Escherichia coli Peptide Binding Protein OppA Has a Preference for Positively Charged Peptides

Klepsch, Mirjam; Kovermann, Michael; Löw, Christian; Balbach, Jochen; Permentier, Hjalmar P.; Fusetti, Fabrizia; Gier, J.W. de; Slotboom, Dirk Jan; Berntsson, R.P.-A.

doi:10.1016/j.jmb.2011.09.043

Cited by 65 publications

(70 citation statements)

References 33 publications

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“…However, for high-affinity binding of a given peptide, the physicochemical properties of the side chains (size and hydrophobicity) should match those of the PrgZ pockets. Further support for this notion comes from the observation that water molecules reside in all side chain pockets, and these could form bridging hydrogen bonds to bound peptides, as seen previously in OppA (14,15,29). The more hydrophilic pockets harbor more defined water molecules inside compared with the more hydrophobic ones (Table 2).…”

Section: Discussionsupporting

confidence: 53%

“…It is clear that iCF10 and cCF10 compete for the same binding site in PrgX, but it has not been shown to date whether iCF10 also competes with cCF10 for binding to PrgZ. Furthermore, it is unknown what discriminates PrgZ from OppA in terms of structure determinants that allow the pheromone receptor to bind cCF10 with high affinity, whereas OppA, based on studies of its homologs in Salmonella typhimurium, Escherichia coli, and Lactococcus lactis, is highly promiscuous and binds a wide variety of peptides with moderate affinity (13)(14)(15). To gain detailed insight in how PrgZ binds its ligands, we present here the structure of PrgZ complexed with cCF10, as well as ligand-binding studies.…”

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confidence: 99%

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Structure and Mode of Peptide Binding of Pheromone Receptor PrgZ

Berntsson

Schuurman-Wolters

Dunny

et al. 2012

Journal of Biological Chemistry

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Background: A sex pheromone system controls bacterial conjugation. Results: The initial receptor PrgZ has been crystallized in complex with the sex pheromone cCF10. Conclusion: An extensive network of hydrogen bonds explains the high peptide specificity of PrgZ. Significance: The sex pheromone and inhibitor peptide compete for binding to PrgZ, providing new insight into the regulation of conjugation.

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Section: Discussionsupporting

confidence: 53%

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confidence: 99%

Structure and Mode of Peptide Binding of Pheromone Receptor PrgZ

Berntsson

Schuurman-Wolters

Dunny

et al. 2012

Journal of Biological Chemistry

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“…This may explain why PsDppA exhibits a high affinity for Ala-Phe but not for Phe-Ala. Second, the peptides are bound in an extended, identical conformation due to the interactions between their backbones and PsDppA, in particular by anchoring their N and C termini through ion-pair interactions. This result is consistent with the peptide binding mode of EcDppA and the OppA of E. coli and S. Typhimurium (7)(8)(9)(10)16). However, for the OppA of L. lactis, the peptide termini are not fixed with salt bridges, explaining the wide tolerance of peptides with varied lengths and sequences (11,32).…”

Section: Discussionsupporting

confidence: 83%

“…OppA, the periplasmic binding protein of Opp, has been widely studied in both Gram-negative bacteria and Gram-positive bacteria (5,(7)(8)(9)(10)(11)(12)(13). The OppA of Salmonella enterica serovar Typhimurium had a higher affinity for tri-and tetrapeptides than for di-and pentapeptides (7)(8)(9).…”

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confidence: 99%

Structural Insights into the Multispecific Recognition of Dipeptides of Deep-Sea Gram-Negative Bacterium Pseudoalteromonas sp. Strain SM9913

