PDBsum entry: 1odv

Signalling

PDB id: 1odv

Contents

Protein chains

100 a.a. *

Ligands

HC4 ×2

Waters ×364

* Residue conservation analysis

PDB id:

1odv

Name:

Signalling

Title:

Photoactive yellow protein 1-25 deletion mutant

Structure:

Photoactive yellow protein. Chain: a, b. Fragment: residues 26-125. Synonym: pyp. Engineered: yes. Other_details: p-coumaric acid

Source:

Ectothiorhodospira halophila. Organism_taxid: 1053. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.14Å R-factor: 0.147 R-free: 0.177

Authors:

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

Key ref:

J.Vreede et al. (2003). PAS domains. Common structure and common flexibility. J Biol Chem, 278, 18434-18439. PubMed id: 12639952 DOI: 10.1074/jbc.M301701200

Date:

14-Mar-03 Release date: 18-Mar-03

Protein chains

P16113  (PYP_HALHA) -  Photoactive yellow protein

Seq: 125 a.a.

Struc: 100 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: signal transduction (4 terms)
• Biochemical function: signal transducer activity (2 terms)

DOI no: 10.1074/jbc.M301701200

J Biol Chem 278:18434-18439 (2003)

PubMed id: 12639952

PAS domains. Common structure and common flexibility.

J.Vreede, M.A.van der Horst, K.J.Hellingwerf, W.Crielaard, D.M.van Aalten.

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 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.

Selected figure(s)

Figure 2.
Fig. 2. Conformational changes. Positional shifts of equivalent C[ ]atoms after superposition of the two [25]PYP monomers in the asymmetric unit on wtPYP and on each other.

Figure 6.
Fig. 6. PYP conformational changes. Atomic positional shifts as described by the first three eigenvectors of [25]PYP are depicted as structures in Cartesian space. Two structures are depicted corresponding to 2 nm (colored) and +2 nm (transparent) along the eigenvectors. Relative degrees of positional shifts are indicated from blue (smallest fluctuations) to red (largest fluctuations). The transparent structures indicate the direction of the motion.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 18434-18439) copyright 2003.

Figures were selected by an automated process.