PDBsum entry 1t1c

Photoreceptor

PDB id: 1t1c

Contents

Protein chain

125 a.a. *

Ligands

HC4

* Residue conservation analysis

PDB id:

1t1c

Name:

Photoreceptor

Title:

Late intermediate il3 from time-resolved crystallography of the e46q mutant of pyp

Structure:

Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes. Mutation: yes

Source:

Halorhodospira halophila. Organism_taxid: 1053. Gene: pyp. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.60Å R-factor: 0.129 R-free: 0.139

Ensemble:

2 models

Authors:

S.Rajagopal,S.Anderson,V.Srajer,M.Schmidt,R.Pahl,K.Moffat

Key ref:

S.Rajagopal et al. (2005). A structural pathway for signaling in the E46Q mutant of photoactive yellow protein. Structure, 13, 55-63. PubMed id: 15642261 DOI: 10.1016/j.str.2004.10.016

Date:

15-Apr-04 Release date: 18-Jan-05

Protein chain

P16113  (PYP_HALHA) -  Photoactive yellow protein from Halorhodospira halophila

Seq: 125 a.a.

Struc: 125 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/j.str.2004.10.016

Structure 13:55-63 (2005)

PubMed id: 15642261

A structural pathway for signaling in the E46Q mutant of photoactive yellow protein.

S.Rajagopal, S.Anderson, V.Srajer, M.Schmidt, R.Pahl, K.Moffat.

ABSTRACT

In the bacterial photoreceptor photoactive yellow protein (PYP), absorption of blue light by its chromophore leads to a conformational change in the protein associated with differential signaling activity, as it executes a reversible photocycle. Time-resolved Laue crystallography allows structural snapshots (as short as 150 ps) of high crystallographic resolution (approximately 1.6 A) to be taken of a protein as it functions. Here, we analyze by singular value decomposition a comprehensive time-resolved crystallographic data set of the E46Q mutant of PYP throughout the photocycle spanning 10 ns-100 ms. We identify and refine the structures of five distinct intermediates and provide a plausible chemical kinetic mechanism for their inter conversion. A clear structural progression is visible in these intermediates, in which a signal generated at the chromophore propagates through a distinct structural pathway of conserved residues and results in structural changes near the N terminus, over 20 A distant from the chromophore.

Selected figure(s)

Figure 5.
Figure 5. The Chemical Kinetic Mechanism of E46Q PYP in the Crystal
(A) Chemical kinetic mechanism of E46Q PYP in the crystal, with rate coefficients (s -1) of 3.0 × 10^6 (IE1->IE2), 5.0 × 10^5 (IE2->IL1), 5.0 × 10^3 (IL1->IL2), 3.0 × 10^3 (IL1->G), 50 (IL2->IL3), and 0 (IL3->G).
(B) Predicted concentrations of IE1 (red), IE2 (magenta), IL1 (blue), IL2 (cyan), IL3 (dashed), and the ground state (black) with the mechanism in (A).
(C) Predicted concentration profiles for spectroscopic intermediates pR (IE1 and IE2) shown in red, pB (IL1 and IL2) shown in blue, and the ground state (IL3 and pG) shown in black with the mechanism in (A).

The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 55-63) copyright 2005.

Figure was selected by an automated process.