1OTD

STRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN AND THEIR ROLE IN ITS PHOTOCYCLE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Short hydrogen bonds in photoactive yellow protein.

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

(2004) Acta Crystallogr.,Sect.D 60: 1008-1016

  • DOI: 10.1107/S090744490400616X
  • Primary Citation of Related Structures:  1OT9, 1OTA, 1OTB, 1OTI, 1OT6, 1OTE

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Consortium for Advanced Radiation Sources, University of Chicago, USA. smander@midway.uchicago.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photoactive yellow protein
A, B
125Halorhodospira 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: 1.25 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 33.983α = 90.00
b = 91.102β = 92.67
c = 36.756γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXL-97refinement
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation