Crystal structure of the triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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This is version 1.3 of the entry. See complete history


Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity

Lee, Y.Nishizawa, T.Takemoto, M.Kumazaki, K.Yamashita, K.Hirata, K.Minoda, A.Nagatoishi, S.Tsumoto, K.Ishitani, R.Nureki, O.

(2017) Nat Plants 3: 825-832

  • DOI: https://doi.org/10.1038/s41477-017-0022-8
  • Primary Citation of Related Structures:  
    5Y78, 5Y79

  • PubMed Abstract: 

    The triose-phosphate/phosphate translocator (TPT) catalyses the strict 1:1 exchange of triose-phosphate, 3-phosphoglycerate and inorganic phosphate across the chloroplast envelope, and plays crucial roles in photosynthesis. Despite rigorous study for more than 40 years, the molecular mechanism of TPT is poorly understood because of the lack of structural information. Here we report crystal structures of TPT bound to two different substrates, 3-phosphoglycerate and inorganic phosphate, in occluded conformations. The structures reveal that TPT adopts a 10-transmembrane drug/metabolite transporter fold. Both substrates are bound within the same central pocket, where conserved lysine, arginine and tyrosine residues recognize the shared phosphate group. A structural comparison with the outward-open conformation of the bacterial drug/metabolite transporter suggests a rocker-switch motion of helix bundles, and molecular dynamics simulations support a model in which this rocker-switch motion is tightly coupled to the substrate binding, to ensure strict 1:1 exchange. These results reveal the unique mechanism of sugar phosphate/phosphate exchange by TPT.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative hexose phosphate translocator
A, B
329Galdieria sulphurariaMutation(s): 0 
Gene Names: Gasu_48050Gs48050.1
Membrane Entity: Yes 
Find proteins for B5AJT1 (Galdieria sulphuraria)
Explore B5AJT1 
Go to UniProtKB:  B5AJT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5AJT1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OLC

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on FLC

Download Ideal Coordinates CCD File 
C6 H5 O7
3PG (Subject of Investigation/LOI)
Query on 3PG

Download Ideal Coordinates CCD File 
KA [auth B],
R [auth A]
C3 H7 O7 P
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.05α = 90
b = 165.33β = 90
c = 41.14γ = 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: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description