synthetase (a key enzyme in glutathione biosynthesis), were only up-regulated by Cd in cv. Jitka, indicating that Cd tolerance mechanisms in this cultivar may include maintenance of low Cd levels at sensitive sites by ferritin and low-molecular weight thiol peptides binding Cd. The identified changes could facilitate marker-assisted breeding for Cd tolerance and the development of transgenic flax lines with enhanced Cd tolerance and accumulation capacities for phytoremediating Cd-contaminated soils.

show abstract

Structural and dynamic roles of permanent water molecules in ligand molecular recognition by chicken liver bile acid binding protein

Ricchiuto¹,

Rocco²,

Gianazza³

et al. 2008

J of Molecular Recognition

View full text Add to dashboard Cite

Chicken liver bile acid binding protein (cL-BABP) crystallizes with water molecules in its binding site. To obtain insights on the role of internal water, we performed two 100 ns molecular dynamics (MD) simulations in explicit solvent for cL-BABP, as apo form and as a complex with two molecules of cholic acid, and analyzed in detail the dynamics properties of all water molecules. The diffusion coefficients of the more persistent internal water molecules are significantly different from the bulk, but similar between the two protein forms. A different number of molecules and a different organization are observed for apo- and holo-cL-BABP. Most water molecules identified in the binding site of the apo-crystal diffuse to the bulk during the simulation. In contrast, almost all the internal waters of the holo-crystal maintain the same interactions with internal sidechains and ligands, which suggests they have a relevant role in protein-ligand molecular recognition. Only in the presence of these water molecules we were able to reproduce, by a classical molecular docking approach, the structure of the complex cL-BABP::cholic acid with a low ligand root mean square deviation (RMSD) with respect to its reference positioning. Literature data reported a conserved pattern of hydrogen bonds between a single water molecule and three amino acid residues of the binding site in a series of crystallized FABP. In cL-BABP, the interactions between this conserved water molecule and the three residues are present in the crystal of both apo- and holo-cL-BABP but are lost immediately after the start of molecular dynamics.

show abstract

YodA from Escherichia coli Is a Metal-binding, Lipocalin-like Protein

Cited by 57 publications

References 56 publications

The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc

The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc

Comparative analysis of proteomic changes in contrasting flax cultivars upon cadmium exposure

Structural and dynamic roles of permanent water molecules in ligand molecular recognition by chicken liver bile acid binding protein

Contact Info

Product

Resources

About