6GHJ | pdb_00006ghj

PepTSt in complex with tripeptide Phe-Ala-Gln

• PDB DOI: https://doi.org/10.2210/pdb6GHJ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Streptococcus thermophilus LMG 18311, synthetic construct
• Expression System: Escherichia coli, synthetic construct
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2018-05-08 Released: 2018-09-19 
• Deposition Author(s): Martinez Molledo, M., Quistgaard, E.M., Loew, C.
• Funding Organization(s): European Union, Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.222 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Tripeptide binding in a proton-dependent oligopeptide transporter.

Martinez Molledo, M., Quistgaard, E.M., Low, C.

(2018) FEBS Lett 592: 3239-3247

• PubMed: 30194725 
• DOI: https://doi.org/10.1002/1873-3468.13246
• Primary Citation Related Structures: 
  6GHJ


• PubMed Abstract: 
  

  Proton-dependent oligopeptide transporters (POTs) are important for the uptake of di-/tripeptides in many organisms and for drug transport in humans. The binding mode of dipeptides has been well described. However, it is still debated how tripeptides are recognized. Here, we show that tripeptides of the sequence Phe-Ala-Xxx bind with similar affinities as dipeptides to the POT transporter from Streptococcus thermophilus (PepT _{S t} ). We furthermore determined a 2.3-Å structure of PepT _{S t} in complex with Phe-Ala-Gln. The phenylalanine and alanine residues of the peptide adopt the same positions as previously observed for the Phe-Ala dipeptide, while the glutamine side chain extends into a hitherto uncharacterized pocket. This pocket is adaptable in size and can likely accommodate a wide variety of peptide side chains.

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Organizational Affiliation: 
• Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany.
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 58.33 kDa 
• Atom Count: 4,005 
• Modeled Residue Count: 460 
• Deposited Residue Count: 486 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Di-or tripeptide:H+ symporter	A	483	Streptococcus thermophilus LMG 18311	Mutation(s): 0  Gene Names: dtpT, stu0970 Membrane Entity: Yes
UniProt
Find proteins for Q5M4H8 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M4H8  Go to UniProtKB:  Q5M4H8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHE-ALA-GLN	B	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
78M	J [auth A], L [auth A], V [auth A]	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE C18 H34 O4 BJMLBVHMHXYQFS-JJEJIETFSA-N
78N	I [auth A], K [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE C18 H34 O4 BJMLBVHMHXYQFS-XZVRFQMRSA-N
EPE	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
1PE	F [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PO4	C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.222 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.55	α = 90
b = 108.22	β = 90
c = 111.61	γ = 90

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: 2018-09-19 
Deposition Author(s): Martinez Molledo, M., Quistgaard, E.M., Loew, C.

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Funding Organization	Location	Grant Number
European Union		653706
Swedish Research Council		621-2013-5905

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description