1SW1

Crystal structure of ProX from Archeoglobus fulgidus in complex with proline betaine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for the binding of compatible solutes by ProX from the hyperthermophilic archaeon Archaeoglobus fulgidus.

Schiefner, A.Holtmann, G.Diederichs, K.Welte, W.Bremer, E.

(2004) J.Biol.Chem. 279: 48270-48281

  • DOI: 10.1074/jbc.M403540200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Compatible solutes such as glycine betaine and proline betaine serve as protein stabilizers because of their preferential exclusion from protein surfaces. To use extracellular sources of this class of compounds as osmo-, cryo-, or thermoprotectants, ...

    Compatible solutes such as glycine betaine and proline betaine serve as protein stabilizers because of their preferential exclusion from protein surfaces. To use extracellular sources of this class of compounds as osmo-, cryo-, or thermoprotectants, Bacteria and Archaea have developed high affinity uptake systems of the ATP-binding cassette type. These transport systems require periplasmic- or extracellular-binding proteins that are able to bind the transported substance with high affinity. Therefore, binding proteins that bind compatible solutes have to avoid the exclusion of their ligands within the binding pocket. In the present study we addressed the question to how compatible solutes can be effectively bound by a protein at temperatures around 83 degrees C as this is done by the ligand-binding protein ProX from the hyperthermophilic archaeon Archaeoglobus fulgidus. We solved the structures of ProX without ligand and in complex with both of its natural ligands glycine betaine and proline betaine, as well as in complex with the artificial ligand trimethylammonium. Cation-pi interactions and non-classical hydrogen bonds between four tyrosine residues, a main chain carbonyl oxygen, and the ligand have been identified to be the key determinants in binding the quaternary amines of the three investigated ligands. The comparison of the ligand binding sites of ProX from A. fulgidus and the recently solved structure of ProX from Escherichia coli revealed a very similar solution for the problem of compatible solute binding, although both proteins share only a low degree of sequence identity. The residues involved in ligand binding are functionally equivalent but not conserved in the primary sequence.


    Organizational Affiliation

    Fachbereich Biologie, Universität Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany. andre.schiefner@uni-konstanz.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
osmoprotection protein (proX)
A, B
275Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 1 
Find proteins for O29280 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O29280
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PBE
Query on PBE

Download SDF File 
Download CCD File 
A, B
1,1-DIMETHYL-PROLINIUM
PROLINE BETAINE
C7 H14 N O2
CMUNUTVVOOHQPW-LURJTMIESA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PBEKd: 50 nM BINDINGMOAD
PBEKd: 50 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.400α = 90.00
b = 78.400β = 91.70
c = 67.800γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
MAR345data collection
XDSdata scaling
SHELXDphasing
SHARPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description