2WX5

Hexa-coordination of a bacteriochlorophyll cofactor in the Rhodobacter sphaeroides reaction centre


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Spectroscopic Consequences of Hexa-Coordination of a Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre

Frolov, D.Marsh, M.Crouch, L.I.Fyfe, P.K.Robert, B.van Grondelle, R.Hadfield, A.T.Jones, M.R.

(2010) Biochemistry 49: 1882

  • DOI: 10.1021/bi901922t
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structural and functional consequences of changing the coordination state of one of the bacteriochlorophyll (BChl) cofactors in the purple bacterial reaction center have been explored. A combination of steady state spectroscopy and X-ray crystall ...

    The structural and functional consequences of changing the coordination state of one of the bacteriochlorophyll (BChl) cofactors in the purple bacterial reaction center have been explored. A combination of steady state spectroscopy and X-ray crystallography was used to demonstrate that mutagenesis of residue 181 of the L-polypeptide from Phe to Arg (FL181R) causes the BChl at the accessory (B(B)) position on the so-called inactive cofactor branch to become hexacoordinated, with no significant changes to the structure of the surrounding protein. This change was accompanied by the appearance of a distinctive absorbance band at 631 nm in the room-temperature absorbance spectrum. The ligand donor was not the Arg side chain but rather an intervening water molecule, and contrary to expectations, the Mg of B(B) did not adopt a more in-plane geometry in response to hexacoordination. The mutation caused a disturbance to the detailed conformation of the BChl macrocycle that manifested in a number of subtle changes to the resonance Raman spectrum. Hexacoordination of B(B) produced a small increase in the lifetime of the excited electronic state of the primary donor bacteriochlorophylls (P*), indicating some disturbance to light-driven energy and/or electron transfer events on the time scale of a few picoseconds after light excitation. The B(B) bacteriochlorophyll returned to a pentacoordinated state in a double mutant where the FL181R mutation was combined with removal of the native axial ligand through mutation of His M182 to Leu. Experimental evidence of hexacoordinated bacteriochlorophylls in the literature on antenna proteins is considered, and possible reasons why hexacoordinated bacteriochlorophylls and chlorophylls appear to be avoided in photosynthetic proteins are discussed.


    Organizational Affiliation

    Department of Physics and Astronomy, Free University of Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTER PROTEIN H CHAINH260Rhodobacter sphaeroidesMutation(s): 0 
Find proteins for Q3J170 (Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
Explore Q3J170 
Go to UniProtKB:  Q3J170
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTRE PROTEIN L CHAINL281Rhodobacter sphaeroidesMutation(s): 1 
Find proteins for Q3J1A5 (Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
Explore Q3J1A5 
Go to UniProtKB:  Q3J1A5
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
REACTION CENTRE PROTEIN M CHAINM307Rhodobacter sphaeroidesMutation(s): 0 
Find proteins for Q3J1A6 (Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
Explore Q3J1A6 
Go to UniProtKB:  Q3J1A6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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

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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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M
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
SPN
Query on SPN

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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
HTO
Query on HTO

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L, M
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
GOL
Query on GOL

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L
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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M
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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H, M
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.18α = 90
b = 140.18β = 90
c = 185.401γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references, Version format compliance
  • Version 1.2: 2017-12-13
    Changes: Database references, Structure summary