spacer
spacer

PDBsum entry 3prc
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Photosynthetic reaction center PDB id
3prc

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
332 a.a. *
273 a.a. *
323 a.a. *
258 a.a. *
Ligands
HEM ×4
BCB ×4
BPB ×2
LDA ×7
SO4 ×4
MQ7
NS5
Metals
FE2
Waters ×425
* Residue conservation analysis
PDB id:
3prc
Name: Photosynthetic reaction center
Title: Photosynthetic reaction center from rhodopseudomonas viridis (qb- depleted)
Structure: Photosynthetic reaction center. Chain: c. Photosynthetic reaction center. Chain: l. Photosynthetic reaction center. Chain: m. Photosynthetic reaction center. Chain: h
Source: Blastochloris viridis. Organism_taxid: 1079. Atcc: dsm 133. Collection: dsm 133. Cellular_location: intracytoplasmic membrane (icm). Cellular_location: intracytoplasmic membrane (icm)
Biol. unit: Octamer (from PQS)
Resolution:
2.40Å     R-factor:   0.178     R-free:   0.215
Authors: C.R.D.Lancaster,H.Michel
Key ref:
C.R.Lancaster and H.Michel (1997). The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB. Structure, 5, 1339-1359. PubMed id: 9351808 DOI: 10.1016/S0969-2126(97)00285-2
Date:
29-Jul-97     Release date:   11-Nov-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07173  (CYCR_BLAVI) -  Photosynthetic reaction center cytochrome c subunit from Blastochloris viridis
Seq:
Struc: 		356 a.a.
332 a.a.
Protein chain
Pfam   ArchSchema ?
P06009  (RCEL_BLAVI) -  Reaction center protein L chain from Blastochloris viridis
Seq:
Struc: 		274 a.a.
273 a.a.
Protein chain
Pfam   ArchSchema ?
P06010  (RCEM_BLAVI) -  Reaction center protein M chain from Blastochloris viridis
Seq:
Struc: 		324 a.a.
323 a.a.
Protein chain
Pfam   ArchSchema ?
P06008  (RCEH_BLAVI) -  Reaction center protein H chain from Blastochloris viridis
Seq:
Struc: 		258 a.a.
258 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1016/S0969-2126(97)00285-2 Structure 5:1339-1359 (1997)
PubMed id: 9351808  
 
 
The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB.
C.R.Lancaster, H.Michel.
 
  ABSTRACT  
 
BACKGROUND: In a reaction of central importance to the energetics of photosynthetic bacteria, light-induced electron transfer in the reaction centre (RC) is coupled to the uptake of protons from the cytoplasm at the binding site of the secondary quinone (QB). In the original structure of the RC from Rhodopseudomonas viridis (PDB entry code 1PRC), the QB site was poorly defined because in the standard RC crystals it was only approximately 30% occupied with ubiquinone-9 (UQ9). We report here the structural characterization of the QB site by crystallographic refinement of UQ9-depleted RCs and of complexes of the RC either with ubiquinone-2 (UQ2) or the electron-transfer inhibitor stigmatellin in the QB site. RESULTS: The structure of the RC complex with UQ2, refined at 2.45 A resolution, constitutes the first crystallographically reliably defined binding site for quinones from the bioenergetically important quinone pool of biological, energy-transducing membranes. In the UQ9-depleted QB site of the RC structure, refined at 2.4 A resolution, apparently five (and possibly six) water molecules are bound instead of the ubiquinone head group, and a detergent molecule binds in the region of the isoprenoid tail. All of the protein-cofactor interactions implicated in the binding of the ubiquinone head group are also implicated in the binding of the stigmatellin head group. In the structure of the stigmatellin-RC complex, refined at 2.4 A resolution, additional hydrogen bonds stabilize the binding of stigmatellin over that of ubiquinone. The tentative position of UQ9 in the QB site in the original data set (1PRC) was re-examined using the structure of the UQ9-depleted RC as a reference. A modified QB site model, which exhibits greater similarity to the distal ubiquinone-10 (UQ10) positioning in the structure of the RC from Rhodobacter sphaeroides (PDB entry code 1PCR), is suggested as the dominant binding site for native UQ9. CONCLUSIONS: The structures reported here can provide models of quinone reduction cycle intermediates. The binding pattern observed for the stigmatellin complex, where the ligand donates a hydrogen bond to Ser L223 (where 'L' represents the L subunit of the RC), can be viewed as a model for the stabilization of a monoprotonated reduced intermediate (QBH or QBH-). The presence of Ser L223 in the QB site indicates that the QB site is not optimized for QB binding, but for QB reduction to the quinol.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Comparison of the structure at the Q[B] site. (a-c) The RC-UQ2 complex (in black) compared to the original structure 1PRC [13] (in green). (d) The Q[B]-depleted RC (in pink) compared to the RC-UQ2 complex (in black). (e,f) The RC-stigmatellin complex (in orange) compared to that of the RC-UQ2 complex (in black). Prospective hydrogen bonds are represented as dashed lines. (Figure made with the program MOLSCRIPT [96].)
