1PSS

CRYSTALLOGRAPHIC ANALYSES OF SITE-DIRECTED MUTANTS OF THE PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic analyses of site-directed mutants of the photosynthetic reaction center from Rhodobacter sphaeroides.

Chirino, A.J.Lous, E.J.Huber, M.Allen, J.P.Schenck, C.C.Paddock, M.L.Feher, G.Rees, D.C.

(1994) Biochemistry 33: 4584-4593

  • Primary Citation of Related Structures:  1PST

  • PubMed Abstract: 
  • Seven site-directed mutants of the bacterial photosynthetic reaction center (RC) from the 2.4.1 and WS 231 wild-type strains of Rhodobacter sphaeroides have been crystallized and their X-ray diffraction analyzed to resolutions between 3.0 and 4.0 A. ...

    Seven site-directed mutants of the bacterial photosynthetic reaction center (RC) from the 2.4.1 and WS 231 wild-type strains of Rhodobacter sphaeroides have been crystallized and their X-ray diffraction analyzed to resolutions between 3.0 and 4.0 A. The mutations can be divided into four distinct categories: (1) mutations altering cofactor composition that affect electron transfer and quantum yield, His M202-->Leu (M202HL), His L173-->Leu (L173HL), and Leu M214-->His (M214LH); (2) a mutation in the proposed pathway of electron transfer altering electron-transfer kinetics, Tyr M210-->Phe (M210YF); (3) a mutation around the non-heme iron resulting in an iron-less reaction center, His M219-->Cys (M219HC); and (4) mutations around the secondary electron acceptor, a ubiquinone, affecting proton transfer and quinone turnover, Glu L212-->Gln (L212EQ) and Asp L213-->Asn (L213DN). Residues L173 and M202 are within bonding distance of the respective magnesiums of the two bacteriochlorophylls of the BChl special pair, while M214 is close to the bacteriopheophytin on the active A branch of the RC. The L173HL and M202HL crystal structures show that the respective bacteriochlorophylls are replaced with bacteriopheophytins (i.e., loss of magnesium) without significant structural perturbations to the surrounding main-chain or side-chain atoms. In the M214LH mutant, the bacteriopheophytin has been replaced by a bacteriochlorophyll, and the side chain of His M214 is within ligand distance of the magnesium. The M210YF, L212EQ, and L213DN mutants show no significant tertiary structure changes near the mutation sites. The M219HC diffraction data indicate that the overall tertiary structure of the reaction center is maintained in the absence of the non-heme iron.


    Related Citations: 
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26 and 2.4.1:Protein-Cofactor (Bacteriochlorophyll,Bacteriopheophytin, and Carotenoid) Interactions
      Yeates, T.O.,Komiya, H.,Chirino, A.,Rees, D.C.,Allen, J.P.,Feher, G.
      (1988) Proc.Natl.Acad.Sci.USA 85: 7993
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: The Protein Subunits
      Allen, J.P.,Feher, G.,Yeates, T.O.,Komiya, H.,Rees, D.C.
      (1987) Proc.Natl.Acad.Sci.USA 84: 6162
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: Membrane-Protein Interactions
      Yeates, T.O.,Komiya, H.,Rees, D.C.,Allen, J.P.,Feher, G.
      (1987) Proc.Natl.Acad.Sci.USA 84: 6438
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: The Cofactors
      Allen, J.P.,Feher, G.,Yeates, T.O.,Komiya, H.,Rees, D.C.
      (1987) Proc.Natl.Acad.Sci.USA 84: 5730
    • Structure and Function of Bacterial Photosynthetic Reaction Centers
      Feher, G.,Allen, J.P.,Okamura, M.Y.,Rees, D.C.
      (1989) Nature 339: 111
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26 and 2.4.1: Symmetry Relations and Sequence Comparisons between Different Species
      Komiya, H.,Yeates, T.O.,Rees, D.C.,Allen, J.P.,Feher, G.
      (1988) Proc.Natl.Acad.Sci.USA 85: 9012
    • The Bacterial Photosynthetic Reaction Center as a Model for Membrane Proteins
      Rees, D.C.,Komiya, H.,Yeates, T.O.,Allen, J.P.,Feher, G.
      (1989) Annu.Rev.Biochem. 58: 607
    • Structure Homology of the Reaction Center from Rhodopseudomonas Sphaeroides and Rhodopseudomonas Viridis as Determined by X-Ray Diffraction
      Allen, J.P.,Feher, G.,Yeates, T.O.,Rees, D.C.,Desenhofer, J.,Michel, H.,Huber, R.
      (1986) Proc.Natl.Acad.Sci.USA 83: 8589
    • Structure of the Reaction Center from Rhodobacter Sphaeroides R-26: Protein-Cofactor (Quinones and Fe2+) Interactions
      Allen, J.P.,Feher, G.,Yeates, T.O.,Komiya, H.,Rees, D.C.
      (1988) Proc.Natl.Acad.Sci.USA 85: 8487


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
L
266Rhodobacter sphaeroidesGene Names: pufL
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
M
296Rhodobacter sphaeroidesGene Names: pufM
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
H
237Rhodobacter sphaeroidesGene Names: puhA
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U10
Query on U10

Download SDF File 
Download CCD File 
L, M
UBIQUINONE-10
Coenzyme Q10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
BCL
Query on BCL

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

Download SDF File 
Download CCD File 
M
SPIRILLOXANTHIN
RHODOVIOLASCIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
 Ligand Interaction
FE
Query on FE

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

Download SDF File 
Download CCD File 
L, M
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 138.000α = 90.00
b = 77.500β = 90.00
c = 141.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance