The ectoine binding protein of the TeaABC TRAP transporter TeaA in the Apo-State

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins

Marinelli, F.Kuhlmann, S.I.Grell, E.Kunte, H.J.Ziegler, C.Faraldo-Gomez, J.D.

(2011) Proc Natl Acad Sci U S A 108: E1285-E1292

  • DOI: https://doi.org/10.1073/pnas.1112534108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Numerous membrane importers rely on accessory water-soluble proteins to capture their substrates. These substrate-binding proteins (SBP) have a strong affinity for their ligands; yet, substrate release onto the low-affinity membrane transporter must occur for uptake to proceed. It is generally accepted that release is facilitated by the association of SBP and transporter, upon which the SBP adopts a conformation similar to the unliganded state, whose affinity is sufficiently reduced. Despite the appeal of this mechanism, however, direct supporting evidence is lacking. Here, we use experimental and theoretical methods to demonstrate that an allosteric mechanism of enhanced substrate release is indeed plausible. First, we report the atomic-resolution structure of apo TeaA, the SBP of the Na(+)-coupled ectoine TRAP transporter TeaBC from Halomonas elongata DSM2581(T), and compare it with the substrate-bound structure previously reported. Conformational free-energy landscape calculations based upon molecular dynamics simulations are then used to dissect the mechanism that couples ectoine binding to structural change in TeaA. These insights allow us to design a triple mutation that biases TeaA toward apo-like conformations without directly perturbing the binding cleft, thus mimicking the influence of the membrane transporter. Calorimetric measurements demonstrate that the ectoine affinity of the conformationally biased triple mutant is 100-fold weaker than that of the wild type. By contrast, a control mutant predicted to be conformationally unbiased displays wild-type affinity. This work thus demonstrates that substrate release from SBPs onto their membrane transporters can be facilitated by the latter through a mechanism of allosteric modulation of the former.

  • Organizational Affiliation

    Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic substrate binding protein
A, B, C, D
341Halomonas elongataMutation(s): 0 
Gene Names: teaA
Find proteins for E1VBK1 (Halomonas elongata (strain ATCC 33173 / DSM 2581 / NBRC 15536 / NCIMB 2198 / 1H9))
Explore E1VBK1 
Go to UniProtKB:  E1VBK1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1VBK1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
E [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth B],
LA [auth D],
M [auth B],
MA [auth D],
N [auth B],
NA [auth D],
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 C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.74α = 90
b = 64.98β = 91.06
c = 121.5γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-30
    Changes: Database references
  • Version 1.3: 2013-11-20
    Changes: Database references
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description