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PDBsum entry 2qjk

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protein ligands metals Protein-protein interface(s) links
Electron transport PDB id
2qjk
Jmol
Contents
Protein chains
(+ 0 more) 428 a.a. *
(+ 0 more) 256 a.a. *
(+ 0 more) 179 a.a. *
Ligands
BGL ×6
HEM ×18
FES ×6
SMA ×6
LOP ×6
ANJ ×6
Metals
_SR ×6
* Residue conservation analysis
PDB id:
2qjk
Name: Electron transport
Title: Crystal structure analysis of mutant rhodobacter sphaeroides bc1 with stigmatellin and antimycin
Structure: Cytochrome b. Chain: a, d, g, j, m, p. Engineered: yes. Mutation: yes. Cytochrome c1. Chain: b, e, h, k, n, q. Engineered: yes. Ubiquinol-cytochromE C reductase iron-sulfur subunit.
Source: Rhodobacter sphaeroides. Organism_taxid: 1063. Gene: petb, fbcb. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: fbcc. Gene: peta, fbcf.
Resolution:
3.10Å     R-factor:   0.239     R-free:   0.266
Authors: L.Esser
Key ref:
L.Esser et al. (2008). Inhibitor-complexed Structures of the Cytochrome bc1 from the Photosynthetic Bacterium Rhodobacter sphaeroides. J Biol Chem, 283, 2846-2857. PubMed id: 18039651 DOI: 10.1074/jbc.M708608200
Date:
07-Jul-07     Release date:   25-Dec-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q02761  (CYB_RHOSH) -  Cytochrome b
Seq:
Struc:
445 a.a.
428 a.a.*
Protein chains
Pfam   ArchSchema ?
Q02760  (CY1_RHOSH) -  Cytochrome c1
Seq:
Struc:
285 a.a.
256 a.a.*
Protein chains
Pfam   ArchSchema ?
Q02762  (UCRI_RHOSH) -  Ubiquinol-cytochrome c reductase iron-sulfur subunit
Seq:
Struc:
187 a.a.
179 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains C, F, I, L, O, 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: 10.1074/jbc.M708608200 J Biol Chem 283:2846-2857 (2008)
PubMed id: 18039651  
 
 
Inhibitor-complexed Structures of the Cytochrome bc1 from the Photosynthetic Bacterium Rhodobacter sphaeroides.
L.Esser, M.Elberry, F.Zhou, C.A.Yu, L.Yu, D.Xia.
 
  ABSTRACT  
 
The cytochrome bc(1) complex (bc(1)) is a major contributor to the proton motive force across the membrane by coupling electron transfer to proton translocation. The crystal structures of wild type and mutant bc(1) complexes from the photosynthetic purple bacterium Rhodobacter sphaeroides (Rsbc(1)), stabilized with the quinol oxidation (Q(P)) site inhibitor stigmatellin alone or in combination with the quinone reduction (Q(N)) site inhibitor antimycin, were determined. The high quality electron density permitted assignments of a new metal-binding site to the cytochrome c(1) subunit and a number of lipid and detergent molecules. Structural differences between Rsbc(1) and its mitochondrial counterparts are mostly extra membranous and provide a basis for understanding the function of the predominantly longer sequences in the bacterial subunits. Functional implications for the bc(1) complex are derived from analyses of 10 independent molecules in various crystal forms and from comparisons with mitochondrial complexes.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Structure of the Rsbc[1] complex. The subunits are colored as follows: green, cyt b; blue, cyt c[1], and yellow, ISP. Insertions and extensions that distinguish Rsbc[1] from Btbc[1] are in red. Heme groups, 2Fe2S, stigmatellin, and ubiquinone are shown as stick models with black carbon, red oxygen, blue nitrogen, green sulfur, and brown iron atoms. Ribbon diagrams were produced with the graphics programs Molscript (57), Bobscript (58), Povray, and Glr. A, ribbon representation of the dimeric Rsbc[1] with the bound Q[P] site inhibitor stigmatellin and Q[N] site substrate quinone. The boundary of lipid bilayer is indicated with two parallel lines. The transmembrane domain (TM), the periplasmic (PP), and cytoplasmic (CP) space are labeled. Modeled lipid and detergent molecules are shown as stick models in red. B, ribbon diagram of the cyt b subunit with labeled TM helices and connecting loop. C, structure of cyt c[1] in the ribbon form showing all secondary structure elements. Residues important for Sr^2+ binding are drawn in stick models with carbon atoms in yellow, oxygen red, and sulfur green. The Sr^2+ ion is shown as a metallic sphere. D, putative metal-binding site in cyt c[1] subunit. The electron density is shown as a semi-transparent hull contoured at 1 level. The Sr^2+ ion is coordinated by three acidic residues and one backbone carbonyl oxygen atom. Residues in the vicinity of the binding site are given in the ball-and-stick form. E, structure of ISP in the ribbon form.
Figure 2.
FIGURE 2. Inhibitor binding sites in cyt b. A, stereoscopic diagram showing electron density for stigmatellin (white) and its binding environment (blue). Stigmatellin and its surrounding residues are portrayed in the stick model with yellow carbon, red oxygen and blue nitrogen, green sulfur and brown iron atoms. His^161 of ISP is 2.64 Å away from the atom O4 of stigmatellin and its phenolic oxygen atom O8 is 3.01 Å away from OE1 of Glu^295. The electron density is contoured at 1.5 . B, stereoscopic view of the Q[N] site. The bound antimycin in yellow forms two hydrogen bonds (red dotted lines) with the 3-FASA moiety of the inhibitor. The b[H] heme is shown as a stick model in gray. The inhibitor displays anti conformation as in 1PPJ (27).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 2846-2857) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19689132 A.I.Twigg, D.Baniulis, W.A.Cramer, and M.P.Hendrich (2009).
EPR detection of an O(2) surrogate bound to heme c(n) of the cytochrome b(6)f complex.
  J Am Chem Soc, 131, 12536-12537.  
19189962 D.Baniulis, E.Yamashita, J.P.Whitelegge, A.I.Zatsman, M.P.Hendrich, S.S.Hasan, C.M.Ryan, and W.A.Cramer (2009).
Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120.
  J Biol Chem, 284, 9861-9869.
PDB code: 2zt9
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.  
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.  
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.  
18713733 S.Yang, H.W.Ma, L.Yu, and C.A.Yu (2008).
On the mechanism of quinol oxidation at the QP site in the cytochrome bc1 complex: studied using mutants lacking cytochrome bL or bH.
  J Biol Chem, 283, 28767-28776.  
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.  
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.