6EI3

Crystal structure of auto inhibited POT family peptide transporter

• PDB DOI:  https://doi.org/10.2210/pdb6EI3/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Xanthomonas campestris
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2017-09-17 Released: 2017-11-22 
• Deposition Author(s): Newstead, S., Brinth, A., Vogeley, L., Caffrey, M.
• Funding Organization(s): Wellcome Trust, Science Foundation Ireland, National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.213 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Proton movement and coupling in the POT family of peptide transporters.

Parker, J.L., Li, C., Brinth, A., Wang, Z., Vogeley, L., Solcan, N., Ledderboge-Vucinic, G., Swanson, J.M.J., Caffrey, M., Voth, G.A., Newstead, S.

(2017) Proc Natl Acad Sci U S A 114: 13182-13187

• PubMed: 29180426 
• DOI: https://doi.org/10.1073/pnas.1710727114
• Primary Citation of Related Structures:  
  6EI3


• PubMed Abstract: 
  

POT transporters represent an evolutionarily well-conserved family of proton-coupled transport systems in biology. An unusual feature of the family is their ability to couple the transport of chemically diverse ligands to an inwardly directed proton electrochemical gradient. For example, in mammals, fungi, and bacteria they are predominantly peptide transporters, whereas in plants the family has diverged to recognize nitrate, plant defense compounds, and hormones. Although recent structural and biochemical studies have identified conserved sites of proton binding, the mechanism through which transport is coupled to proton movement remains enigmatic. Here we show that different POT transporters operate through distinct proton-coupled mechanisms through changes in the extracellular gate. A high-resolution crystal structure reveals the presence of ordered water molecules within the peptide binding site. Multiscale molecular dynamics simulations confirm proton transport occurs through these waters via Grotthuss shuttling and reveal that proton binding to the extracellular side of the transporter facilitates a reorientation from an inward- to outward-facing state. Together these results demonstrate that within the POT family multiple mechanisms of proton coupling have likely evolved in conjunction with variation of the extracellular gate.

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Organizational Affiliation: 

Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 61.98 kDa 
• Atom Count: 4,641 
• Modelled Residue Count: 511 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton-dependent oligopeptide transporter family protein	A	514	Xanthomonas campestris	Mutation(s): 0  Gene Names: XCCB100_2892 Membrane Entity: Yes
UniProt
Find proteins for Q8PAS2 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8PAS2  Go to UniProtKB:  Q8PAS2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
78M	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE C18 H34 O4 BJMLBVHMHXYQFS-JJEJIETFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.213 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.06	α = 90
b = 65.23	β = 96.84
c = 70.34	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Newstead, S., Brinth, A., Vogeley, L., Caffrey, M.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	102890/Z/13/Z
Science Foundation Ireland	Ireland	12/IA/1255
National Institutes of Health	United States	R01GM053148

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 1.2: 2017-12-20
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Source and taxonomy