2Y5Y

Crystal structure of LacY in complex with an affinity inactivator

• PDB DOI: https://doi.org/10.2210/pdb2Y5Y/pdb

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


• Deposited: 2011-01-19 Released: 2011-06-15 
• Deposition Author(s): Chaptal, V., Kwon, S., Sawaya, M.R., Guan, L., Kaback, H.R., Abramson, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free: 0.303 
• R-Value Work: 0.286 
• R-Value Observed: 0.287 

Starting Model: experimental

Literature

Crystal Structure of Lactose Permease in Complex with an Affinity Inactivator Yields Unique Insight Into Sugar Recognition.

Chaptal, V., Kwon, S., Sawaya, M.R., Guan, L., Kaback, H.R., Abramson, J.

(2011) Proc Natl Acad Sci U S A 108: 9361

• PubMed: 21593407 
• DOI: https://doi.org/10.1073/pnas.1105687108
• Primary Citation of Related Structures:  
  2Y5Y


• PubMed Abstract: 
  

  Lactose permease of Escherichia coli (LacY) with a single-Cys residue in place of A122 (helix IV) transports galactopyranosides and is specifically inactivated by methanethiosulfonyl-galactopyranosides (MTS-gal), which behave as unique suicide substrates. In order to study the mechanism of inactivation more precisely, we solved the structure of single-Cys122 LacY in complex with covalently bound MTS-gal. This structure exhibits an inward-facing conformation similar to that observed previously with a slight narrowing of the cytoplasmic cavity. MTS-gal is bound covalently, forming a disulfide bond with C122 and positioned between R144 and W151. E269, a residue essential for binding, coordinates the C-4 hydroxyl of the galactopyranoside moiety. The location of the sugar is in accord with many biochemical studies.

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Organizational Affiliation: 

Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 95.3 kDa 
• Atom Count: 6,209 
• Modelled Residue Count: 780 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LACTOSE PERMEASE	A, B	423	Escherichia coli K-12	Mutation(s): 9  Membrane Entity: Yes
UniProt
Find proteins for P02920 (Escherichia coli (strain K12)) Explore P02920  Go to UniProtKB:  P02920

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TGA	D [auth A], F [auth B]	2-sulfanylethyl beta-D-galactopyranoside C8 H16 O6 S HUYFGRHVKQZODJ-DWOUCZDBSA-N
BA	C [auth A], E [auth B]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free: 0.303 
• R-Value Work: 0.286 
• R-Value Observed: 0.287 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.56	α = 90
b = 127.84	β = 90
c = 189.87	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
Deposition Author(s): Chaptal, V., Kwon, S., Sawaya, M.R., Guan, L., Kaback, H.R., Abramson, J.

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-06-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2024-10-23
  Changes: Structure summary