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PDBsum entry 1kf6

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1kf6
Jmol
Contents
Protein chains
577 a.a. *
243 a.a. *
130 a.a. *
119 a.a. *
Ligands
OAA ×2
ACT ×3
FAD ×2
1PE
FES ×2
F3S ×2
SF4 ×2
HQO ×2
CE1 ×5
Metals
__K ×2
Waters ×16
* Residue conservation analysis
PDB id:
1kf6
Name: Oxidoreductase
Title: E. Coli quinol-fumarate reductase with bound inhibitor hqno
Structure: Fumarate reductase flavoprotein. Chain: a, m. Engineered: yes. Fumarate reductase iron-sulfur protein. Chain: b, n. Engineered: yes. Fumarate reductase 15 kda hydrophobic protein. Chain: c, o. Engineered: yes.
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PQS)
Resolution:
2.70Å     R-factor:   0.231     R-free:   0.280
Authors: T.M.Iverson,C.Luna-Chavez,L.R.Croal,G.Cecchini,D.C.Rees
Key ref:
T.M.Iverson et al. (2002). Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site. J Biol Chem, 277, 16124-16130. PubMed id: 11850430 DOI: 10.1074/jbc.M200815200
Date:
19-Nov-01     Release date:   13-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00363  (FRDA_ECOLI) -  Fumarate reductase flavoprotein subunit
Seq:
Struc:
 
Seq:
Struc:
602 a.a.
577 a.a.
Protein chains
Pfam   ArchSchema ?
P0AC47  (FRDB_ECOLI) -  Fumarate reductase iron-sulfur subunit
Seq:
Struc:
244 a.a.
243 a.a.
Protein chains
Pfam   ArchSchema ?
P0A8Q0  (FRDC_ECOLI) -  Fumarate reductase subunit C
Seq:
Struc:
131 a.a.
130 a.a.
Protein chains
Pfam   ArchSchema ?
P0A8Q3  (FRDD_ECOLI) -  Fumarate reductase subunit D
Seq:
Struc:
119 a.a.
119 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chains A, M: E.C.1.3.5.4  - Fumarate reductase (quinol).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Succinate + a quinone = fumarate + a quinol
Succinate
Bound ligand (Het Group name = OAA)
matches with 88.89% similarity
+ quinone
= fumarate
+ quinol
   Enzyme class 3: Chains B, N: E.C.1.3.5.1  - Succinate dehydrogenase (quinone).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: Succinate + a quinone = fumarate + a quinol
Succinate
+ quinone
= fumarate
+ quinol
      Cofactor: FAD; Iron-sulfur
FAD
Iron-sulfur
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
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     response to DNA damage stimulus   9 terms 
  Biochemical function     electron carrier activity     11 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M200815200 J Biol Chem 277:16124-16130 (2002)
PubMed id: 11850430  
 
 
Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site.
T.M.Iverson, C.Luna-Chavez, L.R.Croal, G.Cecchini, D.C.Rees.
 
  ABSTRACT  
 
The quinol-fumarate reductase (QFR) respiratory complex of Escherichia coli is a four-subunit integral-membrane complex that catalyzes the final step of anaerobic respiration when fumarate is the terminal electron acceptor. The membrane-soluble redox-active molecule menaquinol (MQH(2)) transfers electrons to QFR by binding directly to the membrane-spanning region. The crystal structure of QFR contains two quinone species, presumably MQH(2), bound to the transmembrane-spanning region. The binding sites for the two quinone molecules are termed Q(P) and Q(D), indicating their positions proximal (Q(P)) or distal (Q(D)) to the site of fumarate reduction in the hydrophilic flavoprotein and iron-sulfur protein subunits. It has not been established whether both of these sites are mechanistically significant. Co-crystallization studies of the E. coli QFR with the known quinol-binding site inhibitors 4,6-dinitrophenol establish that both inhibitors block the binding of MQH(2) at the Q(P) site. In the structures with the inhibitor bound at Q(P), no density is observed at Q(D), which suggests that the occupancy of this site can vary and argues against a structurally obligatory role for quinol binding to Q(D). A comparison of the Q(P) site of the E. coli enzyme with quinone-binding sites in other respiratory enzymes shows that an acidic residue is structurally conserved. This acidic residue, Glu-C29, in the E. coli enzyme may act as a proton shuttle from the quinol during enzyme turnover.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Polypeptide -fold and electron transfer distances in QFR. A, ribbon diagram views of the E. coli QFR separated by a 90° rotation about a vertical axis. The flavoprotein is shown in blue, the iron protein is in red, and the transmembrane anchors are in dark green (FrdC) and purple (FrdD). The approximate boundary of the membrane is indicated with a black line. B, inter-cofactor distances of the E. coli enzyme. The known cofactors are superimposed onto an outline of the enzyme. C, inter-cofactor distances in the W. succinogenes enzyme. The b-type hemes associated with the membrane anchor reduce the electron transfer distance between a predicted distal quinol-binding site (data not shown). Figs. 1, 3, and 4 were made using Molscript (56), Bobscript (57), and Raster3D (58).
Figure 2.
Fig. 2. Chemical structures for oxidized menaquinone-8 (MQ-8) (A), reduced menaquinol-8 (B), HQNO (C), and DNP-19 (D). MQ-8 is the primary menaquinone found in E. coli membranes, but smaller proportions of MQ-6, MQ-7, and MQ-9 are additionally present in the organism (59).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 16124-16130) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20802208 Z.Itzhaki, E.Akiva, and H.Margalit (2010).
Preferential use of protein domain pairs as interaction mediators: order and transitivity.
  Bioinformatics, 26, 2564-2570.  
19170876 H.D.Juhnke, H.Hiltscher, H.R.Nasiri, H.Schwalbe, and C.R.Lancaster (2009).
Production, characterization and determination of the real catalytic properties of the putative 'succinate dehydrogenase' from Wolinella succinogenes.
  Mol Microbiol, 71, 1088-1101.  
19820092 Y.L.Chiang, Y.C.Hsieh, J.Y.Fang, E.H.Liu, Y.C.Huang, P.Chuankhayan, J.Jeyakanthan, M.Y.Liu, S.I.Chan, and C.J.Chen (2009).
Crystal structure of Adenylylsulfate reductase from Desulfovibrio gigas suggests a potential self-regulation mechanism involving the C terminus of the beta-subunit.
  J Bacteriol, 191, 7597-7608.
PDB code: 3gyx
17972330 K.Jantama, M.J.Haupt, S.A.Svoronos, X.Zhang, J.C.Moore, K.T.Shanmugam, and L.O.Ingram (2008).
Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate.
  Biotechnol Bioeng, 99, 1140-1153.  
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
17989224 Q.M.Tran, R.A.Rothery, E.Maklashina, G.Cecchini, and J.H.Weiner (2007).
Escherichia coli succinate dehydrogenase variant lacking the heme b.
  Proc Natl Acad Sci U S A, 104, 18007-18012.  
17534481 X.Liang, D.J.Campopiano, and P.J.Sadler (2007).
Metals in membranes.
  Chem Soc Rev, 36, 968-992.  
16815920 A.Oberai, Y.Ihm, S.Kim, and J.U.Bowie (2006).
A limited universe of membrane protein families and folds.
  Protein Sci, 15, 1723-1734.  
16371358 L.S.Huang, G.Sun, D.Cobessi, A.C.Wang, J.T.Shen, E.Y.Tung, V.E.Anderson, and E.A.Berry (2006).
3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.
  J Biol Chem, 281, 5965-5972.
PDB codes: 1yq3 1yq4 2fbw
17139260 M.L.Rodrigues, T.F.Oliveira, I.A.Pereira, and M.Archer (2006).
X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination.
  EMBO J, 25, 5951-5960.
PDB code: 2j7a
16603087 S.S.Krishna, R.I.Sadreyev, and N.V.Grishin (2006).
A tale of two ferredoxins: sequence similarity and structural differences.
  BMC Struct Biol, 6, 8.  
16098782 A.Sevilla, J.W.Schmid, K.Mauch, J.L.Iborra, M.Reuss, and M.Cánovas (2005).
Model of central and trimethylammonium metabolism for optimizing L-carnitine production by E. coli.
  Metab Eng, 7, 401-425.  
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.  
15654871 R.A.Rothery, A.M.Seime, A.M.Spiers, E.Maklashina, I.Schröder, R.P.Gunsalus, G.Cecchini, and J.H.Weiner (2005).
Defining the Q-site of Escherichia coli fumarate reductase by site-directed mutagenesis, fluorescence quench titrations and EPR spectroscopy.
  FEBS J, 272, 313-326.  
15182355 R.Giordani, and J.Buc (2004).
Evidence for two different electron transfer pathways in the same enzyme, nitrate reductase A from Escherichia coli.
  Eur J Biochem, 271, 2400-2407.  
12592029 B.D.Silverman (2003).
Hydrophobicity of transmembrane proteins: spatially profiling the distribution.
  Protein Sci, 12, 586-599.  
14527321 G.Cecchini (2003).
Function and structure of complex II of the respiratory chain.
  Annu Rev Biochem, 72, 77.  
12515859 H.Miyadera, K.Shiomi, H.Ui, Y.Yamaguchi, R.Masuma, H.Tomoda, H.Miyoshi, A.Osanai, K.Kita, and S.Omura (2003).
Atpenins, potent and specific inhibitors of mitochondrial complex II (succinate-ubiquinone oxidoreductase).
  Proc Natl Acad Sci U S A, 100, 473-477.  
14511372 M.G.Almeida, S.Macieira, L.L.Gonçalves, R.Huber, C.A.Cunha, M.J.Romão, C.Costa, J.Lampreia, J.J.Moura, and I.Moura (2003).
The isolation and characterization of cytochrome c nitrite reductase subunits (NrfA and NrfH) from Desulfovibrio desulfuricans ATCC 27774. Re-evaluation of the spectroscopic data and redox properties.
  Eur J Biochem, 270, 3904-3915.  
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.