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PDBsum entry 2fyu

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2fyu
Jmol
Contents
Protein chains
446 a.a. *
423 a.a. *
378 a.a. *
241 a.a. *
196 a.a. *
106 a.a. *
75 a.a. *
64 a.a. *
57 a.a. *
60 a.a. *
53 a.a. *
Ligands
HEM ×3
FDN
FES
Waters ×267
* Residue conservation analysis
PDB id:
2fyu
Name: Oxidoreductase
Title: Crystal structure of bovine heart mitochondrial bc1 with jg1 inhibitor
Structure: Ubiquinol-cytochromE-C reductase complex core pro mitochondrial. Chain: a. Fragment: core1. Ubiquinol-cytochromE-C reductase complex core pro mitochondrial. Chain: b. Fragment: core2. Synonym: complex iii subunit ii.
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organism_taxid: 9913
Biol. unit: 22mer (from PDB file)
Resolution:
2.26Å     R-factor:   0.249     R-free:   0.283
Authors: D.Xia,L.Esser
Key ref:
L.Esser et al. (2006). Surface-modulated motion switch: capture and release of iron-sulfur protein in the cytochrome bc1 complex. Proc Natl Acad Sci U S A, 103, 13045-13050. PubMed id: 16924113 DOI: 10.1073/pnas.0601149103
Date:
08-Feb-06     Release date:   29-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P31800  (QCR1_BOVIN) -  Cytochrome b-c1 complex subunit 1, mitochondrial
Seq:
Struc:
480 a.a.
446 a.a.
Protein chain
Pfam   ArchSchema ?
P23004  (QCR2_BOVIN) -  Cytochrome b-c1 complex subunit 2, mitochondrial
Seq:
Struc:
453 a.a.
423 a.a.
Protein chain
Pfam   ArchSchema ?
P00157  (CYB_BOVIN) -  Cytochrome b
Seq:
Struc:
379 a.a.
378 a.a.
Protein chain
Pfam   ArchSchema ?
P00125  (CY1_BOVIN) -  Cytochrome c1, heme protein, mitochondrial
Seq:
Struc:
325 a.a.
241 a.a.
Protein chain
Pfam   ArchSchema ?
P13272  (UCRI_BOVIN) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
274 a.a.
196 a.a.
Protein chain
Pfam   ArchSchema ?
P00129  (QCR7_BOVIN) -  Cytochrome b-c1 complex subunit 7
Seq:
Struc:
111 a.a.
106 a.a.*
Protein chain
Pfam   ArchSchema ?
P13271  (QCR8_BOVIN) -  Cytochrome b-c1 complex subunit 8
Seq:
Struc:
82 a.a.
75 a.a.
Protein chain
Pfam   ArchSchema ?
P00126  (QCR6_BOVIN) -  Cytochrome b-c1 complex subunit 6, mitochondrial
Seq:
Struc:
91 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
P13272  (UCRI_BOVIN) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
274 a.a.
57 a.a.
Protein chain
Pfam   ArchSchema ?
P00130  (QCR9_BOVIN) -  Cytochrome b-c1 complex subunit 9
Seq:
Struc:
64 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
P07552  (QCR10_BOVIN) -  Cytochrome b-c1 complex subunit 10
Seq:
Struc:
56 a.a.
53 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains E, I: 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
+
2 × ferricytochrome c
Bound ligand (Het Group name = HEM)
matches with 63.64% 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   8 terms 
  Biological process     oxidation-reduction process   13 terms 
  Biochemical function     catalytic activity     10 terms  

 

 
    Added reference    
 
 
DOI no: 10.1073/pnas.0601149103 Proc Natl Acad Sci U S A 103:13045-13050 (2006)
PubMed id: 16924113  
 
 
Surface-modulated motion switch: capture and release of iron-sulfur protein in the cytochrome bc1 complex.
L.Esser, X.Gong, S.Yang, L.Yu, C.A.Yu, D.Xia.
 
