Crystal structure of VcSiaP bound to sialic acid

Experimental Data Snapshot

  • Resolution: 1.68 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

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Triggering Closure of a Sialic Acid TRAP Transporter Substrate Binding Protein through Binding of Natural or Artificial Substrates.

Peter, M.F.Gebhardt, C.Glaenzer, J.Schneberger, N.de Boer, M.Thomas, G.H.Cordes, T.Hagelueken, G.

(2020) J Mol Biol 433: 166756-166756

  • DOI: https://doi.org/10.1016/j.jmb.2020.166756
  • Primary Citation of Related Structures:  
    7A5C, 7A5Q

  • PubMed Abstract: 

    The pathogens Vibrio cholerae and Haemophilus influenzae use tripartite ATP-independent periplasmic transporters (TRAPs) to scavenge sialic acid from host tissues. They use it as a nutrient or to evade the innate immune system by sialylating surface lipopolysaccharides. An essential component of TRAP transporters is a periplasmic substrate binding protein (SBP). Without substrate, the SBP has been proposed to rest in an open-state, which is not recognised by the transporter. Substrate binding induces a conformational change of the SBP and it is thought that this closed state is recognised by the transporter, triggering substrate translocation. Here we use real time single molecule FRET experiments and crystallography to investigate the open- to closed-state transition of VcSiaP, the SBP of the sialic acid TRAP transporter from V. cholerae. We show that the conformational switching of VcSiaP is strictly substrate induced, confirming an important aspect of the proposed transport mechanism. Two new crystal structures of VcSiaP provide insights into the closing mechanism. While the first structure contains the natural ligand, sialic acid, the second structure contains an artificial peptide in the sialic acid binding site. Together, the two structures suggest that the ligand itself stabilises the closed state and that SBP closure is triggered by physically bridging the gap between the two lobes of the SBP. Finally, we demonstrate that the affinity for the artificial peptide substrate can be substantially increased by varying its amino acid sequence and by this, serve as a starting point for the development of peptide-based inhibitors of TRAP transporters.

  • Organizational Affiliation

    Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DctP family TRAP transporter solute-binding subunit
A, B
299Vibrio choleraeMutation(s): 0 
Gene Names: C9J66_17385GQX72_05445
Find proteins for Q9KR64 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KR64 
Go to UniProtKB:  Q9KR64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KR64
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SLB (Subject of Investigation/LOI)
Query on SLB

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
N-acetyl-beta-neuraminic acid
C11 H19 N O9
Query on BGC

Download Ideal Coordinates CCD File 
DA [auth B]beta-D-glucopyranose
C6 H12 O6
Query on PGE

Download Ideal Coordinates CCD File 
CA [auth B],
L [auth A]
C6 H14 O4
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
D [auth A]
E [auth A]
F [auth A]
AA [auth B],
BA [auth B],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
SLB Binding MOAD:  7A5Q Kd: 300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.68 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.354α = 90
b = 106.738β = 90
c = 134.506γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyHA 6805/5-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description