1E6D

PHOTOSYNTHETIC REACTION CENTER MUTANT WITH TRP M115 REPLACED WITH PHE (CHAIN M, WM115F) PHE M197 REPLACED WITH ARG (CHAIN M, FM197R)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An Examination of How Structural Changes Can Affect the Rate of Electron Transfer in a Mutated Bacterial Photoreaction Centre

Ridge, J.P.Fyfe, P.K.Mcauley, K.E.Van Brederode, M.E.Robert, B.Van Grondelle, R.Isaacs, N.W.Cogdell, R.J.Jones, M.R.

(2000) Biochem J 351: 567

  • Primary Citation of Related Structures:  
    1E6D

  • PubMed Abstract: 
  • A series of reaction centres bearing mutations at the (Phe) M197 position were constructed in the photosynthetic bacterium Rhodobacter sphaeroides. This residue is adjacent to the pair of bacteriochlorophyll molecules (P(L) and P(M)) that is the primary donor of electrons (P) in photosynthetic light-energy transduction ...

    A series of reaction centres bearing mutations at the (Phe) M197 position were constructed in the photosynthetic bacterium Rhodobacter sphaeroides. This residue is adjacent to the pair of bacteriochlorophyll molecules (P(L) and P(M)) that is the primary donor of electrons (P) in photosynthetic light-energy transduction. All of the mutations affected the optical and electrochemical properties of the P bacteriochlorophylls. A mutant reaction centre with the change Phe M197 to Arg (FM197R) was crystallized, and a structural model constructed at 2.3 A (1 A=0.1 nm) resolution. The mutation resulted in a change in the structure of the protein at the interface region between the P bacteriochlorophylls and the monomeric bacteriochlorophyll that is the first electron acceptor (B(L)). The new Arg residue at the M197 position undergoes a significant reorientation, creating a cavity at the interface region between P and B(L). The acetyl carbonyl substituent group of the P(M) bacteriochlorophyll undergoes an out-of-plane rotation, which decreases the edge-to-edge distance between the macrocycles of P(M) and B(L). In addition, two new buried water molecules partially filled the cavity that is created by the reorientation of the Arg residue. These waters are in a suitable position to connect the macrocycles of P and B(L) via three hydrogen bonds. Transient absorption measurements show that, despite an inferred decrease in the driving force for primary electron transfer in the FM197R reaction centre, there is little effect on the overall rate of the primary reaction in the bulk of the reaction-centre population. Examination of the X-ray crystal structure reveals a number of small changes in the structure of the reaction centre in the interface region between the P and B(L) bacteriochlorophylls that could account for this faster-than-predicted rate of primary electron transfer.


    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
    • Structural Studies of Wild-Type and Mutant Reaction Centers from an Antenna-Deficient Strain of Rhodobacter Sphaeroides: Monitoring the Optical Properties of the Complex from Bacterial Cell to Crystal
      Mcauley, K.E., Fyfe, P.K., Ridge, J.P., Prince, S.M., Hunter, C.N., Isaacs, N.W., Cogdell, R.J., Jones, M.R.
      (1998) Biochemistry 37: 4740
    • Crystallographic Studies of Mutant Reaction Centers from Rhodobacter Sphaeroides
      Fyfe, P.K., Mcauley-Hecht, K.E., Ridge, J.P., Prince, S.M., Fritzsch, G., Isaacs, N.W., Cogdell, R.J., Jones, M.R.
      (1998) Photosynth Res 55: 133

    Organizational Affiliation

    Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2UH, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER H SUBUNITA [auth H]260Cereibacter sphaeroidesMutation(s): 0 
Gene Names: PUFQLMXpuhA
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER L SUBUNITB [auth L]281Cereibacter sphaeroidesMutation(s): 0 
Gene Names: PUFQLMXpufL
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y8
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTER M SUBUNITC [auth M]307Cereibacter sphaeroidesMutation(s): 2 
Gene Names: PUFQLMXpufM
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

Download Ideal Coordinates CCD File 
F [auth L],
G [auth L],
J [auth M],
K [auth M]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
BPH
Query on BPH

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

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I [auth L],
N [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
SPN
Query on SPN

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O [auth M]SPEROIDENONE
C41 H70 O2
GWQAMGYOEYXWJF-YCDPMLDASA-N
 Ligand Interaction
LDA
Query on LDA

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D [auth H],
E [auth H],
P [auth M],
Q [auth M],
R [auth M],
D [auth H],
E [auth H],
P [auth M],
Q [auth M],
R [auth M],
S [auth M],
T [auth M]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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U [auth M],
V [auth M]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.2α = 90
b = 141.2β = 90
c = 187.3γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-30
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance