PDBsum entry: 1otb

Signaling protein

PDB id: 1otb

Contents

Protein chain

125 a.a. *

Ligands

HC4

Waters ×113

* Residue conservation analysis

PDB id:

1otb

Name:

Signaling protein

Title:

Wild type photoactive yellow protein, p63 at 295k

Structure:

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

Source:

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

Resolution:

1.10Å R-factor: 0.133 R-free: 0.161

Authors:

S.Anderson,S.Crosson,K.Moffat

Key ref:

S.Anderson et al. (2004). Short hydrogen bonds in photoactive yellow protein. Acta Crystallogr D Biol Crystallogr, 60, 1008-1016. PubMed id: 15159559 DOI: 10.1107/S090744490400616X

Date:

21-Mar-03 Release date: 11-May-04

Protein chain

P16113  (PYP_HALHA) -  Photoactive yellow protein

Seq: 125 a.a.

Struc: 125 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: response to stimulus (5 terms)
• Biochemical function: signal transducer activity (3 terms)

DOI no: 10.1107/S090744490400616X

Acta Crystallogr D Biol Crystallogr 60:1008-1016 (2004)

PubMed id: 15159559

Short hydrogen bonds in photoactive yellow protein.

S.Anderson, S.Crosson, K.Moffat.

ABSTRACT

Eight high-resolution crystal structures of the ground state of photoactive yellow protein (PYP) solved under a variety of conditions reveal that its chromophore is stabilized by two unusually short hydrogen bonds. Both Tyr42 Oeta and Glu46 Oepsilon are separated from the chromophore phenolate oxygen by less than the sum of their atomic van der Waals radii, 2.6 angstroms. This is characteristic of strong hydrogen bonding, in which hydrogen bonds acquire significant covalent character. The hydrogen bond from the protonated Glu46 to the negatively charged phenolate oxygen is 2.58 +/- 0.01 angstroms in length, while that from Tyr42 is considerably shorter, 2.49 +/- 0.01 angstroms. The E46Q mutant was solved to 0.95 angstroms resolution; the isosteric mutation increased the length of the hydrogen bond from Glx46 to the chromophore by 0.29 +/- 0.01 angstroms to that of an average hydrogen bond, 2.88 +/- 0.01 angstroms. The very short hydrogen bond from Tyr42 explains why mutating this residue has such a severe effect on the ground-state structure and PYP photocycle. The effect of isosteric mutations on the photocycle can be largely explained by the alterations to the length and strength of these hydrogen bonds.

Selected figure(s)

Figure 1.
Figure 1 The ground-state coumaric acid chromophore (pCA) and its binding pocket in wild-type PYP. Hydrogen bonds are shown as dashed lines.

Figure 5.
Figure 5 Difference electron-density maps between wild type and E46Q mutant in space group P6[3] superimposed on the wild-type structure. Red contours denote negative difference electron density and blue denote positive. The entire molecule contoured at ±5 is shown at (a) 110 K and (b) at 295 K. The chromophore-binding pocket contoured at ±4 and ±8 is shown at (c) 110 K and (d) at 295 K.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 1008-1016) copyright 2004.

Figures were selected by an automated process.