5LTC

Crystal structure of doubly spin labelled VcSiaP R125


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

PELDOR Spectroscopy Reveals Two Defined States of a Sialic Acid TRAP Transporter SBP in Solution.

Glaenzer, J.Peter, M.F.Thomas, G.H.Hagelueken, G.

(2017) Biophys. J. 112: 109-120

  • DOI: 10.1016/j.bpj.2016.12.010

  • PubMed Abstract: 
  • The tripartite ATP-independent periplasmic (TRAP) transporters are a widespread class of membrane transporters in bacteria and archaea. Typical substrates for TRAP transporters are organic acids including the sialic acid N-acetylneuraminic acid. The ...

    The tripartite ATP-independent periplasmic (TRAP) transporters are a widespread class of membrane transporters in bacteria and archaea. Typical substrates for TRAP transporters are organic acids including the sialic acid N-acetylneuraminic acid. The substrate binding proteins (SBP) of TRAP transporters are the best studied component and are responsible for initial high-affinity substrate binding. To better understand the dynamics of the ligand binding process, pulsed electron-electron double resonance (PELDOR, also known as DEER) spectroscopy was applied to study the conformational changes in the N-acetylneuraminic acid-specific SBP VcSiaP. The protein is the SBP of VcSiaPQM, a sialic acid TRAP transporter from Vibrio cholerae. Spin-labeled double-cysteine mutants of VcSiaP were analyzed in the substrate-bound and -free state and the measured distances were compared to available crystal structures. The data were compatible with two clear states only, which are consistent with the open and closed forms seen in TRAP SBP crystal structures. Substrate titration experiments demonstrated the transition of the population from one state to the other with no other observed forms. Mutants of key residues involved in ligand binding and/or proposed to be involved in domain closure were produced and the corresponding PELDOR experiments reveal important insights into the open-closed transition. The results are in excellent agreement with previous in vivo sialylation experiments. The structure of the spin-labeled Q54R1/L173R1 R125A mutant was solved at 2.1 Å resolution, revealing no significant changes in the protein structure. Thus, the loss of domain closure appears to be solely due to loss of binding. In conclusion, these data are consistent with TRAP SBPs undergoing a simple two-state transition from an open-unliganded to closed-liganded state during the transport cycle.


    Organizational Affiliation

    Institute for Physical & Theoretical Chemistry, University of Bonn, Bonn, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C4-dicarboxylate-binding periplasmic protein
B, A
326Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: siaP
Find proteins for Q9KR64 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KR64
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
R1A
Query on R1A
A, B
L-PEPTIDE LINKINGC12 H21 N2 O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 72.270α = 90.00
b = 78.100β = 90.00
c = 116.240γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
PHENIXrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanyHA6805/4-1

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references