2JJ0

PHOTOSYNTHETIC REACTION CENTER MUTANT WITH ALA M248 REPLACED WITH TRP (CHAIN M, AM248W)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Responses to Cavity-Creating Mutations in an Integral Membrane Protein.

Fyfe, P.K.Potter, J.A.Cheng, J.Williams, C.M.Watson, A.J.Jones, M.R.

(2007) Biochemistry 46: 10461

  • DOI: 10.1021/bi701085w
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • X-ray crystallography has been used to investigate the extent of structural changes in mutants of the purple bacterial reaction center that assemble without a particular ubiquinone or bacteriopheophytin cofactor. In the case of the bacteriopheophytin ...

    X-ray crystallography has been used to investigate the extent of structural changes in mutants of the purple bacterial reaction center that assemble without a particular ubiquinone or bacteriopheophytin cofactor. In the case of the bacteriopheophytin-exclusion mutant, in which Ala M149 was replaced by Trp (AM149W), the quality of protein crystals was improved over that seen in previous work by minimizing illumination, time, and temperature during the purification protocol and carrying out crystal growth at 4 degrees C after overnight incubation at 18 degrees C. The X-ray crystal structure of the AM149W mutant, determined to a resolution of 2.2 A, showed very little change in protein structure despite the absence of the bacteriopheophytin cofactor. Changes in the electron density map in the region of the cofactor binding site could be accounted for by changes in the conformation of the phytol side chains of adjacent cofactors and the presence of a buried water molecule. Residues lining the vacated binding pocket did not show any significant changes in conformation or increases in disorder as assessed through crystallographic atomic displacement parameters (B-factors). The X-ray crystal structure of a reaction center lacking the primary acceptor ubiquinone through mutation of Ala M248 to Trp (AM248W) was also determined, to a resolution of 2.8 A. Again, despite the absence of an internal cofactor only very minor changes in protein structure were observed. This is in contrast to a previous report on a reaction center lacking this ubiquinone through mutation of Ala M260 to Trp (AM260W) where more extensive changes in structure were apparent. All three mutant reaction centers showed a decrease in thermal stability when housed in the native membrane, but this decrease was smaller for the AM260W mutant than the AM248W complex, possibly due to beneficial effects of the observed changes in protein structure. The lack of major changes in protein structure despite the absence of large internal cofactors is discussed in terms of protein rigidity, the protective influence of the adaptable membrane environment, and the role of small molecules and ions as packing material in the internal cavities created by this type of mutation.


    Related Citations: 
    • On the Role of Basic Residues in Adapting the Purple Bacterial Reaction Centre-Lh1 Photosystem for Growth at Elevated Temperature
      Watson, A.J., Hughes, A.V., Fyfe, P.K., Wakeham, M.C., Holden-Dye, K., Heathcote, P., Jones, M.R.
      (2005) Photosynth Res 86: 81
    • Structural Details of an Interaction between Cardiolipin and an Integral Membrane Protein.
      Mcauley, K.E., Fyfe, P.K., Ridge, J.P., Isaacs, N.W., Cogdell, R.J., Jones, M.R.
      (1999) Proc Natl Acad Sci U S A 96: 14706
    • Ubiquinone Binding, Ubiquinone Exclusion, and Detailed Cofactor Conformation in a Mutant Bacterial Reaction Center.
      Mcauley, K.E., Fyfe, P.K., Ridge, J.P., Cogdell, R.J., Isaacs, N.W., Jones, M.R.
      (2000) Biochemistry 39: 15032

    Organizational Affiliation

    Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN H CHAIN
H
260RHODOBACTER SPHAEROIDESMutation(s): 0 
Gene Names: puhA
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y7

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN L CHAIN
L
281RHODOBACTER SPHAEROIDESMutation(s): 0 
Gene Names: pufL
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y8

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN M CHAIN
M
308RHODOBACTER SPHAEROIDESMutation(s): 1 
Gene Names: pufM
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y9
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download CCD File 
M
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
BCL
Query on BCL

Download CCD File 
L, M
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
BPH
Query on BPH

Download CCD File 
L, M
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
U10
Query on U10

Download CCD File 
L
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
SPN
Query on SPN

Download CCD File 
M
SPEROIDENONE
C41 H70 O2
GWQAMGYOEYXWJF-YCDPMLDASA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
M
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
M
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.81α = 90
b = 139.81β = 90
c = 185.153γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance