4QFL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.749 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1128/JB.02600-14
  • Primary Citation of Related Structures:  

  • 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 prote ...

    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.,State Key Laboratory of Microbial Technology, Shandong University, Jinan, China Marine Biotechnology Research Center, Shandong University, Jinan, China.,State Key Laboratory of Microbial Technology, Shandong University, Jinan, China Marine Biotechnology Research Center, Shandong University, Jinan, China Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China.,State Key Laboratory of Microbial Technology, Shandong University, Jinan, China Marine Biotechnology Research Center, Shandong University, Jinan, China zhangxiying@sdu.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABC transporter periplasmic peptide-binding protein
A, B
541Pseudoalteromonas sp. (strain SM9913)Mutation(s): 0 
Gene Names: dppA
Find proteins for A7Y7W1 (Pseudoalteromonas sp. (strain SM9913))
Go to UniProtKB:  A7Y7W1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PHE
Query on PHE

Download SDF File 
Download CCD File 
A, B
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
ALA
Query on ALA

Download SDF File 
Download CCD File 
A, B
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.749 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 106.142α = 90.00
b = 106.142β = 90.00
c = 100.981γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-05-21 
  • Released Date: 2015-01-28 
  • Deposition Author(s): Li, C.Y., Zhang, Y.Z.

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references