1ODV

Photoactive yellow protein 1-25 deletion mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pas Domains.Common Structure and Common Flexibility

Vreede, J.Van Der Horst, M.A.Hellingwerf, K.J.Crielaard, W.Van Aalten, D.M.F.

(2003) J.Biol.Chem. 278: 18434

  • DOI: 10.1074/jbc.M301701200

  • PubMed Abstract: 
  • PAS (PER-ARNT-SIM) domains are a family of sensor protein domains involved in signal transduction in a wide range of organisms. Recent structural studies have revealed that these domains contain a structurally conserved alpha/beta-fold, whereas almos ...

    PAS (PER-ARNT-SIM) domains are a family of sensor protein domains involved in signal transduction in a wide range of organisms. Recent structural studies have revealed that these domains contain a structurally conserved alpha/beta-fold, whereas almost no conservation is observed at the amino acid sequence level. The photoactive yellow protein, a bacterial light sensor, has been proposed as the PAS structural prototype yet contains an N-terminal helix-turn-helix motif not found in other PAS domains. Here we describe the atomic resolution structure of a photoactive yellow protein deletion mutant lacking this motif, revealing that the PAS domain is indeed able to fold independently and is not affected by the removal of these residues. Computer simulations of currently known PAS domain structures reveal that these domains are not only structurally conserved but are also similar in their conformational flexibilities. The observed motions point to a possible common mechanism for communicating ligand binding/activation to downstream transducer proteins.


    Organizational Affiliation

    Department of Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1018WV, Amsterdam, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOACTIVE YELLOW PROTEIN
A, B
100Halorhodospira halophilaGene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Go to UniProtKB:  P16113
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC4
Query on HC4

Download SDF File 
Download CCD File 
A, B
4'-HYDROXYCINNAMIC ACID
PARA-COUMARIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.177 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 82.566α = 90.00
b = 82.566β = 90.00
c = 63.453γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance