4M8J

Crystal structure of CaiT R262E bound to gamma-butyrobetaine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Arginine oscillation explains Na+ independence in the substrate/product antiporter CaiT.

Kalayil, S.Schulze, S.Kuhlbrandt, W.

(2013) Proc Natl Acad Sci U S A 110: 17296-17301

  • DOI: https://doi.org/10.1073/pnas.1309071110
  • Primary Citation of Related Structures:  
    4M8J

  • PubMed Abstract: 

    Most secondary-active transporters transport their substrates using an electrochemical ion gradient. In contrast, the carnitine transporter (CaiT) is an ion-independent, l-carnitine/γ-butyrobetaine antiporter belonging to the betaine/carnitine/choline transporter family of secondary transporters. Recently determined crystal structures of CaiT from Escherichia coli and Proteus mirabilis revealed an inverted five-transmembrane-helix repeat similar to that in the amino acid/Na(+) symporter LeuT. The ion independence of CaiT makes it unique in this family. Here we show that mutations of arginine 262 (R262) make CaiT Na(+)-dependent. The transport activity of R262 mutants increased by 30-40% in the presence of a membrane potential, indicating substrate/Na(+) cotransport. Structural and biochemical characterization revealed that R262 plays a crucial role in substrate binding by stabilizing the partly unwound TM1' helix. Modeling CaiT from P. mirabilis in the outward-open and closed states on the corresponding structures of the related symporter BetP reveals alternating orientations of the buried R262 sidechain, which mimic sodium binding and unbinding in the Na(+)-coupled substrate symporters. We propose that a similar mechanism is operative in other Na(+)/H(+)-independent transporters, in which a positively charged amino acid replaces the cotransported cation. The oscillation of the R262 sidechain in CaiT indicates how a positive charge triggers the change between outward-open and inward-open conformations as a unifying critical step in LeuT-type transporters.


  • Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-carnitine/gamma-butyrobetaine antiporter504Proteus mirabilis ATCC 29906Mutation(s): 3 
Gene Names: caiTHMPREF0693_2800
Membrane Entity: Yes 
UniProt
Find proteins for B4EY22 (Proteus mirabilis (strain HI4320))
Explore B4EY22 
Go to UniProtKB:  B4EY22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4EY22
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NM2
Query on NM2

Download Ideal Coordinates CCD File 
B [auth A]3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM
C7 H16 N O2
JHPNVNIEXXLNTR-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.075α = 90
b = 129.075β = 90
c = 160.717γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2013-10-09 
  • Deposition Author(s): Kalayil, S.

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references
  • Version 1.2: 2013-11-06
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description