Crystal structure of dipeptide binding protein from pseudoalteromonas sp. SM9913 in complex with Ala-Phe

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

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Structural insights into the multispecific recognition of dipeptides of deep-sea gram-negative bacterium Pseudoalteromonas sp. strain SM9913

Li, C.Y.Chen, X.L.Qin, Q.L.Wang, P.Zhang, W.X.Xie, B.B.Su, H.N.Zhang, X.Y.Zhou, B.C.Zhang, Y.Z.

(2015) J Bacteriol 197: 1125-1134

  • DOI: https://doi.org/10.1128/JB.02600-14
  • Primary Citation of Related Structures:  
    4QFK, 4QFL, 4QFN, 4QFO, 4QFP

  • PubMed Abstract: 

    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 Gram-negative bacterial DppA, which provides a better understanding of the mechanisms of marine bacterial peptide uptake.

  • Organizational Affiliation

    Marine Biotechnology Research Center, Shandong University, Jinan, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter periplasmic peptide-binding protein
A, B
541Pseudoalteromonas sp. SM9913Mutation(s): 0 
Gene Names: dppA
Find proteins for A7Y7W1 (Pseudoalteromonas sp. (strain SM9913))
Explore A7Y7W1 
Go to UniProtKB:  A7Y7W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7Y7W1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.142α = 90
b = 106.142β = 90
c = 100.981γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description