2Y5Y

Crystal structure of LacY in complex with an affinity inactivator

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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • DOI: 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 ...

    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.

    Related Citations: 
    • Probing the Mechanism of a Membrane Transport Protein with Affinity Inactivators.
      Guan, L., Sahin-Toth, M., Kalai, T., Hideg, K., Kaback, H.R.
      (2003) J Biol Chem 278: 10641
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LACTOSE PERMEASEA, B423Escherichia coli K-12Mutation(s): 9 
Gene Names: lacY, b0343, JW0334
Membrane Entity: Yes 
UniProt
Find proteins for P02920 (Escherichia coli (strain K12))
Explore P02920 
Go to UniProtKB:  P02920
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02920
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TGA
Query on TGA
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		2-sulfanylethyl beta-D-galactopyranoside
C8 H16 O6 S
HUYFGRHVKQZODJ-DWOUCZDBSA-N		 Ligand Interaction
BA
Query on BA
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N		 Ligand Interaction
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 = 102.56α = 90
b = 127.84β = 90
c = 189.87γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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