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PDBsum entry 2h89

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2h89
Jmol
Contents
Protein chains
613 a.a. *
241 a.a. *
139 a.a. *
102 a.a. *
Ligands
FAD
MLI
UNL ×40
FES
SF4
F3S
BHG
HEM
PEE ×2
Metals
__K ×2
Waters ×580
* Residue conservation analysis
PDB id:
2h89
Name: Oxidoreductase
Title: Avian respiratory complex ii with malonate bound
Structure: Succinate dehydrogenase flavoprotein subunit. Chain: a. Succinate dehydrogenase ip subunit. Chain: b. Succinate dehydrogenase cytochrome b, large subunit. Chain: c. Succinate dehydrogenase cytochrome b, small subunit.
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organism_taxid: 9031
Biol. unit: Tetramer (from PQS)
Resolution:
2.40Å     R-factor:   0.226     R-free:   0.279
Authors: L.S.Huang,J.T.Shen,A.C.Wang,E.A.Berry
Key ref: L.S.Huang et al. (2006). Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state. Biochim Biophys Acta, 1757, 1073-1083. PubMed id: 16935256 DOI: 10.1016/j.bbabio.2006.06.015
Date:
06-Jun-06     Release date:   20-Jun-06    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9YHT1  (DHSA_CHICK) -  Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Seq:
Struc:
 
Seq:
Struc:
665 a.a.
613 a.a.*
Protein chain
Pfam   ArchSchema ?
Q9YHT2  (DHSB_CHICK) -  Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
Seq:
Struc:
290 a.a.
241 a.a.
Protein chain
Pfam   ArchSchema ?
D0VWW3  (D0VWW3_CHICK) -  Succinate dehydrogenase cytochrome b, large subunit
Seq:
Struc:
140 a.a.
139 a.a.
Protein chain
Pfam   ArchSchema ?
Q5ZIS0  (DHSD_CHICK) -  Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
Seq:
Struc:
157 a.a.
102 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: 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
Bound ligand (Het Group name = MLI)
matches with 50.00% similarity
+ quinone
Bound ligand (Het Group name = PEE)
matches with 47.00% similarity
= fumarate
+ quinol
      Cofactor: FAD; Iron-sulfur
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Iron-sulfur
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   7 terms 
  Biological process     small molecule metabolic process   6 terms 
  Biochemical function     electron carrier activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.bbabio.2006.06.015 Biochim Biophys Acta 1757:1073-1083 (2006)
PubMed id: 16935256  
 
 
Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state.
L.S.Huang, J.T.Shen, A.C.Wang, E.A.Berry.
 
  ABSTRACT  
 
Mitochondrial Complex II (succinate:ubiquinone oxidoreductase) is purified in a partially inactivated state, which can be activated by removal of tightly bound oxaloacetate (E.B. Kearney, et al., Biochem. Biophys. Res. Commun. 49 1115-1121). We crystallized Complex II in the presence of oxaloacetate or with the endogenous inhibitor bound. The structure showed a ligand essentially identical to the "malate-like intermediate" found in Shewanella Flavocytochrome c crystallized with fumarate (P. Taylor, et al., Nat. Struct. Biol. 6 1108-1112) Crystallization of Complex II in the presence of excess fumarate also gave the malate-like intermediate or a mixture of that and fumarate at the active site. In order to more conveniently monitor the occupation state of the dicarboxylate site, we are developing a library of UV/Vis spectral effects induced by binding different ligands to the site. Treatment with fumarate results in rapid development of the fumarate difference spectrum and then a very slow conversion into a species spectrally similar to the OAA-liganded complex. Complex II is known to be capable of oxidizing malate to the enol form of oxaloacetate (Y.O. Belikova, et al., Biochim. Biophys. Acta 936 1-9). The observations above suggest it may also be capable of interconverting fumarate and malate. It may be useful for understanding the mechanism and regulation of the enzyme to identify the malate-like intermediate and its pathway of formation from oxaloacetate or fumarate.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19821037 F.Zoccarato, L.Cavallini, and A.Alexandre (2009).
Succinate is the controller of O2-/H2O2 release at mitochondrial complex I : negative modulation by malate, positive by cyanide.
  J Bioenerg Biomembr, 41, 387-393.  
19536822 G.Zoppellaro, K.L.Bren, A.A.Ensign, E.Harbitz, R.Kaur, H.P.Hersleth, U.Ryde, L.Hederstedt, and K.K.Andersson (2009).
Review: studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis-histidine and histidine-methionine axial iron coordination.
  Biopolymers, 91, 1064-1082.  
19710024 J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, and G.Cecchini (2009).
Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.
  J Biol Chem, 284, 29836-29846.
PDB codes: 2wdq 2wdr 2wdv
18385138 T.M.Tomasiak, E.Maklashina, G.Cecchini, and T.M.Iverson (2008).
A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II.
  J Biol Chem, 283, 15460-15468.
PDB code: 3cir
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