Crystal Structures of Two Solute Receptors for l-Cystine and l-Cysteine, Respectively, of the Human Pathogen Neisseria gonorrhoeae

Bulut, Haydar; Moniot, S.; Licht, Anke; Scheffel, F.; Gathmann, S.; Saenger, Wolfram; Schneider, Erwin

doi:10.1016/j.jmb.2011.11.030

Cited by 38 publications

(27 citation statements)

References 36 publications

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“…The biophysical analysis revealed the low affinity of CLasTcyA for cystine as compared to reported cystine‐binding protein from Ngo ( K D 0.021 μ m ) . The dissociation constant for other ligands could not be determined suggesting much lower affinity.…”

Section: Discussionmentioning

confidence: 77%

“…There is one other structure from Gram‐positive bacteria L. monocytogenes (PDB id http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4GVO) that has been submitted to PDB database. N. gonorrhoeae Ngo belongs to cluster group F‐IV of Class II SBPs . This cluster comprises of many other amino acid‐binding proteins such as cysteine, arginine or glutamine, histidine, lysine, etc.…”

Section: Resultsmentioning

confidence: 99%

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Crystal structures of a putative periplasmic cystine‐binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding

et al. 2019

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The amino acid‐binding receptors, a component of ABC transporters, have evolved to cater to different specificities and functions. Of particular interest are cystine‐binding receptors, which have shown broad specificity. In the present study, a putative periplasmic cystine‐binding protein from Candidatus Liberibacter asiaticus (CLasTcyA) was characterized. Analysis of the CLasTcyA sequence and crystal structures in the ligand‐bound state revealed novel features of CLasTcyA in comparison to related proteins. One of the unique features found in CLasTcyA structure was the positioning of the C‐terminal extended loop of one chain very close to the substrate‐binding site of the adjacent monomer in the asymmetric unit. The presence of a disulphide bond, unique to Candidatus Liberibacter family, holds the C‐terminal extended loop in position. Analysis of the substrate‐binding pocket of CLasTcyA suggested a broad specificity and a completely different orientation of the bound substrates in comparison to related protein structures. The open conformation for one of the two chains of the asymmetric unit in the Arg‐bound structure revealed a limited open state (18.4°) for CLasTcyA as compared to open state of other related proteins (~ 60°). The strong interaction between Asp126 on helix‐α5 of small domain and Arg82 (bigger domain) restricts the degree of opening in ligand‐free open state. The dissociation constant of 1.26 μm by SPR and 3.7 μm by MST exhibited low affinity for the cystine. This is the first structural characterization of an l‐cystine ABC transporter from plant pathogen and our results suggest that CLasTcyA may have evolved to cater to its specific needs for its survival in the host.

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Section: Discussionmentioning

confidence: 77%

Section: Resultsmentioning

confidence: 99%

Crystal structures of a putative periplasmic cystine‐binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding

et al. 2019

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“…Statistics are presented in Table 2. Molecular replacement was performed using Phaser [17] with the structure of the cysteine-binding protein from N. gonorrhoea [8] as the search model. Model refinement was performed using Phenix [18].…”

Section: Crystallisation Preliminary X-ray Diffraction Data Collectimentioning

confidence: 99%

“…A molecular replacement search was performed with Phaser using data at a resolution range of 20.0-2.5 Å. The monomers of the homologous protein from N. gonorrhoeae [8] in the closed (PBD ID: 2YLN) and open (PDB ID: 3ZSF) conformation were used as search models, and the protocol parameters were set to allow a search for a mix of the two. The molecular replacement (MR) solution contained three subunits: two in an open and one in the closed conformation.…”

Section: Crystallisation and Preliminary Crystallographic Analysismentioning

confidence: 99%

“…An amino acid sequence similarity search in the RCSB Protein Data Bank with the sequence of YckK from H. pylori strain SS1 [7] revealed 54% overall sequence identity to a cysteine-binding protein from Neisseria gonorrhoea [8] (PDB ID 2YLN). In all sequenced H. pylori strains, the 3' end of the yckK gene overlaps with the 5' end of a gene on the same strand, annotated tcyB, a polar amino acid transport system permease, indicating that yckK and tcyB are co-transcribed.…”

