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PDBsum entry 1orz

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protein Protein-protein interface(s) links
Oxidoreductase PDB id
1orz
Jmol
Contents
Protein chains
612 a.a.
246 a.a.
148 a.a.
150 a.a.
Theoretical model
PDB id:
1orz
Name: Oxidoreductase
Title: Three-dimensional model of the saccharomyces cerevisiae succinate dehydrogenase
Structure: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial. Chain: a. Synonym: fp, flavoprotein subunit of complex ii, sdh1p. Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial. Chain: b. Synonym: ip, sdh2p. Succinate dehydrogenase cytochrome b subunit,
Source: Saccharomyces cerevisiae. Yeast. Yeast
Authors: K.S.Oyedotun,B.D.Lemire
Key ref:
K.S.Oyedotun and B.D.Lemire (2004). The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies. J Biol Chem, 279, 9424-9431. PubMed id: 14672929 DOI: 10.1074/jbc.M311876200
Date:
17-Mar-03     Release date:   09-Mar-04    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q00711  (DHSA_YEAST) -  Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Seq:
Struc:
 
Seq:
Struc:
640 a.a.
612 a.a.
Protein chain
Pfam   ArchSchema ?
P21801  (DHSB_YEAST) -  Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
Seq:
Struc:
266 a.a.
246 a.a.
Protein chain
Pfam   ArchSchema ?
P33421  (SDH3_YEAST) -  Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
Seq:
Struc:
198 a.a.
148 a.a.
Protein chain
Pfam   ArchSchema ?
P37298  (DHSD_YEAST) -  Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
Seq:
Struc:
181 a.a.
150 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.1.3.5.1  - Succinate dehydrogenase (quinone).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Citric acid cycle
      Reaction: Succinate + a quinone = fumarate + a quinol
Succinate
+ quinone
= fumarate
+ quinol
      Cofactor: FAD; Iron-sulfur
FAD
Iron-sulfur
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M311876200 J Biol Chem 279:9424-9431 (2004)
PubMed id: 14672929  
 
 
The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies.
K.S.Oyedotun, B.D.Lemire.
 
  ABSTRACT  
 
Succinate dehydrogenases and fumarate reductases are complex mitochondrial or bacterial respiratory chain proteins with remarkably similar structures and functions. Succinate dehydrogenase oxidizes succinate and reduces ubiquinone using a flavin adenine dinucleotide cofactor and iron-sulfur clusters to transport electrons. A model of the quaternary structure of the tetrameric Saccharomyces cerevisiae succinate dehydrogenase was constructed based on the crystal structures of the Escherichia coli succinate dehydrogenase, the E. coli fumarate reductase, and the Wolinella succinogenes fumarate reductase. One FAD and three iron-sulfur clusters were docked into the Sdh1p and Sdh2p catalytic dimer. One b-type heme and two ubiquinone or inhibitor analog molecules were docked into the Sdh3p and Sdh4p membrane dimer. The model is consistent with numerous experimental observations. The calculated free energies of inhibitor binding are in excellent agreement with the experimentally determined inhibitory constants. Functionally important residues identified by mutagenesis of the SDH3 and SDH4 genes are located near the two proposed quinone-binding sites, which are separated by the heme. The proximal quinone-binding site, located nearest the catalytic dimer, has a considerably more polar environment than the distal site. Alternative low energy conformations of the membrane subunits were explored in a molecular dynamics simulation of the dimer embedded in a phospholipid bilayer. The simulation offers insight into why Sdh4p Cys-78 may be serving as the second axial ligand for the heme instead of a histidine residue. We discuss the possible roles of heme and of the two quinone-binding sites in electron transport.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. Quaternary structure model of the S. cerevisiae SDH. A, ribbon representation of SDH. Sdh1p, Sdh2p, Sdh3p, and Sdh4p are shown in gold, green, red, and blue, respectively. The iron-sulfur clusters are shown as cyan (S atoms) and red (Fe atoms); FAD and heme b are shown as purple; quinones are shown in yellow. B, superposition of the S. cerevisiae SDH (blue) with the E. coli SDH (yellow). C, structure of the flavoprotein (Sdh1p). His-62, which is covalently linked to the FAD is shown in red. D, the iron-sulfur protein (Sdh2p) with the three iron-sulfur clusters.
Figure 7.
FIG. 7. A, averaged structure of the Sdh2p-Sdh3p-Sdh4p trimer calculated after MD simulation and the pathway of electron transfer. A, superimposition of the SDH trimer structure after molecular dynamics (blue) with the starting conformation (yellow). Sdh4p residues that are most mobile during molecular dynamics simulation are colored red. The average structure was calculated from the equilibrium ensemble of the last 500 ps using the g_rmsf utility of GROMACS. B, structure of the heme-binding site after a 5-ns molecular dynamics simulation. C, cofactor location and pathway of electron transfer. Edge-to-edge distances (Å) between the cofactors are indicated.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 9424-9431) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20938771 H.Cao, M.Yue, S.Li, X.Bai, X.Zhao, and Y.Du (2011).
The impact of MIG1 and/or MIG2 disruption on aerobic metabolism of succinate dehydrogenase negative Saccharomyces cerevisiae.
  Appl Microbiol Biotechnol, 89, 733-738.  
21241518 J.Zheng, C.Wei, L.Zhao, L.Liu, W.Leng, W.Li, and Q.Jin (2011).
Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin.
  BMC Genomics, 12, 40.  
21283140 R.Costenoble, P.Picotti, L.Reiter, R.Stallmach, M.Heinemann, U.Sauer, and R.Aebersold (2011).
Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics.
  Mol Syst Biol, 7, 464.  
21136603 T.van Alen, H.Claus, R.P.Zahedi, J.Groh, H.Blazyca, M.Lappann, A.Sickmann, and U.Vogel (2010).
Comparative proteomic analysis of biofilm and planktonic cells of Neisseria meningitidis.
  Proteomics, 10, 4512-4521.  
18498664 W.Sun, S.Yuan, and K.C.Li (2008).
Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study.
  BMC Genomics, 9, 242.  
16648166 L.R.Forrest, C.L.Tang, and B.Honig (2006).
On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins.
  Biophys J, 91, 508-517.  
15805592 L.S.Huang, T.M.Borders, J.T.Shen, C.J.Wang, and E.A.Berry (2005).
Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A.
  Acta Crystallogr D Biol Crystallogr, 61, 380-387.  
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.