 
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 1339-1359) copyright 1997.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21433296 X.Wang, W.Ma, Y.Ying, J.Liang, and Y.T.Long (2011).
Bis-coenzyme q(0) : synthesis, characteristics, and application.
  Chem Asian J, 6, 1064-1073.  
19072873 S.Wolf, E.Freier, and K.Gerwert (2008).
How does a membrane protein achieve a vectorial proton transfer via water molecules?
  Chemphyschem, 9, 2772-2778.  
18721136 T.Kleinschroth, O.Anderka, M.Ritter, A.Stocker, T.A.Link, B.Ludwig, and P.Hellwig (2008).
Characterization of mutations in crucial residues around the Q(o) binding site of the cytochrome bc complex from Paracoccus denitrificans.
  FEBS J, 275, 4773-4785.  
17200733 A.Y.Mulkidjanian (2007).
Proton translocation by the cytochrome bc1 complexes of phototrophic bacteria: introducing the activated Q-cycle.
  Photochem Photobiol Sci, 6, 19-34.  
17164531 G.J.Kleywegt (2007).
Crystallographic refinement of ligand complexes.
  Acta Crystallogr D Biol Crystallogr, 63, 94.  
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.  
16829675 E.Maklashina, P.Hellwig, R.A.Rothery, V.Kotlyar, Y.Sher, J.H.Weiner, and G.Cecchini (2006).
Differences in protonation of ubiquinone and menaquinone in fumarate reductase from Escherichia coli.
  J Biol Chem, 281, 26655-26664.  
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.  
16380425 C.R.Lancaster, U.S.Sauer, R.Gross, A.H.Haas, J.Graf, H.Schwalbe, W.Mäntele, J.Simon, and M.G.Madej (2005).
Experimental support for the "E pathway hypothesis" of coupled transmembrane e- and H+ transfer in dihemic quinol:fumarate reductase.
  Proc Natl Acad Sci U S A, 102, 18860-18865.
PDB codes: 2bs3 2bs4
15908429 J.A.Potter, P.K.Fyfe, D.Frolov, M.C.Wakeham, R.van Grondelle, B.Robert, and M.R.Jones (2005).
Strong effects of an individual water molecule on the rate of light-driven charge separation in the Rhodobacter sphaeroides reaction center.
  J Biol Chem, 280, 27155-27164.
PDB code: 2boz
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
15041635 E.Olkhova, M.C.Hutter, M.A.Lill, V.Helms, and H.Michel (2004).
Dynamic water networks in cytochrome C oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations.
  Biophys J, 86, 1873-1889.  
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.  
15073325 R.H.Baxter, N.Ponomarenko, V.Srajer, R.Pahl, K.Moffat, and J.R.Norris (2004).
Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center.
  Proc Natl Acad Sci U S A, 101, 5982-5987.
PDB code: 1r2c
15313239 S.Iwata, and J.Barber (2004).
Structure of photosystem II and molecular architecture of the oxygen-evolving centre.
  Curr Opin Struct Biol, 14, 447-453.  
