3GA5

X-ray structure of glucose/galactose receptor from Salmonella typhimurium in complex with (2R)-glyceryl-beta-D-galactopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray structure of glucose/galactose receptor from Salmonella typhimurium in complex with the physiological ligand, (2R)-glyceryl-beta-D-galactopyranoside

Sooriyaarachchi, S.Ubhayasekera, W.Boos, W.Mowbray, S.L.

(2009) Febs J. 276: 2116-2124

  • DOI: 10.1111/j.1742-4658.2009.06945.x

  • PubMed Abstract: 
  • Periplasmic binding proteins are abundant in bacteria by virtue of their essential roles as high-affinity receptors in ABC transport systems and chemotaxis. One of the best studied of these receptors is the so-called glucose/galactose-binding protein ...

    Periplasmic binding proteins are abundant in bacteria by virtue of their essential roles as high-affinity receptors in ABC transport systems and chemotaxis. One of the best studied of these receptors is the so-called glucose/galactose-binding protein. Here, we report the X-ray structure of the Salmonella typhimurium protein bound to the physiologically relevant ligand, (2R)-glyceryl-beta-D-galactopyranoside, solved by molecular replacement, and refined to 1.87 A resolution with R and R-free values of 17% and 22%. The structure identifies three amino acid residues that are diagnostic of (2R)-glyceryl-beta-D-galactopyranoside binding (Thr110, Asp154 and Gln261), as opposed to binding to the monosaccharides glucose and galactose. These three residues are conserved in essentially all available glucose/galactose-binding protein sequences, indicating that the binding of (2R)-glyceryl-beta-D-galactopyranoside is the rule rather than the exception for receptors of this type. The role of (2R)-glyceryl-beta-D-galactopyranoside in bacterial biology is discussed. Further, comparison of the available structures provides the most complete description of the conformational changes of glucose/galactose-binding protein to date. The structures follow a smooth and continuous path from the most closed structure [that bound to (2R)-glyceryl-beta-D-galactopyranoside] to the most open (an apo structure).


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-galactose-binding periplasmic protein
A, B
309Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: mglB
Find proteins for P23905 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P23905
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

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A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
RGG
Query on RGG

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A, B
(2R)-2,3-dihydroxypropyl beta-D-galactopyranoside
(2R)-glyceryl-beta-D-galactopyranoside
C9 H18 O8
NHJUPBDCSOGIKX-NTXXKDEISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RGGKd: 3200 nM BINDINGMOAD
RGGKd: 3200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.458α = 90.00
b = 109.275β = 90.00
c = 150.703γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance