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PDBsum entry 1zrt

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protein ligands Protein-protein interface(s) links
Oxidoreductase/metal transport PDB id
1zrt
Jmol
Contents
Protein chains
427 a.a. *
252 a.a. *
181 a.a. *
Ligands
HEM ×4
SMA ×2
HEC ×2
FES ×2
* Residue conservation analysis
PDB id:
1zrt
Name: Oxidoreductase/metal transport
Title: Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound
Structure: Cytochrome b. Chain: c, p. Engineered: yes. Cytochrome c1. Chain: d, q. Engineered: yes. Ubiquinol-cytochromE C reductase iron-sulfur subunit. Chain: e, r.
Source: Rhodobacter capsulatus. Organism_taxid: 1061. Expressed in: rhodobacter capsulatus. Expression_system_taxid: 1061. Other_details: the strain pmts1/mt-rbc1 corresponds to a deletion strain mt-rbc1 complemented in trans with the plasmid pmts1 bearing a wild-type copy of the petabc operon encoding the bc1 complex. Operon encoding the bc1 complex
Biol. unit: Hexamer (from PQS)
Resolution:
3.50Å     R-factor:   0.300     R-free:   0.358
Authors: E.A.Berry,L.S.Huang,L.K.Saechao,N.G.Pon,M.Valkova-Valchanov, F.Daldal
Key ref: E.A.Berry et al. (2004). X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc (1): Comparison with its Mitochondrial and Chloroplast Counterparts. Photosynth Res, 81, 251-275. PubMed id: 16034531 DOI: 10.1023/B:PRES.0000036888.18223.0e
Date:
22-May-05     Release date:   07-Jun-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0CY47  (CYB_RHOCA) -  Cytochrome b
Seq:
Struc:
437 a.a.
427 a.a.*
Protein chains
Pfam   ArchSchema ?
P0CY49  (CY1_RHOCA) -  Cytochrome c1
Seq:
Struc:
280 a.a.
252 a.a.*
Protein chains
Pfam   ArchSchema ?
P0CY48  (UCRI_RHOCA) -  Ubiquinol-cytochrome c reductase iron-sulfur subunit
Seq:
Struc:
191 a.a.
181 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 30 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains E, R: E.C.1.10.2.2  - Quinol--cytochrome-c reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Quinol + 2 ferricytochrome c = quinone + 2 ferrocytochrome c + 2 H+
Quinol
Bound ligand (Het Group name = SMA)
matches with 46.00% similarity
+
2 × ferricytochrome c
Bound ligand (Het Group name = HEM)
matches with 63.00% similarity
= quinone
+ 2 × ferrocytochrome c
+ 2 × H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     electron carrier activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1023/B:PRES.0000036888.18223.0e Photosynth Res 81:251-275 (2004)
PubMed id: 16034531  
 
 
X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc (1): Comparison with its Mitochondrial and Chloroplast Counterparts.
E.A.Berry, L.S.Huang, L.K.Saechao, N.G.Pon, M.Valkova-Valchanova, F.Daldal.
 
  ABSTRACT  
 
Ubihydroquinone: cytochrome (cyt)c oxidoreductase, or cyt bc (1), is a widespread, membrane integral enzyme that plays a crucial role during photosynthesis and respiration. It is one of the major contributors of the electrochemical proton gradient, which is subsequently used for ATP synthesis. The simplest form of the cyt bc (1) is found in bacteria, and it contains only the three ubiquitously conserved catalytic subunits: the Fe-S protein, cyt b and cyt c (1). Here we present a preliminary X-ray structure of Rhodobacter capsulatus cyt bc (1) at 3.8 A and compare it to the available structures of its homologues from mitochondria and chloroplast. Using the bacterial enzyme structure, we highlight the structural similarities and differences that are found among the three catalytic subunits between the members of this family of enzymes. In addition, we discuss the locations of currently known critical mutations, and their implications in terms of the cyt bc (1) catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19910368 A.Marsico, K.Scheubert, A.Tuukkanen, A.Henschel, C.Winter, R.Winnenburg, and M.Schroeder (2010).
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins.
  Nucleic Acids Res, 38, D181-D189.  
19917265 E.Cieluch, K.Pietryga, M.Sarewicz, and A.Osyczka (2010).
Visualizing changes in electron distribution in coupled chains of cytochrome bc(1) by modifying barrier for electron transfer between the FeS cluster and heme c(1).
  Biochim Biophys Acta, 1797, 296-303.  
19826804 K.McLuskey, A.W.Roszak, Y.Zhu, and N.W.Isaacs (2010).
Crystal structures of all-alpha type membrane proteins.
  Eur Biophys J, 39, 723-755.  
19892700 M.Castellani, R.Covian, T.Kleinschroth, O.Anderka, B.Ludwig, and B.L.Trumpower (2010).
Direct demonstration of half-of-the-sites reactivity in the dimeric cytochrome bc1 complex: enzyme with one inactive monomer is fully active but unable to activate the second ubiquinol oxidation site in response to ligand binding at the ubiquinone reduction site.
  J Biol Chem, 285, 502-510.  
20651150 M.Swierczek, E.Cieluch, M.Sarewicz, A.Borek, C.C.Moser, P.L.Dutton, and A.Osyczka (2010).
An electronic bus bar lies in the core of cytochrome bc1.
  Science, 329, 451-454.  
19099453 D.R.Kolling, R.I.Samoilova, A.A.Shubin, A.R.Crofts, and S.A.Dikanov (2009).
Proton environment of reduced Rieske iron-sulfur cluster probed by two-dimensional ESEEM spectroscopy.
  J Phys Chem A, 113, 653-667.  
19254042 J.W.Cooley, D.W.Lee, and F.Daldal (2009).
Across membrane communication between the Q(o) and Q(i) active sites of cytochrome bc(1).
  Biochemistry, 48, 1888-1899.  
19415898 M.Sarewicz, M.Dutka, W.Froncisz, and A.Osyczka (2009).
Magnetic interactions sense changes in distance between heme b(L) and the iron-sulfur cluster in cytochrome bc(1).
  Biochemistry, 48, 5708-5720.  
19176478 R.Covian, and B.L.Trumpower (2009).
Ilicicolin Inhibition and Binding at Center N of the Dimeric Cytochrome bc1 Complex Reveal Electron Transfer and Regulatory Interactions between Monomers.
  J Biol Chem, 284, 8614-8620.  
18343816 D.W.Lee, Y.Oztürk, A.Osyczka, J.W.Cooley, and F.Daldal (2008).
Cytochrome bc1-cy fusion complexes reveal the distance constraints for functional electron transfer between photosynthesis components.
  J Biol Chem, 283, 13973-13982.  
18953640 D.Xia, L.Esser, M.Elberry, F.Zhou, L.Yu, and C.A.Yu (2008).
The road to the crystal structure of the cytochrome bc (1) complex from the anoxigenic, photosynthetic bacterium Rhodobacter sphaeroides.
  J Bioenerg Biomembr, 40, 485-492.  
18418633 E.A.Berry, and F.A.Walker (2008).
Bis-histidine-coordinated hemes in four-helix bundles: how the geometry of the bundle controls the axial imidazole plane orientations in transmembrane cytochromes of mitochondrial complexes II and III and related proteins.
  J Biol Inorg Chem, 13, 481-498.  
18022381 F.A.Rotsaert, M.G.Ding, and B.L.Trumpower (2008).
Differential efficacy of inhibition of mitochondrial and bacterial cytochrome bc1 complexes by center N inhibitors antimycin, ilicicolin H and funiculosin.
  Biochim Biophys Acta, 1777, 211-219.  
18039651 L.Esser, M.Elberry, F.Zhou, C.A.Yu, L.Yu, and D.Xia (2008).
Inhibitor-complexed Structures of the Cytochrome bc1 from the Photosynthetic Bacterium Rhodobacter sphaeroides.
  J Biol Chem, 283, 2846-2857.