12872158 A.Remy, and K.Gerwert (2003).
Coupling of light-induced electron transfer to proton uptake in photosynthesis.
  Nat Struct Biol, 10, 637-644.  
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.  
14622246 F.Milano, A.Agostiano, F.Mavelli, and M.Trotta (2003).
Kinetics of the quinone binding reaction at the QB site of reaction centers from the purple bacteria Rhodobacter sphaeroides reconstituted in liposomes.
  Eur J Biochem, 270, 4595-4605.  
12962624 G.J.Kleywegt, K.Henrick, E.J.Dodson, and D.M.van Aalten (2003).
Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement?
  Structure, 11, 1051-1059.  
12975370 P.Voigt, and E.W.Knapp (2003).
Tuning heme redox potentials in the cytochrome C subunit of photosynthetic reaction centers.
  J Biol Chem, 278, 51993-52001.  
11883600 J.Tandori, J.Miksovska, M.Valerio-Lepiniec, M.Schiffer, P.Maróti, D.K.Hanson, and P.Sebban (2002).
Proton uptake of rhodobacter capsulatus reaction center mutants modified in the primary quinone environment.
  Photochem Photobiol, 75, 126-133.  
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.  
12023243 P.Huppman, T.Arlt, H.Penzkofer, S.Schmidt, M.Bibikova, B.Dohse, D.Oesterhelt, J.Wachtveit, and W.Zinth (2002).
Kinetics, energetics, and electronic coupling of the primary electron transfer reactions in mutated reaction centers of Blastochloris viridis.
  Biophys J, 82, 3186-3197.  
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.  
12081951 S.Ouchane, I.Agalidis, and C.Astier (2002).
Natural resistance to inhibitors of the ubiquinol cytochrome c oxidoreductase of Rubrivivax gelatinosus: sequence and functional analysis of the cytochrome bc(1) complex.
  J Bacteriol, 184, 3815-3822.  
12169656 W.Kühlbrandt, J.Zeelen, and J.Dietrich (2002).
Structure, mechanism, and regulation of the Neurospora plasma membrane H+-ATPase.
  Science, 297, 1692-1696.
PDB code: 1mhs
12081322 Z.Tokaji, J.Tandori, and P.Maróti (2002).
Light- and redox-dependent thermal stability of the reaction center of the photosynthetic Bacterium rhodobacter sphaeroides.
  Photochem Photobiol, 75, 605-612.  
11284681 A.Kuglstatter, U.Ermler, H.Michel, L.Baciou, and G.Fritzsch (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.
PDB codes: 1f6n 1fnp 1fnq
11248702 C.R.Lancaster, R.Gross, and J.Simon (2001).
A third crystal form of Wolinella succinogenes quinol:fumarate reductase reveals domain closure at the site of fumarate reduction.
  Eur J Biochem, 268, 1820-1827.
PDB code: 1e7p
11322886 I.Fathir, T.Mori, T.Nogi, M.Kobayashi, K.Miki, and T.Nozawa (2001).
Structure of the H subunit of the photosynthetic reaction center from the thermophilic purple sulfur bacterium, Thermochromatium tepidum Implications for the specific binding of the lipid molecule to the membrane protein complex.
  Eur J Biochem, 268, 2652-2657.  
11352751 L.M.Utschig, O.Poluektov, S.L.Schlesselman, M.C.Thurnauer, and D.M.Tiede (2001).
Cu2+ site in photosynthetic bacterial reaction centers from Rhodobacter sphaeroides, Rhodobacter capsulatus, and Rhodopseudomonas viridis.
  Biochemistry, 40, 6132-6141.  
11222300 M.C.Wakeham, R.B.Sessions, M.R.Jones, and P.K.Fyfe (2001).
Is there a conserved interaction between cardiolipin and the type II bacterial reaction center?
  Biophys J, 80, 1395-1405.  
11761330 P.J.O'Malley (2001).
Electronic structure studies of quinones and semiquinones: accurate calculation of spin densities and electron paramagnetic resonance parameters.
  Antioxid Redox Signal, 3, 825-838.  
11166568 P.K.Fyfe, K.E.McAuley, A.W.Roszak, N.W.Isaacs, R.J.Cogdell, and M.R.Jones (2001).
Probing the interface between membrane proteins and membrane lipids by X-ray crystallography.
  Trends Biochem Sci, 26, 106-112.  
11303880 S.Arndt, U.Emde, S.Bäurle, T.Friedrich, L.Grubert, and U.Koert (2001).
Quinone-annonaceous acetogenins: synthesis and complex I inhibition studies of a new class of natural product hybrids.
  Chemistry, 7, 993.  
11148037 S.Keller, J.T.Beatty, M.Paddock, J.Breton, and W.Leibl (2001).
Effect of metal binding on electrogenic proton transfer associated with reduction of the secondary electron acceptor (QB) in Rhodobacter sphaeroides chromatophores.
  Biochemistry, 40, 429-439.  
11334792 U.Zachariae, and C.R.Lancaster (2001).
Proton uptake associated with the reduction of the primary quinone Q(A) influences the binding site of the secondary quinone Q(B) in Rhodopseudomonas viridis photosynthetic reaction centers.
  Biochim Biophys Acta, 1505, 280-290.  
10924900 A.Spyridaki, G.Fritzsch, E.Kouimtzoglou, L.Baciou, and D.Ghanotakis (2000).
The natural product capsaicin inhibits photosynthetic electron transport at the reducing side of photosystem II and purple bacterial reaction center: structural details of capsaicin binding.
  Biochim Biophys Acta, 1459, 69-76.  
10956039 B.Rabenstein, G.M.Ullmann, and E.W.Knapp (2000).
Electron transfer between the quinones in the photosynthetic reaction center and its coupling to conformational changes.
  Biochemistry, 39, 10487-10496.  
10873857 C.Hunte, J.Koepke, C.Lange, T.Rossmanith, and H.Michel (2000).
Structure at 2.3 A resolution of the cytochrome bc(1) complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment.
  Structure, 8, 669-684.
PDB code: 1ezv
11186225 C.R.Lancaster, R.Gorss, A.Haas, M.Ritter, W.Mäntele, J.Simon, and A.Kröger (2000).
Essential role of Glu-C66 for menaquinol oxidation indicates transmembrane electrochemical potential generation by Wolinella succinogenes fumarate reductase.
  Proc Natl Acad Sci U S A, 97, 13051-13056.  
10924896 D.A.Cherepanov, S.I.Bibikov, M.V.Bibikova, D.A.Bloch, L.A.Drachev, O.A.Gopta, D.Oesterhelt, A.Y.Semenov, and A.Y.Mulkidjanian (2000).
Reduction and protonation of the secondary quinone acceptor of Rhodobacter sphaeroides photosynthetic reaction center: kinetic model based on a comparison of wild-type chromatophores with mutants carrying Arg-->Ile substitution at sites 207 and 217 in the L-subunit.
  Biochim Biophys Acta, 1459, 10-34.  
10821665 E.Alexov, J.Miksovska, L.Baciou, M.Schiffer, D.K.Hanson, P.Sebban, and M.R.Gunner (2000).
Modeling the effects of mutations on the free energy of the first electron transfer from QA- to QB in photosynthetic reaction centers.
  Biochemistry, 39, 5940-5952.  
11087422 E.Nabedryk, J.Breton, H.M.Joshi, and D.K.Hanson (2000).
Fourier transform infrared evidence of proton uptake by glutamate L212 upon reduction of the secondary quinone QB in the photosynthetic reaction center from Rhodobacter capsulatus.
  Biochemistry, 39, 14654-14663.  
10736158 I.P.Chen, P.Mathis, J.Koepke, and H.Michel (2000).
Uphill electron transfer in the tetraheme cytochrome subunit of the Rhodopseudomonas viridis photosynthetic reaction center: evidence from site-directed mutagenesis.
  Biochemistry, 39, 3592-3602.  
10966478 J.L.Popot, and D.M.Engelman (2000).
Helical membrane protein folding, stability, and evolution.
  Annu Rev Biochem, 69, 881-922.  
