5XAS

Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.47 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS

Kim, J.W., Kim, S., Kim, S., Lee, H., Lee, J.O., Jin, M.S.

(2017) Sci Rep 7: 2548-2548

  • DOI: 10.1038/s41598-017-02794-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The sodium-dependent citrate transporter of Klebsiella pneumoniae (KpCitS) belongs to the 2-hydroxycarboxylate transporter (2-HCT) family and allows the cell to use citrate as sole carbon and energy source in anaerobic conditions. Here we present cry ...

    The sodium-dependent citrate transporter of Klebsiella pneumoniae (KpCitS) belongs to the 2-hydroxycarboxylate transporter (2-HCT) family and allows the cell to use citrate as sole carbon and energy source in anaerobic conditions. Here we present crystal structures of KpCitS in citrate-bound outward-facing, citrate-bound asymmetric, and citrate-free inward-facing state. The structures reveal that the KpCitS dimerization domain remains stationary throughout the transport cycle due to a hydrogen bond network as well as extensive hydrophobic interactions. In contrast, its transport domain undergoes a ~35° rigid-body rotation and a ~17 Å translocation perpendicular to the membrane to expose the substrate-binding site alternately to either side of the membrane. Furthermore, homology models of two other 2-HCT proteins based on the KpCitS structure offer structural insights into their differences in substrate specificity at a molecular level. On the basis of our results and previous biochemical data, we propose that the activity of the 2-HCT CitS involves an elevator-like movement in which the transport domain itself traverses the lipid bilayer, carrying the substrate into the cell in a sodium-dependent manner.

    Organizational Affiliation: 

    Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Citrate-sodium symporter
A, B
438Klebsiella pneumoniaeGene Names: citS
Find proteins for P31602 (Klebsiella pneumoniae)
Go to UniProtKB:  P31602
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC
Download SDF File 
Download CCD File 
A, B
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
BOG
Query on BOG
Download SDF File 
Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.47 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.246 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 51.705α = 97.14
b = 83.340β = 100.16
c = 81.060γ = 94.59
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationCountryGrant Number
National Research FoundationKorea, Republic OfNRF-2014R1A1A3050966
National Research FoundationKorea, Republic OfNRF-2015M2A2A4A03044653
National Research FoundationKorea, Republic OfNRF-2014R1A2A1A10050436

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release