2CFQ | pdb_00002cfq

Sugar Free Lactose Permease at neutral pH

• PDB DOI: https://doi.org/10.2210/pdb2CFQ/pdb

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


• Deposited: 2006-02-22 Released: 2006-03-13 
• Deposition Author(s): Mirza, O., Guan, L., Verner, G., Iwata, S., Kaback, H.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.298 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.262 (Depositor), 0.264 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: experimental

Literature

Structural Evidence for Induced Fit and a Mechanism for Sugar/H(+) Symport in Lacy.

Mirza, O., Guan, L., Verner, G., Iwata, S., Kaback, H.R.

(2006) EMBO J 25: 2038

• PubMed: 16525509 
• DOI: https://doi.org/10.1038/sj.emboj.7601028
• Primary Citation Related Structures: 
  2CFP, 2CFQ


• PubMed Abstract: 
  

  Cation-coupled active transport is an essential cellular process found ubiquitously in all living organisms. Here, we present two novel ligand-free X-ray structures of the lactose permease (LacY) of Escherichia coli determined at acidic and neutral pH, and propose a model for the mechanism of coupling between lactose and H+ translocation. No sugar-binding site is observed in the absence of ligand, and deprotonation of the key residue Glu269 is associated with ligand binding. Thus, substrate induces formation of the sugar-binding site, as well as the initial step in H+ transduction.

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Organizational Affiliation: 
• Department of Biological Sciences, Membrane Protein Crystallography Group, Imperial College London, London, UK.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 47.49 kDa 
• Atom Count: 3,295 
• Modeled Residue Count: 417 
• Deposited Residue Count: 417 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LACTOSE PERMEASE	A	417	Escherichia coli	Mutation(s): 1  Membrane Entity: Yes
UniProt
Find proteins for P02920 (Escherichia coli (strain K12)) Explore P02920  Go to UniProtKB:  P02920

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.298 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.262 (Depositor), 0.264 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.47	α = 90
b = 122.47	β = 90
c = 187.78	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-13 
Deposition Author(s): Mirza, O., Guan, L., Verner, G., Iwata, S., Kaback, H.R.

Revision History  

• Version 1.0: 2006-03-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description