10812030 M.Y.Okamura, M.L.Paddock, M.S.Graige, and G.Feher (2000).
Proton and electron transfer in bacterial reaction centers.
  Biochim Biophys Acta, 1458, 148-163.  
11095707 T.Nogi, I.Fathir, M.Kobayashi, T.Nozawa, and K.Miki (2000).
Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer.
  Proc Natl Acad Sci U S A, 97, 13561-13566.
PDB codes: 1eys 1eyt
10625446 A.R.Crofts, B.Barquera, R.B.Gennis, R.Kuras, M.Guergova-Kuras, and E.A.Berry (1999).
Mechanism of ubiquinol oxidation by the bc(1) complex: different domains of the quinol binding pocket and their role in the mechanism and binding of inhibitors.
  Biochemistry, 38, 15807-15826.  
10625445 A.R.Crofts, M.Guergova-Kuras, L.Huang, R.Kuras, Z.Zhang, and E.A.Berry (1999).
Mechanism of ubiquinol oxidation by the bc(1) complex: role of the iron sulfur protein and its mobility.
  Biochemistry, 38, 15791-15806.  
10468555 A.R.Crofts, S.Hong, N.Ugulava, B.Barquera, R.Gennis, M.Guergova-Kuras, and E.A.Berry (1999).
Pathways for proton release during ubihydroquinone oxidation by the bc(1) complex.
  Proc Natl Acad Sci U S A, 96, 10021-10026.  
10387071 E.G.Alexov, and M.R.Gunner (1999).
Calculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centers.
  Biochemistry, 38, 8253-8270.  
10216167 E.Nabedryk (1999).
Characterization of the photoreduction of the secondary quinone QB in the photosynthetic reaction center from rhodobacter capsulatus with FTIR spectroscopy
  Biochim Biophys Acta, 1411, 206-213.  
10588708 J.Miksovska, M.Schiffer, D.K.Hanson, and P.Sebban (1999).
Proton uptake by bacterial reaction centers: the protein complex responds in a similar manner to the reduction of either quinone acceptor.
  Proc Natl Acad Sci U S A, 96, 14348-14353.  
10611277 K.E.McAuley, P.K.Fyfe, J.P.Ridge, N.W.Isaacs, R.J.Cogdell, and M.R.Jones (1999).
Structural details of an interaction between cardiolipin and an integral membrane protein.
  Proc Natl Acad Sci U S A, 96, 14706-14711.
PDB code: 1qov
10512801 S.Izrailev, A.R.Crofts, E.A.Berry, and K.Schulten (1999).
Steered molecular dynamics simulation of the Rieske subunit motion in the cytochrome bc(1) complex.
  Biophys J, 77, 1753-1768.  
9729743 A.R.Crofts, and E.A.Berry (1998).
Structure and function of the cytochrome bc1 complex of mitochondria and photosynthetic bacteria.
  Curr Opin Struct Biol, 8, 501-509.  
9772172 E.Nabedryk, J.Breton, M.Y.Okamura, and M.L.Paddock (1998).
Proton uptake by carboxylic acid groups upon photoreduction of the secondary quinone (QB) in bacterial reaction centers from Rhodobacter sphaeroides: FTIR studies on the effects of replacing Glu H173.
  Biochemistry, 37, 14457-14462.  
9729741 M.Wikström (1998).
Proton translocation by bacteriorhodopsin and heme-copper oxidases.
  Curr Opin Struct Biol, 8, 480-488.  
9651245 S.Iwata, J.W.Lee, K.Okada, J.K.Lee, M.Iwata, B.Rasmussen, T.A.Link, S.Ramaswamy, and B.K.Jap (1998).
Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex.
  Science, 281, 64-71.
PDB codes: 1be3 1bgy
9694819 Z.Zhao, and J.H.Weiner (1998).
Interaction of 2-n-heptyl-4-hydroxyquinoline-N-oxide with dimethyl sulfoxide reductase of Escherichia coli.
  J Biol Chem, 273, 20758-20763.  
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 codes are shown on the right.

 

spacer
spacer