3PGU

Phe3Glu mutant of EcFadL

• PDB DOI:  https://doi.org/10.2210/pdb3PGU/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2010-11-02 Released: 2011-05-25 
• Deposition Author(s): Lepore, B.W., Indic, M., Pham, H., Hearn, E., Patel, D., van den Berg, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.180 
• R-Value Work: 0.168 
• R-Value Observed: 0.168 

Literature

From the Cover: Ligand-gated diffusion across the bacterial outer membrane.

Lepore, B.W., Indic, M., Pham, H., Hearn, E.M., Patel, D.R., van den Berg, B.

(2011) Proc Natl Acad Sci U S A 108: 10121-10126

• PubMed: 21593406 
• DOI: https://doi.org/10.1073/pnas.1018532108
• Primary Citation of Related Structures:  
  2R89, 2R8A, 3PF1, 3PGR, 3PGS, 3PGU


• PubMed Abstract: 
  

Ligand-gated channels, in which a substrate transport pathway is formed as a result of the binding of a small-molecule chemical messenger, constitute a diverse class of membrane proteins with important functions in prokaryotic and eukaryotic organisms. Despite their widespread nature, no ligand-gated channels have yet been found within the outer membrane (OM) of Gram-negative bacteria. Here we show, using in vivo transport assays, intrinsic tryptophan fluorescence and X-ray crystallography, that high-affinity (submicromolar) substrate binding to the OM long-chain fatty acid transporter FadL from Escherichia coli causes conformational changes in the N terminus that open up a channel for substrate diffusion. The OM long-chain fatty acid transporter FadL from E. coli is a unique paradigm for OM diffusion-driven transport, in which ligand gating within a β-barrel membrane protein is a prerequisite for channel formation.

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Organizational Affiliation: 

University of Massachusetts Medical School, Program in Molecular Medicine, 373 Plantation Street, Worcester, MA 01605, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 52.73 kDa 
• Atom Count: 3,945 
• Modelled Residue Count: 408 
• Deposited Residue Count: 427 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Long-chain fatty acid transport protein	A	427	Escherichia coli K-12	Mutation(s): 1  Gene Names: b2344, fadL, JW2341, ttr Membrane Entity: Yes
UniProt
Find proteins for P10384 (Escherichia coli (strain K12)) Explore P10384  Go to UniProtKB:  P10384

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	J [auth A], K [auth A], L [auth A]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
C8E	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth A], Q [auth A], R [auth A], T [auth A], U [auth A], W [auth A]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N
OLA	V [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
NI	N [auth A], O [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
NA	P [auth A], S [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OLA	PDBBind:  3PGU	Kd: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.180 
• R-Value Work: 0.168 
• R-Value Observed: 0.168 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.2	α = 90
b = 65.2	β = 90
c = 280.28	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Lepore, B.W., Indic, M., Pham, H., Hearn, E., Patel, D., van den Berg, B.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2015-01-07
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description