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PDBsum entry 2nve

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Oxidoreductase PDB id
2nve
Jmol
Contents
Protein chain
141 a.a. *
Ligands
FES
GOL ×2
Waters ×181
* Residue conservation analysis
PDB id:
2nve
Name: Oxidoreductase
Title: Soluble domain of rieske iron sulfur protein
Structure: Ubiquinol-cytochromE C reductase iron-sulfur subu chain: a. Fragment: residues 47-187. Synonym: rieske iron-sulfur protein, risp. Engineered: yes. Mutation: yes
Source: Rhodobacter sphaeroides. Organism_taxid: 1063. Gene: peta, fbcf. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.50Å     R-factor:   0.136     R-free:   0.174
Authors: D.K.Kolling,J.S.Brunzelle,S.Lhee,A.R.Crofts,S.K.Nair
Key ref:
D.J.Kolling et al. (2007). Atomic resolution structures of rieske iron-sulfur protein: role of hydrogen bonds in tuning the redox potential of iron-sulfur clusters. Structure, 15, 29-38. PubMed id: 17223530 DOI: 10.1016/j.str.2006.11.012
Date:
12-Nov-06     Release date:   06-Feb-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q02762  (UCRI_RHOSH) -  Ubiquinol-cytochrome c reductase iron-sulfur subunit
Seq:
Struc:
187 a.a.
141 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: 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
= 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   1 term 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2006.11.012 Structure 15:29-38 (2007)
PubMed id: 17223530  
 
 
Atomic resolution structures of rieske iron-sulfur protein: role of hydrogen bonds in tuning the redox potential of iron-sulfur clusters.
D.J.Kolling, J.S.Brunzelle, S.Lhee, A.R.Crofts, S.K.Nair.
 
  ABSTRACT  
 
The Rieske [2Fe-2S] iron-sulfur protein of cytochrome bc(1) functions as the initial electron acceptor in the rate-limiting step of the catalytic reaction. Prior studies have established roles for a number of conserved residues that hydrogen bond to ligands of the [2Fe-2S] cluster. We have constructed site-specific variants at two of these residues, measured their thermodynamic and functional properties, and determined atomic resolution X-ray crystal structures for the native protein at 1.2 A resolution and for five variants (Ser-154-->Ala, Ser-154-->Thr, Ser-154-->Cys, Tyr-156-->Phe, and Tyr-156-->Trp) to resolutions between 1.5 A and 1.1 A. These structures and complementary biophysical data provide a molecular framework for understanding the role hydrogen bonds to the cluster play in tuning thermodynamic properties, and hence the rate of this bioenergetic reaction. These studies provide a detailed structure-function dissection of the role of hydrogen bonds in tuning the redox potentials of [2Fe-2S] clusters.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Orthogonal Views of the Overall Structure of the Rieske Iron-Sulfur Protein from R. sphaeroides
(A) A ribbon representation of the polypeptide is shown and is labeled with the corresponding secondary structural elements as defined in the text. Atoms within the [2Fe-2S] cluster are shown as white and yellow spheres.
(B) The structure shown is rotated 90° about the vertical axis and is viewed at the location of the [2Fe-2S] cluster.
Figure 2.
Figure 2. Close-Up View of Mutations at Residue 156
(A–C) Difference Fourier maps shown around residue 156 of wild-type and variant Rieske ISPs, calculated with coefficients F[o] − F[c] by using experimental amplitudes and phases calculated from the final refined structures, minus the coordinates of residue 156. The contour levels of the maps are 2.5σ (blue). Coordinates from the final refined structures are superimposed on the respective maps, and atoms of the [2Fe-2S] cluster are shown as stick figures in magenta and orange. The structures shown are of (A) wild-type, (B) Tyr-156→Phe, and (C) Tyr-156→Trp Rieske ISPs.
(D) Superposition of the structures of wild-type (cyan) and Tyr-156→Trp (yellow) ISPs showing the gross structural movements that accompany the introduction of the Trp-156 side chain.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2007, 15, 29-38) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20445237 C.A.Behnke, I.Le Trong, J.W.Godden, E.A.Merritt, D.C.Teller, J.Bajorath, and R.E.Stenkamp (2010).
Atomic resolution studies of carbonic anhydrase II.
  Acta Crystallogr D Biol Crystallogr, 66, 616-627.
PDB codes: 1lug 3k34
20023300 S.Lhee, D.R.Kolling, S.K.Nair, S.A.Dikanov, and A.R.Crofts (2010).
Modifications of protein environment of the [2Fe-2S] cluster of the bc1 complex: effects on the biophysical properties of the rieske iron-sulfur protein and on the kinetics of the complex.
  J Biol Chem, 285, 9233-9248.  
  20885930 T.Iwasaki (2010).
Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus.
  Archaea, 2010, 0.  
20737532 Y.El Khoury, A.Trivella, J.Gross, and P.Hellwig (2010).
Probing the hydrogen bonding structure in the Rieske protein.
  Chemphyschem, 11, 3313-3319.  
18996897 A.L.Cuff, I.Sillitoe, T.Lewis, O.C.Redfern, R.Garratt, J.Thornton, and C.A.Orengo (2009).
The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
  Nucleic Acids Res, 37, D310-D314.  
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.  
19715344 H.Li, D.T.Mapolelo, N.N.Dingra, S.G.Naik, N.S.Lees, B.M.Hoffman, P.J.Riggs-Gelasco, B.H.Huynh, M.K.Johnson, and C.E.Outten (2009).
The yeast iron regulatory proteins Grx3/4 and Fra2 form heterodimeric complexes containing a [2Fe-2S] cluster with cysteinyl and histidyl ligation.
  Biochemistry, 48, 9569-9581.  
18766386 Y.El Khoury, and P.Hellwig (2009).
Infrared spectroscopic characterization of copper-polyhistidine from 1,800 to 50 cm(-1): model systems for copper coordination.
  J Biol Inorg Chem, 14, 23-34.  
18719951 E.N.Brown, R.Friemann, A.Karlsson, J.V.Parales, M.M.Couture, L.D.Eltis, and S.Ramaswamy (2008).
Determining Rieske cluster reduction potentials.
  J Biol Inorg Chem, 13, 1301-1313.
PDB code: 2qpz
17712580 H.Bönisch, C.L.Schmidt, P.Bianco, and R.Ladenstein (2007).
Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin: II. Introduction of an O-H...Sgamma-Fe hydrogen bond increased the reduction potential by 65 mV.
  J Biol Inorg Chem, 12, 1163-1171.
PDB code: 2pya
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.