  ABSTRACT  
 
In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein (ISP) between two redox sites constitutes a key component of the mechanism that achieves the separation of the two electrons in a substrate molecule at the quinol oxidation (Q(o)) site. The question remaining is how the motion of ISP is controlled so that only one electron enters the thermodynamically favorable chain via ISP. An analysis of eight structures of mitochondrial bc(1) with bound Q(o) site inhibitors revealed that the presence of inhibitors causes a bidirectional repositioning of the cd1 helix in the cytochrome b subunit. As the cd1 helix forms a major part of the ISP binding crater, any positional shift of this helix modulates the ability of cytochrome b to bind ISP. The analysis also suggests a mechanism for reversal of the ISP fixation when the shape complementarity is significantly reduced after a positional reorientation of the reaction product quinone. The importance of shape complementarity in this mechanism was confirmed by functional studies of bc(1) mutants and by a structure determination of the bacterial form of bc(1). A mechanism for the high fidelity of the bifurcated electron transfer is proposed.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Prosthetic groups and subunit structures of the cyt bc[1] complex. (A) Arrangement of prosthetic groups in the dimeric bc[1] complex and illustration of the electron bifurcation at the Q[o] site. The b[L], b[H], and c[1] heme groups are shown as ball-and-stick models, and the [2Fe2S] clusters are depicted as cpk models. Carbon atoms, black; nitrogen, blue; oxygen, red; sulfur, yellow; iron, brown. The Q[o] pockets near the IMS side of the membrane and the Q[i] pockets near the matrix side are labeled and shaded in gray. Cyt c is shown as a gray shaded oval. Distances between redox centers are given on the left half of the diagram, and the redox potential for each center is given on the right. The high- and low-potential ET paths are depicted with red and green arrows, respectively. Circles in pink and light green within the Q[o] pockets are hypothesized distal-QH[2] and proximal-Q binding sites, respectively. (B) Ribbon diagram of the dimeric cyt b, cyt c[1], and ISP subunit in the mitochondrial bc[1] complex. Two symmetry-related cyt b subunits are shown (green and light green). The eight TM helices of cyt b are denoted with letters A–H. Helices A–E form one bundle in which the two b-type hemes (b[L] and b[H] in ball-and-stick models) reside; helices F–H form the other bundle. The ISP subunit (yellow and red for the symmetry pair) has an extrinsic soluble domain with a [2Fe2S] cluster at its tip, connecting to a TM segment by a flexible neck. The extrinsic domain of cyt c[1] (blue and magenta for the symmetry pair) with its heme group is rigidly attached to its TM helix. The locations for the two active sites (Q[o] and Q[i]) per monomer in cyt b are labeled. The surface depression in cyt b at the IMS side of the membrane is labeled as the ISP-docking crater.
Figure 3.
Fig. 3. Control of the ISP-ED motion switch and the proposed mechanism for electron bifurcation at the Q[o] pocket. The structural components necessary for the control of ISP conformational switch are illustrated in this cartoon rendition of the Q[o] pocket. The PEWY motif and cd1 helix in gray represent a native (Rest) configuration. The ISP in yellow and magenta are of oxidized and reduced form, respectively. The PEWY in blue stands for the open configuration with a bound Q[o] site inhibitor. The cd1 helix in red symbolizes the conformation (On/+) in the presence of a Pf inhibitor occupying the distal site (pink), and the cd1 helix in green shows the conformation (Off/–) when a Pm inhibitor is taking the proximal site (purple). Cyt c[1] and heme b[L] are also shown.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
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.  
  19774111 Q.L.Chen, X.S.Tang, W.J.Yao, and S.Q.Lu (2009).
Bioinformatics analysis of the complete sequences of cytochrome b of Takydromus sylvaticus and modeling the tertiary structure of encoded protein.
  Int J Biol Sci, 5, 596-602.  
19325183 R.Covian, and B.L.Trumpower (2009).
The rate-limiting step in the cytochrome bc1 complex (Ubiquinol-Cytochrome c Oxidoreductase) is not changed by inhibition of cytochrome b-dependent deprotonation: implications for the mechanism of ubiquinol oxidation at center P of the bc1 complex.
  J Biol Chem, 284, 14359-14367.  
18501698 A.R.Crofts, J.T.Holland, D.Victoria, D.R.Kolling, S.A.Dikanov, R.Gilbreth, S.Lhee, R.Kuras, and M.G.Kuras (2008).
The Q-cycle reviewed: How well does a monomeric mechanism of the bc(1) complex account for the function of a dimeric complex?
  Biochim Biophys Acta, 1777, 1001-1019.  
18481000 C.Cai, L.Chang, W.Li, and W.Liu (2008).
Effects of hyperoxia on mitochondrial multienzyme complex III and V in premature newborn rat lung.
  J Huazhong Univ Sci Technolog Med Sci, 28, 207-210.  
18515401 D.E.Chandler, J.Hsin, C.B.Harrison, J.Gumbart, and K.Schulten (2008).
Intrinsic curvature properties of photosynthetic proteins in chromatophores.
  Biophys J, 95, 2822-2836.  
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.  
18258178 H.W.Ma, S.Yang, L.Yu, and C.A.Yu (2008).
Formation of engineered intersubunit disulfide bond in cytochrome bc1 complex disrupts electron transfer activity in the complex.
  Biochim Biophys Acta, 1777, 317-326.  
18996700 P.J.Crowley, E.A.Berry, T.Cromartie, F.Daldal, C.R.Godfrey, D.W.Lee, J.E.Phillips, A.Taylor, and R.Viner (2008).
The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D.
  Bioorg Med Chem, 16, 10345-10355.
PDB code: 3cwb
18318906 R.R.da Fonseca, W.E.Johnson, S.J.O'Brien, M.J.Ramos, and A.Antunes (2008).
The adaptive evolution of the mammalian mitochondrial genome.
  BMC Genomics, 9, 119.  
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
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.  
17516628 S.Devanathan, Z.Salamon, G.Tollin, J.C.Fitch, T.E.Meyer, E.A.Berry, and M.A.Cusanovich (2007).
Plasmon waveguide resonance spectroscopic evidence for differential binding of oxidized and reduced Rhodobacter capsulatus cytochrome c2 to the cytochrome bc1 complex mediated by the conformation of the Rieske iron-sulfur protein.
  Biochemistry, 46, 7138-7145.  
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.

 

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