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Oxidoreductase/metal transport PDB-id
1zrt
Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)
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Contents
Description
Header details
Header records
References
PROCHECK
Protein chains
427 a.a. *
252 a.a. *
181 a.a. *
Ligands
HEM ×4
SMA ×2
HEC ×2
FES ×2

* Residue conservation analysis
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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

Biological unit:
Hexamer (from PQS)

UniProt:
Chains C, P: P08502 (CYB_RHOCA)
Pfam  
Seq:
Struc:
Seq: 437 a.a.
Struc: 427 a.a.

Chains D, Q: P08501 (CY1_RHOCA)
Pfam  
Seq:
Struc:
Seq: 279 a.a.
Struc: 252 a.a.

Chains E, R: P08500 (UCRI_RHOCA)
Pfam  
Seq: 191 a.a.
Struc: 181 a.a.
Key:    PfamA domain
 Secondary structure  CATH domain

Enzyme class:
Chains E, R: E.C.1.10.2.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:
QH2 + 2 ferricytochrome c = Q + 2 ferrocytochrome c + 2 H+ (see diagram below)

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

Related entries:
1pp9
bovine bc1 complex with stigmatellin bound
1kb9
yeast bc1 complex with stigmatellin bound
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Enzyme reaction for E.C.1.10.2.2


QH(2)
+
2 × ferricytochrome c
=
Q
+
2 × ferrocytochrome c
Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

 
    Key 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
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.  
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.  
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.  
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.  
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.  
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.  
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.  
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.