Probing the Putative Active Site of YjdL: An Unusual Proton-Coupled Oligopeptide Transporter from E. coli

Johanne Mørch Jensen, Fouzia Ismat, G. Szakonyi, Moazur Rahman, Osman Mirza

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

YjdL from E. coli is an unusual proton-coupled oligopeptide transporter (POT). Unlike prototypical POTs, dipeptides are preferred over tripeptides, in particular dipeptides with a positively charged C-terminal residue. To further understand this difference in peptide specificity, the sequences of YjdL and YdgR, a prototypical E. coli POT, were compared in light of the crystal structure of a POT from Shewanella oneidensis. Several residues found in the putative active site were mutated and the activities of the mutated variants were assessed in terms of substrate uptake assays, and changes in specificity in terms of uptake inhibition. Most strikingly, changing the YjdL specific Asp392 to the conserved Ser in YjdL obliterated the preference for a positively charged C-terminal residue. Based on this unique finding and previously published results indicating that the dipeptide N-terminus may interact with Glu388, a preliminary orientation model of a dipeptide in the YjdL cavity is presented. Single site mutations of particularly Ala281 and Trp278 support the presented orientation. A dipeptide bound in the cavity of YjdL appears to be oriented such that the N-terminal side chain protrudes into a sub pocket that opens towards the extracellular space. The C-terminal side chain faces in the opposite direction into a sub pocket that faces the cytoplasm. These data indicated a stabilizing effect on a bulky N-terminal residue by an Ala281Phe variant and on the dipeptide backbone by Trp278. In the presented orientation model, Tyr25 and Tyr58 both appear to be in proximity of the dipeptide backbone while Lys117 appears to be in proximity of the peptide C-terminus. Mutational studies of these conserved residues highlight their functional importance.

Original languageEnglish
Article numbere47780
JournalPLoS One
Volume7
Issue number10
DOIs
Publication statusPublished - Oct 22 2012

Fingerprint

oligopeptides
Oligopeptides
dipeptides
Dipeptides
active sites
Escherichia coli
protons
transporters
Protons
Catalytic Domain
Shewanella oneidensis
Shewanella
peptides
uptake mechanisms
tripeptides
extracellular space
Extracellular Space
crystal structure
Assays
Cytoplasm

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Probing the Putative Active Site of YjdL : An Unusual Proton-Coupled Oligopeptide Transporter from E. coli. / Jensen, Johanne Mørch; Ismat, Fouzia; Szakonyi, G.; Rahman, Moazur; Mirza, Osman.

In: PLoS One, Vol. 7, No. 10, e47780, 22.10.2012.

Research output: Contribution to journalArticle

Jensen, Johanne Mørch ; Ismat, Fouzia ; Szakonyi, G. ; Rahman, Moazur ; Mirza, Osman. / Probing the Putative Active Site of YjdL : An Unusual Proton-Coupled Oligopeptide Transporter from E. coli. In: PLoS One. 2012 ; Vol. 7, No. 10.
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