Section: Introductionmentioning

confidence: 99%

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Crystallisation and Preliminary Crystallographic Analysis of Helicobacter pylori Periplasmic Binding Protein YckK

et al. 2017

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Abstract:Helicobacter pylori infection can lead to the development of gastric and duodenal ulcers and gastric cancer. In recent years, the efficacy of the standard therapy has been falling, necessitating ongoing efforts to identify new drug targets. Due to their important role in chemotaxis and nutrient uptake, periplasmic binding proteins (PBPs) represent potential targets for new antimicrobial agents that have not yet been fully explored and exploited. The H. pylori PBP YckK is homologous to polar amino acid-binding proteins from other bacteria. The yckK gene overlaps the gene tcyB-a gene annotated as a polar amino acid-transporting permease. Purified recombinant YckK behaved as a monomer in solution. Crystals of YckK were grown by the hanging drop vapour diffusion method using PEG 3350 as the precipitating agent. The crystals belong to the primitive triclinic space group P1 with unit cell parameters a = 63.0, b = 63.5, c = 74.6 Å, α = 72.5, β = 68.3, γ = 69.4 • . X-ray diffraction data were collected to 1.8 Å resolution using synchrotron radiation. Molecular replacement using this data revealed that the asymmetric unit contains three subunits: two in the open and one in the closed conformation.

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Comparative proteomics reveal the impact of OmcA/MtrC deletion on Shewanella oneidensis MR-1 in response to hexavalent chromium exposure

Chao

Chen

et al. 2014

Appl Microbiol Biotechnol

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Hexavalent chromium [Cr(VI)] is a priority pollutant causing serious environmental issues. Microbial reduction provides an alternative strategy for Cr(VI) remediation. The dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, was employed to study Cr(VI) reduction and toxicity in this work. To understand the effect of membrane cytochromes on Cr(VI) response, a comparative protein profile analysis from S. oneidensis MR-1 wild type and its mutant of deleting OmcA and MtrC (△omcA/mtrC) was conducted using two-dimensional electrophoresis (2-DE) technology. The 2-DE patterns were compared, and the proteins with abundant changes of up to twofold in the Cr(VI) treatment were detected. Using mass spectrometry, 38 and 45 differentially abundant proteins were identified in the wild type and the mutant, respectively. Among them, 25 proteins were shared by the two strains. The biological functions of these identified proteins were analyzed. Results showed that Cr(VI) exposure decreased the abundance of proteins involved in transcription, translation, pyruvate metabolism, energy production, and function of cellular membrane in both strains. There were also significant differences in protein expressions between the two strains under Cr(VI) treatment. Our results suggest that OmcA/MtrC deletion might result in the Cr(VI) toxicity to outer membrane and decrease assimilation of lactate, vitamin B12, and cystine. When carbohydrate metabolism was inhibited by Cr(VI), leucine and sulfur metabolism may act as the important compensatory mechanisms in the mutant. Furthermore, the mutant may regulate electron transfer in the inner membrane and periplasm to compensate for the deletion of OmcA and MtrC in Cr(VI) reduction.

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Crystal Structures of Two Solute Receptors for l-Cystine and l-Cysteine, Respectively, of the Human Pathogen Neisseria gonorrhoeae

Cited by 38 publications

References 36 publications

Crystal structures of a putative periplasmic cystine‐binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding

Crystal structures of a putative periplasmic cystine‐binding protein from Candidatus Liberibacter asiaticus: insights into an adapted mechanism of ligand binding

Crystallisation and Preliminary Crystallographic Analysis of Helicobacter pylori Periplasmic Binding Protein YckK

Comparative proteomics reveal the impact of OmcA/MtrC deletion on Shewanella oneidensis MR-1 in response to hexavalent chromium exposure

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