5I20

Crystal structure of protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for amino acid export by DMT superfamily transporter YddG.

Tsuchiya, H.Doki, S.Takemoto, M.Ikuta, T.Higuchi, T.Fukui, K.Usuda, Y.Tabuchi, E.Nagatoishi, S.Tsumoto, K.Nishizawa, T.Ito, K.Dohmae, N.Ishitani, R.Nureki, O.

(2016) Nature 534: 417-420

  • DOI: https://doi.org/10.1038/nature17991
  • Primary Citation of Related Structures:  
    5I20

  • PubMed Abstract: 

    The drug/metabolite transporter (DMT) superfamily is a large group of membrane transporters ubiquitously found in eukaryotes, bacteria and archaea, and includes exporters for a remarkably wide range of substrates, such as toxic compounds and metabolites. YddG is a bacterial DMT protein that expels aromatic amino acids and exogenous toxic compounds, thereby contributing to cellular homeostasis. Here we present structural and functional analyses of YddG. Using liposome-based analyses, we show that Escherichia coli and Starkeya novella YddG export various amino acids. The crystal structure of S. novella YddG at 2.4 Å resolution reveals a new membrane transporter topology, with ten transmembrane segments in an outward-facing state. The overall structure is basket-shaped, with a large substrate-binding cavity at the centre of the molecule, and is composed of inverted structural repeats related by two-fold pseudo-symmetry. On the basis of this intramolecular symmetry, we propose a structural model for the inward-facing state and a mechanism of the conformational change for substrate transport, which we confirmed by biochemical analyses. These findings provide a structural basis for the mechanism of transport of DMT superfamily proteins.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B, C, D, E
A, B, C, D, E, F
298Ancylobacter novellus DSM 506Mutation(s): 0 
Gene Names: Snov_2734
Membrane Entity: Yes 
UniProt
Find proteins for D7A5Q8 (Ancylobacter novellus (strain ATCC 8093 / DSM 506 / JCM 20403 / CCM 1077 / IAM 12100 / NBRC 12443 / NCIMB 10456))
Explore D7A5Q8 
Go to UniProtKB:  D7A5Q8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7A5Q8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
G [auth A]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
X [auth D],
Y [auth E],
Z [auth E]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.84α = 90
b = 84.65β = 108.46
c = 112.25γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references