PDB codes: 2qjk 2qjp 2qjy
18617515 M.Sarewicz, A.Borek, F.Daldal, W.Froncisz, and A.Osyczka (2008).
Demonstration of Short-lived Complexes of Cytochrome c with Cytochrome bc1 by EPR Spectroscopy: IMPLICATIONS FOR THE MECHANISM OF INTERPROTEIN ELECTRON TRANSFER.
  J Biol Chem, 283, 24826-24836.  
18093133 N.Fisher, and B.Meunier (2008).
Molecular basis of resistance to cytochrome bc1 inhibitors.
  FEMS Yeast Res, 8, 183-192.  
18454936 R.Covian, and B.L.Trumpower (2008).
The dimeric structure of the cytochrome bc(1) complex prevents center P inhibition by reverse reactions at center N.
  Biochim Biophys Acta, 1777, 1044-1052.  
18471987 R.Covian, and B.L.Trumpower (2008).
Regulatory interactions in the dimeric cytochrome bc(1) complex: the advantages of being a twin.
  Biochim Biophys Acta, 1777, 1079-1091.  
18501187 W.Liu, C.E.Rogge, G.F.da Silva, V.P.Shinkarev, A.L.Tsai, Y.Kamensky, G.Palmer, and R.J.Kulmacz (2008).
His92 and His110 selectively affect different heme centers of adrenal cytochrome b(561).
  Biochim Biophys Acta, 1777, 1218-1228.  
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.  
17457691 D.Xia, L.Esser, L.Yu, and C.A.Yu (2007).
Structural basis for the mechanism of electron bifurcation at the quinol oxidation site of the cytochrome bc1 complex.
  Photosynth Res, 92, 17-34.  
17498743 E.Yamashita, H.Zhang, and W.A.Cramer (2007).
Structure of the cytochrome b6f complex: quinone analogue inhibitors as ligands of heme cn.
  J Mol Biol, 370, 39-52.
PDB codes: 2e74 2e75 2e76
18073116 J.Busselez, M.Cottevieille, P.Cuniasse, F.Gubellini, N.Boisset, and D.Lévy (2007).
Structural basis for the PufX-mediated dimerization of bacterial photosynthetic core complexes.
  Structure, 15, 1674-1683.  
17360398 J.Zhu, T.Egawa, S.R.Yeh, L.Yu, and C.A.Yu (2007).
Simultaneous reduction of iron-sulfur protein and cytochrome b(L) during ubiquinol oxidation in cytochrome bc(1) complex.
  Proc Natl Acad Sci U S A, 104, 4864-4869.  
17657404 K.Ogawa, T.Sonoyama, T.Takeda, S.Ichiki, S.Nakamura, Y.Kobayashi, S.Uchiyama, K.Nakasone, S.J.Takayama, H.Mita, Y.Yamamoto, and Y.Sambongi (2007).
Roles of a short connecting disulfide bond in the stability and function of psychrophilic Shewanella violacea cytochrome c (5)*.
  Extremophiles, 11, 797-807.  
17573435 L.Giachini, F.Francia, G.Veronesi, D.W.Lee, F.Daldal, L.S.Huang, E.A.Berry, T.Cocco, S.Papa, F.Boscherini, and G.Venturoli (2007).
X-Ray absorption studies of Zn2+ binding sites in bacterial, avian, and bovine cytochrome bc1 complexes.
  Biophys J, 93, 2934-2951.  
16963124 M.R.Jones (2007).
Lipids in photosynthetic reaction centres: structural roles and functional holes.
  Prog Lipid Res, 46, 56-87.  
17544294 N.Morgner, T.Kleinschroth, H.D.Barth, B.Ludwig, and B.Brutschy (2007).
A novel approach to analyze membrane proteins by laser mass spectrometry: from protein subunits to the integral complex.
  J Am Soc Mass Spectrom, 18, 1429-1438.  
17584742 R.Covian, K.Zwicker, F.A.Rotsaert, and B.L.Trumpower (2007).
Asymmetric and redox-specific binding of quinone and quinol at center N of the dimeric yeast cytochrome bc1 complex. Consequences for semiquinone stabilization.
  J Biol Chem, 282, 24198-24208.  
