2BOZ

Photosynthetic Reaction Center Mutant With Gly M203 Replaced With Leu


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Strong Effects of an Individual Water Molecule on the Rate of Light-Driven Charge Separation in the Rhodobacter Sphaeroides Reaction Center.

Potter, J.A.Fyfe, P.K.Frolov, D.Wakeham, M.C.Van Grondelle, R.Robert, B.Jones, M.R.

(2005) J Biol Chem 280: 27155

  • DOI: 10.1074/jbc.M501961200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The role of a water molecule (water A) located between the primary electron donor (P) and first electron acceptor bacteriochlorophyll (B(A)) in the purple bacterial reaction center was investigated by mutation of glycine M203 to leucine (GM203L). The ...

    The role of a water molecule (water A) located between the primary electron donor (P) and first electron acceptor bacteriochlorophyll (B(A)) in the purple bacterial reaction center was investigated by mutation of glycine M203 to leucine (GM203L). The x-ray crystal structure of the GM203L reaction center shows that the new leucine residue packs in such a way that water A is sterically excluded from the complex, but the structure of the protein-cofactor system around the mutation site is largely undisturbed. The results of absorbance and resonance Raman spectroscopy were consistent with either the removal of a hydrogen bond interaction between water A and the keto carbonyl group of B(A) or a change in the local electrostatic environment of this carbonyl group. Similarities in the spectroscopic properties and x-ray crystal structures of reaction centers with leucine and aspartic acid mutations at the M203 position suggested that the effects of a glycine to aspartic acid substitution at the M203 position can also be explained by steric exclusion of water A. In the GM203L mutant, loss of water A was accompanied by an approximately 8-fold slowing of the rate of decay of the primary donor excited state, indicating that the presence of water A is important for optimization of the rate of primary electron transfer. Possible functions of this water molecule are discussed, including a switching role in which the redox potential of the B(A) acceptor is rapidly modulated in response to oxidation of the primary electron donor.


    Related Citations: 
    • Structural Consequences of the Replacement of Glycine M203 with Aspartic Acid in the Reaction Center from Rhodobacter Sphaeroides
      Fyfe, P.K., Ridge, J.P., Mcauley, K.E., Cogdell, R.J., Isaacs, N.W., Jones, M.R.
      (2000) Biochemistry 39: 5953

    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: 3
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN M CHAINM307Rhodobacter sphaeroidesMutation(s): 1 
Gene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN H CHAINH260Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN L CHAINL281Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

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

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

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L, M
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
LDA
Query on LDA

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H, M
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

Download CCD File 
H
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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M
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FE
Query on FE

Download CCD File 
M
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.613α = 90
b = 138.613β = 90
c = 185.274γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-03-20
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary