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PDBsum entry 1fnp

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protein ligands metals Protein-protein interface(s) links
Photosynthesis PDB id
1fnp
Jmol
Contents
Protein chains
281 a.a. *
301 a.a. *
240 a.a. *
Ligands
BCL ×4
BPH ×2
U10 ×2
LDA ×7
PO4
SPO
Metals
_FE
Waters ×142
* Residue conservation analysis
PDB id:
1fnp
Name: Photosynthesis
Title: Crystal structure analysis of the mutant reaction center pro phe from the photosynthetic purple bacterium rhodobacter sp
Structure: Reaction center protein l chain. Chain: l. Engineered: yes. Mutation: yes. Reaction center protein m chain. Chain: m. Engineered: yes. Reaction center protein h chain. Chain: h.
Source: Rhodobacter sphaeroides. Organism_taxid: 1063. Expressed in: rhodobacter sphaeroides. Expression_system_taxid: 1063.
Biol. unit: Trimer (from PQS)
Resolution:
2.60Å     R-factor:   0.216     R-free:   0.248
Authors: A.Kuglstatter,U.Ermler,H.Michel,L.Baciou,G.Fritzsch
Key ref:
A.Kuglstatter et al. (2001). X-ray structure analyses of photosynthetic reaction center variants from Rhodobacter sphaeroides: structural changes induced by point mutations at position L209 modulate electron and proton transfer. Biochemistry, 40, 4253-4260. PubMed id: 11284681 DOI: 10.1021/bi001589h
Date:
23-Aug-00     Release date:   18-Apr-01    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0C0Y8  (RCEL_RHOSH) -  Reaction center protein L chain
Seq:
Struc:
282 a.a.
281 a.a.*
Protein chain
Pfam   ArchSchema ?
P0C0Y9  (RCEM_RHOSH) -  Reaction center protein M chain
Seq:
Struc:
308 a.a.
301 a.a.
Protein chain
Pfam   ArchSchema ?
P0C0Y7  (RCEH_RHOSH) -  Reaction center protein H chain
Seq:
Struc:
260 a.a.
240 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity     4 terms  

 

 
DOI no: 10.1021/bi001589h Biochemistry 40:4253-4260 (2001)
PubMed id: 11284681  
 
 
X-ray structure analyses of photosynthetic reaction center variants from Rhodobacter sphaeroides: structural changes induced by point mutations at position L209 modulate electron and proton transfer.
A.Kuglstatter, U.Ermler, H.Michel, L.Baciou, G.Fritzsch.
 
  ABSTRACT  
 
The structures of the reaction center variants Pro L209 --> Tyr, Pro L209 --> Phe, and Pro L209 --> Glu from the photosynthetic purple bacterium Rhodobacter sphaeroides have been determined by X-ray crystallography to 2.6-2.8 A resolution. These variants were constructed to interrupt a chain of tightly bound water molecules that was assumed to facilitate proton transfer from the cytoplasm to the secondary quinone Q(B) [Baciou, L., and Michel, H. (1995) Biochemistry 34, 7967-7972]. However, the amino acid exchanges Pro L209 --> Tyr and Pro L209 --> Phe do not interrupt the water chain. Both aromatic side chains are oriented away from this water chain and interact with three surrounding polar side chains (Asp L213, Thr L226, and Glu H173) which are displaced by up to 2.6 A. The conformational changes induced by the bulky aromatic rings of Tyr L209 and Phe L209 lead to unexpected displacements of Q(B) compared to the wild-type protein. In the structure of the Pro L209 --> Tyr variant, Q(B) is shifted by approximately 4 A and is now located at a position similar to that reported for the wild-type reaction center after illumination [Stowell, M. H. B., et al. (1997) Science 276, 812-816]. In the Pro L209 --> Phe variant, the electron density map reveals an intermediate Q(B) position between the binding sites of the wild-type protein in the dark and the Pro L209 --> Tyr protein. In the Pro L209 --> Glu reaction center, the carboxylic side chain of Glu L209 is located within the water chain, and the binding site of Q(B) remains unchanged compared to the wild-type structure.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17590017 M.L.Paddock, M.Flores, R.Isaacson, C.Chang, E.C.Abresch, and M.Y.Okamura (2007).
ENDOR spectroscopy reveals light induced movement of the H-bond from Ser-L223 upon forming the semiquinone (Q(B)(-)(*)) in reaction centers from Rhodobacter sphaeroides.
  Biochemistry, 46, 8234-8243.  
17115698 M.L.Paddock, M.Flores, R.Isaacson, C.Chang, E.C.Abresch, P.Selvaduray, and M.Y.Okamura (2006).
Trapped conformational states of semiquinone (D+*QB-*) formed by B-branch electron transfer at low temperature in Rhodobacter sphaeroides reaction centers.
  Biochemistry, 45, 14032-14042.  
16211505 P.D.Laible, A.N.Hata, A.E.Crawford, and D.K.Hanson (2005).
Incorporation of selenomethionine into induced intracytoplasmic membrane proteins of Rhodobacter species.
  J Struct Funct Genomics, 6, 95.  
15858271 R.H.Baxter, B.L.Seagle, N.Ponomarenko, and J.R.Norris (2005).
Cryogenic structure of the photosynthetic reaction center of Blastochloris viridis in the light and dark.
  Acta Crystallogr D Biol Crystallogr, 61, 605-612.
PDB code: 1vrn
15368575 N.D'Amelio, E.Gaggelli, P.Mlynarz, E.Molteni, G.Valensin, and W.Lubitz (2004).
NMR structural model of the interaction of herbicides with the photosynthetic reaction center from Rhodobacter sphaeroides.
  Chembiochem, 5, 1237-1244.  
12872158 A.Remy, and K.Gerwert (2003).
Coupling of light-induced electron transfer to proton uptake in photosynthesis.
  Nat Struct Biol, 10, 637-644.  
12919324 A.Remy, R.B.Boers, T.Egorova-Zachernyuk, P.Gast, J.Lugtenburg, and K.Gerwert (2003).
Does different orientation of the methoxy groups of ubiquinone-10 in the reaction centre of Rhodobacter sphaeroides cause different binding at QA and QB?
  Eur J Biochem, 270, 3603-3609.  
12609910 A.Taly, P.Sebban, J.C.Smith, and G.M.Ullmann (2003).
The position of QB in the photosynthetic reaction center depends on pH: a theoretical analysis of the proton uptake upon QB reduction.
  Biophys J, 84, 2090-2098.  
14507738 F.Francia, G.Palazzo, A.Mallardi, L.Cordone, and G.Venturoli (2003).
Residual water modulates QA- -to-QB electron transfer in bacterial reaction centers embedded in trehalose amorphous matrices.
  Biophys J, 85, 2760-2775.  
11983861 J.Tandori, P.Maroti, E.Alexov, P.Sebban, and L.Baciou (2002).
Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides.
  Proc Natl Acad Sci U S A, 99, 6702-6706.  
12119028 L.Gerencser, A.Taly, L.Baciou, P.Maroti, and P.Sebban (2002).
Effect of binding of Cd2+ on bacterial reaction center mutants: proton-transfer uses interdependent pathways.
  Biochemistry, 41, 9132-9138.  
12146966 Q.Xu, L.Baciou, P.Sebban, and M.R.Gunner (2002).
Exploring the energy landscape for Q(A)(-) to Q(B) electron transfer in bacterial photosynthetic reaction centers: effect of substrate position and tail length on the conformational gating step.
  Biochemistry, 41, 10021-10025.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.