17561507 R.Covian, T.Kleinschroth, B.Ludwig, and B.L.Trumpower (2007).
Asymmetric binding of stigmatellin to the dimeric Paracoccus denitrificans bc1 complex: evidence for anti-cooperative ubiquinol oxidation and communication between center P ubiquinol oxidation sites.
  J Biol Chem, 282, 22289-22297.  
17616531 S.A.Dikanov, J.T.Holland, B.Endeward, D.R.Kolling, R.I.Samoilova, T.F.Prisner, and A.R.Crofts (2007).
Hydrogen bonds between nitrogen donors and the semiquinone in the Qi-site of the bc1 complex.
  J Biol Chem, 282, 25831-25841.  
17399709 V.P.Shinkarev, and C.A.Wraight (2007).
Intermonomer electron transfer in the bc1 complex dimer is controlled by the energized state and by impaired electron transfer between low and high potential hemes.
  FEBS Lett, 581, 1535-1541.  
16586113 F.A.Walker (2006).
The heme environment of mouse neuroglobin: histidine imidazole plane orientations obtained from solution NMR and EPR spectroscopy as compared with X-ray crystallography.
  J Biol Inorg Chem, 11, 391-397.  
17008316 I.Forquer, R.Covian, M.K.Bowman, B.L.Trumpower, and D.M.Kramer (2006).
Similar transition states mediate the Q-cycle and superoxide production by the cytochrome bc1 complex.
  J Biol Chem, 281, 38459-38465.  
16908520 R.Covian, and B.L.Trumpower (2006).
Regulatory interactions between ubiquinol oxidation and ubiquinone reduction sites in the dimeric cytochrome bc1 complex.
  J Biol Chem, 281, 30925-30932.  
16714339 T.Geyer, and V.Helms (2006).
A spatial model of the chromatophore vesicles of Rhodobacter sphaeroides and the position of the Cytochrome bc1 complex.
  Biophys J, 91, 921-926.  
16714340 T.Geyer, and V.Helms (2006).
Reconstruction of a kinetic model of the chromatophore vesicles from Rhodobacter sphaeroides.
  Biophys J, 91, 927-937.  
16433558 T.Teschner, L.Yatsunyk, V.Schünemann, H.Paulsen, H.Winkler, C.Hu, W.R.Scheidt, F.A.Walker, and A.X.Trautwein (2006).
Models of the membrane-bound cytochromes: mössbauer spectra of crystalline low-spin ferriheme complexes having axial ligand plane dihedral angles ranging from 0 degree to 90 degrees.
  J Am Chem Soc, 128, 1379-1389.  
16756511 W.A.Cramer, H.Zhang, J.Yan, G.Kurisu, and J.L.Smith (2006).
Transmembrane traffic in the cytochrome b6f complex.
  Annu Rev Biochem, 75, 769-790.  
15817393 A.Osyczka, C.C.Moser, and P.L.Dutton (2005).
Fixing the Q cycle.
  Trends Biochem Sci, 30, 176-182.  
16060661 J.W.Cooley, T.Ohnishi, and F.Daldal (2005).
Binding dynamics at the quinone reduction (Qi) site influence the equilibrium interactions of the iron sulfur protein and hydroquinone oxidation (Qo) site of the cytochrome bc1 complex.
  Biochemistry, 44, 10520-10532.  
16024040 L.S.Huang, D.Cobessi, E.Y.Tung, and E.A.Berry (2005).
Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern.
  J Mol Biol, 351, 573-597.
PDB codes: 1pp9 1ppj 2a06
15917236 M.W.Mather, E.Darrouzet, M.Valkova-Valchanova, J.W.Cooley, M.T.McIntosh, F.Daldal, and A.B.Vaidya (2005).
Uncovering the molecular mode of action of the antimalarial drug atovaquone using a bacterial system.
  J Biol Chem, 280, 27458-27465.  
15601770 R.N.Frese, C.A.Siebert, R.A.Niederman, C.N.Hunter, C.Otto, and R.van Grondelle (2004).
The long-range organization of a native photosynthetic membrane.
  Proc Natl Acad Sci U S A, 101, 17994-17999.  
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.