Chen

Qin

et al. 2015

J Bacteriol

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Peptide uptake is important for nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria absorb peptides is still not fully understood. DppA is the periplasmic dipeptide binding protein of dipeptide permease (Dpp; an important peptide transporter in bacteria) and exclusively controls the substrate specificity of Dpp. Here, the substrate binding specificity of deep-sea Pseudoalteromonas sp. strain SM9913 DppA (PsDppA) was analyzed for 25 different dipeptides with various properties by using isothermal titration calorimetry measurements. PsDppA showed binding affinities for 8 dipeptides. To explain the multispecific substrate recognition mechanism of PsDppA, we solved the crystal structures of unliganded PsDppA and of PsDppA in complex with 4 different types of dipeptides (Ala-Phe, Met-Leu, Gly-Glu, and Val-Thr). PsDppA alternates between an "open" and a "closed" form during substrate binding. Structural analyses of the 4 PsDppA-substrate complexes combined with mutational assays indicate that PsDppA binds to different substrates through a precise mechanism: dipeptides are bound mainly by the interactions between their backbones and PsDppA, in particular by anchoring their N and C termini through ion-pair interactions; hydrophobic interactions are important in binding hydrophobic dipeptides; and Lys457 is necessary for the binding of dipeptides with a C-terminal glutamic acid or glutamine. Additionally, sequence alignment suggests that the substrate recognition mechanism of PsDppA may be common in Gram-negative bacteria. All together, our results provide structural insights into the multispecific substrate recognition mechanism of marine Gramnegative bacterial DppA, which provides a better understanding of the mechanisms of marine bacterial peptide uptake. IMPORTANCEPeptide uptake plays a significant role in nutrition supply for marine bacteria. It is also an important step in marine nitrogen cycling. However, how marine bacteria recognize and absorb peptides is still unclear. This study analyzed the substrate binding specificity of deep-sea Pseudoalteromonas sp. strain SM9913 DppA (PsDppA; the dipeptide-binding protein of dipeptide permease) and solved the crystal structures of unliganded PsDppA and PsDppA in complex with 4 different types of dipeptides. The multispecific recognition mechanism of PsDppA for dipeptides is explained based on structural and mutational analyses. We also find that the substrate-binding mechanism of PsDppA may be common in Gram-negative bacteria. This study sheds light on marine Gram-negative bacterial peptide uptake and marine nitrogen cycling.T he largest components of marine organic matter are referred to as detrital proteins (1, 2). The utilization of oceanic nonliving organic nitrogen is vital for marine nitrogen recycling. A portion of this oceanic organic pool is consumed directly by grazers, and bacterial extracellular enzymes degrade the rest into small peptides and amino acids. Bacteria and/or other mi...

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“…The accepted peptide fragments can have two to five residues with no preference for their composition, which confers OppA a broad substrate promiscuity . However, because of the negative charge at its binding site, OppA has a preference toward positively charged substrates, particularly lysine containing tripeptides . Experimental studies revealed that the substrate promiscuity is especially pronounced for the central amino acid of KXK tripeptides, where X may represent 20 natural and 8 non‐natural amino acids .…”

Section: Introductionmentioning

confidence: 99%

Free‐energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling

2016

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Previous free‐energy calculations have shown that the seemingly simple transformation of the tripeptide KXK to KGK in water holds some unobvious challenges concerning the convergence of the forward and backward thermodynamic integration processes (i.e., hysteresis). In the current study, the central residue X was either alanine, serine, glutamic acid, lysine, phenylalanine, or tyrosine. Interestingly, the transformation from alanine to glycine yielded the highest hysteresis in relation to the extent of the chemical change of the side chain. The reason for that could be attributed to poor sampling of φ2/ψ2 dihedral angles along the transformation. Altering the nature of alanine's Cβ atom drastically improved the sampling and at the same time led to the identification of high energy barriers as cause for it. Consequently, simple strategies to overcome these barriers are to increase simulation time (computationally expensive) or to use enhanced sampling techniques such as Hamiltonian replica exchange molecular dynamics and one‐step perturbation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

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Escherichia coli Peptide Binding Protein OppA Has a Preference for Positively Charged Peptides

Cited by 65 publications

References 33 publications

Structure and Mode of Peptide Binding of Pheromone Receptor PrgZ

Structure and Mode of Peptide Binding of Pheromone Receptor PrgZ

Structural Insights into the Multispecific Recognition of Dipeptides of Deep-Sea Gram-Negative Bacterium Pseudoalteromonas sp. Strain SM9913

Free‐energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling

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