1RZH

PHOTOSYNTHETIC REACTION CENTER DOUBLE MUTANT FROM RHODOBACTER SPHAEROIDES WITH ASP L213 REPLACED WITH ASN AND ARG M233 REPLACED WITH CYS IN THE CHARGE-NEUTRAL DQAQB STATE (TRIGONAL FORM)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

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This is version 1.4 of the entry. See complete history. 


Literature

X-Ray Structure Determination of Three Mutants of the Bacterial Photosynthetic Reaction Centers from Rb. sphaeroides; Altered Proton Transfer Pathways.

Xu, Q., Axelrod, H.L., Abresch, E.C., Paddock, M.L., Okamura, M.Y., Feher, G.

(2004) Structure 12: 703-715

  • DOI: 10.1016/j.str.2004.03.001
  • Primary Citation of Related Structures:  
    1RVJ, 1RY5, 1RZH, 1RZZ, 1S00

  • PubMed Abstract: 

    • In the photosynthetic reaction center (RC) from Rhodobacter sphaeroides, the reduction of a bound quinone molecule Q(B) is coupled with proton uptake. When Asp-L213 is replaced by Asn, proton transfer is inhibited. Proton transfer was restored by two second-site revertant mutations, Arg-M233-->Cys and Arg-H177-->His ...

    In the photosynthetic reaction center (RC) from Rhodobacter sphaeroides, the reduction of a bound quinone molecule Q(B) is coupled with proton uptake. When Asp-L213 is replaced by Asn, proton transfer is inhibited. Proton transfer was restored by two second-site revertant mutations, Arg-M233-->Cys and Arg-H177-->His. Kinetic effects of Cd(2+) on proton transfer showed that the entry point in revertant RCs to be the same as in the native RC. The structures of the parental and two revertant RCs were determined at resolutions of 2.10, 1.80, and 2.75 A. From the structures, we were able to delineate alternate proton transfer pathways in the revertants. The main changes occur near Glu-H173, which allow it to substitute for the missing Asp-L213. The electrostatic changes near Glu-H173 cause it to be a good proton donor and acceptor, and the structural changes create a cavity which accommodates water molecules that connect Glu-H173 to other proton transfer components.

    Related Citations: 
    • Characterization of Second Site Mutations Show that Fast Proton Transfer to Qb- is Restored in Bacterial Reaction Centers of Rhodobacter Sphaeroides Containing the Asp-L213->Asn Lesion
      Paddock, M.L., Senft, M.E., Graige, M.S., Rongey, S.H., Turanchik, T., Feher, G., Okamura, M.Y.
      (1998) Photosynth Res 55: 281
    • Determination of the Binding Sites of the Proton Transfer Inhibitors Cd2+ and Zn2+ in Bacterial Reaction Centers
      Axelrod, H.L., Abresch, E.C., Paddock, M.L., Okamura, M.Y., Feher, G.
      (2000) Proc Natl Acad Sci U S A 97: 1542
    • Identification of Proton Transfer Pathways in the X-Ray Crystal Structure of the Bacterial Reaction Center from Rhodobacter Sphaeroides
      Abresch, E.C., Paddock, M.L., Stowell, M.H.B., McPhillips, T.M., Axelrod, H.L., Soltis, S.M., Rees, D.C., Okamura, M.Y., Feher, G.
      (1998) Photosynth Res 55: 119
    Organizational Affiliation: 

    Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein L chainA [auth L]281Cereibacter sphaeroidesMutation(s): 1 
Gene Names: pufL
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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein M chainB [auth M]307Cereibacter sphaeroidesMutation(s): 1 
Gene Names: pufM
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
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Reaction center protein H chainC [auth H]260Cereibacter sphaeroidesMutation(s): 0 
Gene Names: puhA
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
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL
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S [auth M]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L		 Ligand Interaction
BCL
Query on BCL
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D [auth L],
E [auth L],
L [auth M],
M		BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ		 Ligand Interaction
BPH
Query on BPH
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F [auth L],
N [auth M]		BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N		 Ligand Interaction
U10
Query on U10
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G [auth L],
O [auth M]		UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N		 Ligand Interaction
SPO
Query on SPO
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P [auth M]SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N		 Ligand Interaction
LDA
Query on LDA
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Q [auth M],
R [auth M],
U [auth H]		LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N		 Ligand Interaction
HTO
Query on HTO
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H [auth L],
I [auth L]		HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N		 Ligand Interaction
PO4
Query on PO4
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K [auth M]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
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T [auth M]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
FE2
Query on FE2
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J [auth M]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.353α = 90
b = 139.353β = 90
c = 184.962γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2012-04-25
    Changes: Non-polymer description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations