5X9R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.98 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    5X9R, 5XAS, 5XAR, 5XAT

  • 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 crystal ...

    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

    School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, Republic of Korea. misunjin@gist.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Citrate-sodium symporter AB438Klebsiella pneumoniaeMutation(s): 0 
Gene Names: citS
Find proteins for P31602 (Klebsiella pneumoniae)
Explore P31602 
Go to UniProtKB:  P31602
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
A, B
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
BGC
Query on BGC

Download Ideal Coordinates CCD File 
A, B
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.98 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.998α = 90
b = 93.998β = 90
c = 172.947γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF)Korea, Republic OfNRF-2014R1A1A3050966
National Research Foundation (NRF)Korea, Republic OfNRF-2015M2A2A4A03044653
National Research Foundation (NRF)Korea, Republic OfNRF-2014R1A2A1A10050436

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary