1PST

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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

  • DOI: 10.1021/bi00181a020
  • Primary Citation of Related Structures:  
    1PSS, 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. 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) ...

    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 U S A 85: 7993
    • 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 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 U S A 85: 9012
    • 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 U S A 85: 8487
    • 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 U S A 84: 6438
    • 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 U S A 84: 6162
    • 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 U S A 84: 5730
    • 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 U S A 83: 8589

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERA [auth L]266Cereibacter sphaeroidesMutation(s): 0 
Gene Names: pufL
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERB [auth M]296Cereibacter sphaeroidesMutation(s): 0 
Gene Names: pufM
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERC [auth H]237Cereibacter sphaeroidesMutation(s): 0 
Gene Names: puhA
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

Download Ideal Coordinates CCD File 
D [auth L], E [auth L], I [auth M]BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
BPH (Subject of Investigation/LOI)
Query on BPH

Download Ideal Coordinates CCD File 
F [auth L], J [auth M], K [auth M]BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
U10 (Subject of Investigation/LOI)
Query on U10

Download Ideal Coordinates CCD File 
G [auth L], L [auth M]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
CRT (Subject of Investigation/LOI)
Query on CRT

Download Ideal Coordinates CCD File 
MSPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
H [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138α = 90
b = 77.5β = 90
c = 141.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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