3V3Y

Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The site-directed mutation I(L177)H in Rhodobacter sphaeroides reaction center affects coordination of P(A) and B(B) bacteriochlorophylls.

Vasilieva, L.G.Fufina, T.Y.Gabdulkhakov, A.G.Leonova, M.M.Khatypov, R.A.Shuvalov, V.A.

(2012) Biochim Biophys Acta 1817: 1407-1417

  • DOI: 10.1016/j.bbabio.2012.02.008
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • To explore the influence of the I(L177)H single mutation on the properties of the nearest bacteriochlorophylls (BChls), three reaction centers (RCs) bearing double mutations were constructed in the photosynthetic purple bacterium Rhodobacter sphaeroi ...

    To explore the influence of the I(L177)H single mutation on the properties of the nearest bacteriochlorophylls (BChls), three reaction centers (RCs) bearing double mutations were constructed in the photosynthetic purple bacterium Rhodobacter sphaeroides, and their properties and pigment content were compared with those of the correspondent single mutant RCs. Each pair of the mutations comprised the amino acid substitution I(L177)H and another mutation altering histidine ligand of BChl P(A) or BChl B(B). Contrary to expectations, the double mutation I(L177)H+H(L173)L does not bring about a heterodimer RC but causes a 46nm blue shift of the long-wavelength P absorbance band. The histidine L177 or a water molecule were suggested as putative ligands for P(A) in the RC I(L177)H+H(L173)L although this would imply a reorientation of the His backbone and additional rearrangements in the primary donor environment or even a repositioning of the BChl dimer. The crystal structure of the mutant I(L177)H reaction center determined to a resolution of 2.9Å shows changes at the interface region between the BChl P(A) and the monomeric BChl B(B). Spectral and pigment analysis provided evidence for β-coordination of the BChl B(B) in the double mutant RC I(L177)H+H(M182)L and for its hexacoordination in the mutant reaction center I(L177)H. Computer modeling suggests involvement of two water molecules in the β-coordination of the BChl B(B). Possible structural consequences of the L177 mutation affecting the coordination of the two BChls P(A) and B(B) are discussed. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.


    Organizational Affiliation

    Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow, Russia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein H chain
H
241Rhodobacter 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
302Rhodobacter sphaeroidesMutation(s): 0 
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 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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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L, 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
PO4
Query on PO4

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

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L, M
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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

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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: 0.284 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.75α = 90
b = 139.75β = 90
c = 185.604γ = 120
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-06-27
    Changes: Database references