6R7R

Crystal structure of the glutamate transporter homologue GltTk in complex with D-aspartate

• PDB DOI:  https://doi.org/10.2210/pdb6R7R/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2019-03-29 Released: 2019-04-17 
• Deposition Author(s): Arkhipova, V., Guskov, A., Slotboom, D.J.
• Funding Organization(s): Netherlands Organisation for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Literature

Binding and transport of D-aspartate by the glutamate transporter homolog Glt Tk .

Arkhipova, V., Trinco, G., Ettema, T.W., Jensen, S., Slotboom, D.J., Guskov, A.

(2019) Elife 8

• PubMed: 30969168 
• DOI: https://doi.org/10.7554/eLife.45286
• Primary Citation of Related Structures:  
  6R7R


• PubMed Abstract: 
  

Mammalian glutamate transporters are crucial players in neuronal communication as they perform neurotransmitter reuptake from the synaptic cleft. Besides L-glutamate and L-aspartate, they also recognize D-aspartate, which might participate in mammalian neurotransmission and/or neuromodulation. Much of the mechanistic insight in glutamate transport comes from studies of the archeal homologs Glt _Ph from Pyrococcus horikoshii and Glt _Tk from Thermococcus kodakarensis . Here, we show that Glt _Tk transports D-aspartate with identical Na ⁺ : substrate coupling stoichiometry as L-aspartate, and that the affinities ( K _d and K _m ) for the two substrates are similar. We determined a crystal structure of Glt _Tk with bound D-aspartate at 2.8 Å resolution. Comparison of the L- and D-aspartate bound Glt _Tk structures revealed that D-aspartate is accommodated with only minor rearrangements in the structure of the binding site. The structure explains how the geometrically different molecules L- and D-aspartate are recognized and transported by the protein in the same way.

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Organizational Affiliation: 

Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 143.87 kDa 
• Atom Count: 9,512 
• Modelled Residue Count: 1,244 
• Deposited Residue Count: 1,314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton/glutamate symporter, SDF family	A, B, C	438	Thermococcus kodakarensis KOD1	Mutation(s): 0  Gene Names: TK0986 Membrane Entity: Yes
UniProt
Find proteins for Q5JID0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JID0  Go to UniProtKB:  Q5JID0

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMU	L [auth A]	DECYL-BETA-D-MALTOPYRANOSIDE C22 H42 O11 WOQQAWHSKSSAGF-WXFJLFHKSA-N
P6G	V [auth B], W [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE	Z [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	K [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	M [auth A], X [auth B], Y [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
DAS (Subject of Investigation/LOI)	DA [auth C], G [auth A], Q [auth B]	D-ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-UWTATZPHSA-N
PEG	EA [auth C], FA [auth C], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], R [auth B], S [auth B], T [auth B], U [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	AA [auth C], BA [auth C], CA [auth C], D [auth A], E [auth A], F [auth A], N [auth B], O [auth B], P [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.55	α = 90
b = 116.55	β = 90
c = 314.77	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): Arkhipova, V., Guskov, A., Slotboom, D.J.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research	Netherlands	865.11.001

Revision History  

• Version 1.0: 2019-04-17
  Type: Initial release
  
• Version 1.1: 2019-05-01
  Changes: Data collection, Database references
• Version 1.2: 2020-09-30
  Changes: Database references