Structural Basis for Recognition of Dipeptides by Peptide Transporters

Payne, John W.; Grail, Barry M.; Gupta, Sona; Ladbury, John E.; Marshall, N. Justin; O’Brien, Rita Cruise; Payne, Gillian

doi:10.1006/abbi.2000.2084

Cited by 29 publications

(58 citation statements)

References 36 publications

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“…S4). This is not what one would have predicted given that HbpA is 54% identical to E. coli DppA, a PBP known to bind di-and tripeptides (39,40), heme (30), and the heme precursor δ-aminolevulinic acid (δ-ALA) (41). Indeed, many dpp-like proteins exhibit significant ligand-binding promiscuity in terms of peptide length and side-chain content (35).…”

Section: Discussionmentioning

confidence: 94%

Glutathione import in Haemophilus influenzae Rd is primed by the periplasmic heme-binding protein HbpA

Vergauwen

Elegheert

Dansercoer

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

104

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Glutathione (GSH) is a vital intracellular cysteine-containing tripeptide across all kingdoms of life and assumes a plethora of cellular roles. Such pleiotropic behavior relies on a finely tuned spatiotemporal distribution of glutathione and its conjugates, which is not only controlled by synthesis and breakdown, but also by transport. Here, we show that import of glutathione in the obligate human pathogen Haemophilus influenzae , a glutathione auxotrophe, is mediated by the ATP-binding cassette (ABC)-like dipeptide transporter DppBCDF, which is primed for glutathione transport by a dedicated periplasmic-binding protein (PBP). We have identified the periplasmic lipoprotein HbpA, a protein hitherto implicated in heme acquisition, as the cognate PBP that specifically binds reduced (GSH) and oxidized glutathione (GSSG) forms of glutathione with physiologically relevant affinity, while it exhibits marginal binding to hemin. Dissection of the ligand preferences of HbpA showed that HbpA does not recognize bulky glutathione S conjugates or glutathione derivatives with C-terminal modifications, consistent with the need for selective import of useful forms of glutathione and the concomitant exclusion of potentially toxic glutathione adducts. Structural studies of the highly homologous HbpA from Haemophilus parasuis in complex with GSSG have revealed the structural basis of the proposed novel function for HbpA-like proteins, thus allowing a delineation of highly conserved structure-sequence fingerprints for the entire family of HbpA proteins. Taken together, our studies unmask the main physiological role of HbpA and establish a paradigm for glutathione import in bacteria. Accordingly, we propose a name change for HbpA to glutathione-binding protein A.

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Section: Discussionmentioning

confidence: 94%

Glutathione import in Haemophilus influenzae Rd is primed by the periplasmic heme-binding protein HbpA

Vergauwen

Elegheert

Dansercoer

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

104

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“…However, this analysis alone does not permit identification of a unique conformer or combination of conformer types that allows definition of an MRT, although the structurally distinct forms resulting from different Tor6/Tor4 combinations makes it unlikely that a transpeptidase would evolve a specificity able to recognize both conformational classes as substrates. To seek an MRT for transpeptidase, conformational analysis of a range of substrates needs to be performed so that common structural patterns can be identified, as exemplified with the description of unique MRTs for different peptide transport proteins (Grail and Payne, 2000;Payne et al, 2000b (Fig. 2(c, d)); a combined 3DPR plot of their conformers shows that the main overlap in conformational space for the important Tor8 terminal carboxylate region (Laws and Page, 1989;Varetto et al, 1991) is in sector D3 (Fig.…”

Section: Conformational Profiles Of Cell Wall Peptidesmentioning

confidence: 99%

Conformational analysis of bacterial cell wall peptides indicates how particular conformations have influenced the evolution of penicillin‐binding proteins, β‐lactam antibiotics and antibiotic resistance mechanisms

Grail

Payne

2002

J of Molecular Recognition

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Our aim was to use a conformational analysis technique developed for peptides to identify structural relationships between bacterial cell wall peptides and beta-lactam antibiotics that might help to explain their different actions as substrates and inhibitors of penicillin binding proteins (PBPs). The conformational forms of the model cell wall peptide Ac-L-Lys(Ac)-D-Ala-D-Ala are described by just a few backbone torsion combinations: three C-terminal carboxylate regions, with Tor8 (psi(i+1)) ranges of D3 region (50 degrees to 70 degrees ), D6 region (140 degrees to 170 degrees ) and D9 region (-50 degrees to -70 degrees ) are combined with either of two Tor6 (phi(i))-Tor4 (psi(i)) combinations, C4 region (-50 degrees to -80 degrees ) with B8 region (-40 degrees to -70 degrees ) or C11 region (30 degrees to 50 degrees ) with B2 region (30 degrees to 70 degrees ). From these results, and comparisons with conformational analyses of various beta-lactams and Ac-L-Lys(Ac)-D-Ala-D-Lac, it is concluded that molecular recognition of cell wall peptide substrates by PBPs requires conformers with backbone torsion angles of D3C4B8. beta-Lactam antibiotics are constrained compounds with fewer conformational forms; these match well the backbone torsions of cell wall peptides at D3C4, allowing their recognition and acylation by PBPs, whereas their unique Tor4 produces differently orientated CO and N atoms that appear to prevent subsequent deacylation, leading to their action as suicide substrates. The results are also related to the selective pressures involved in evolution of beta-lactamases from PBPs. From analysis of conformers of Ac-L-Lys(Ac)-D-Ala-D-Ala and the vancomycin-resistant analogue Ac-L-Lys(Ac)-D-Ala-D-Lac, it is concluded that vancomycin may recognise D6C11B2 conformers, giving it complementary substrate specificity to PBPs. This approach could have applications in the rational design of antibiotics targeted against PBPs and their substrates.

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“…2) Dipeptides must be in zwitterionic forms, and the intramolecular distance between oppositely charged NH 2 and COOH head groups is > 500 and < 630 picometers (46)(47)(48);…”

Section: Basic Structural Characteristics Of the Substratesmentioning

confidence: 99%

“…3) A correctly positioned backbone carbonyl group (28,41,48); 4) A free amino group in α or β position; 5) Stereoselectivity with L-amino acids and transconformers being preferred (37,39,40); 6) Chiral centers at α-carbons and backbone torsion angles ψ, φ, and ω (23,48);…”

Section: Basic Structural Characteristics Of the Substratesmentioning

confidence: 99%