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PDBsum entry 1kek

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1kek
Jmol
Contents
Protein chains
1231 a.a. *
Ligands
SF4 ×6
HTL ×2
CO2 ×2
Metals
_MG ×2
_CA ×2
Waters ×1893
* Residue conservation analysis
PDB id:
1kek
Name: Oxidoreductase
Title: Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase
Structure: Pyruvate-ferredoxin oxidoreductase. Chain: a, b. Ec: 1.2.7.1
Source: Desulfovibrio africanus. Organism_taxid: 873
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.178     R-free:   0.227
Authors: E.Chabriere,X.Vernede,B.Guigliarelli,M.-H.Charon, E.C.Hatchikian,J.C.Fontecilla-Camps
Key ref:
E.Chabrière et al. (2001). Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase. Science, 294, 2559-2563. PubMed id: 11752578 DOI: 10.1126/science.1066198
Date:
16-Nov-01     Release date:   21-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P94692  (P94692_DESAF) -  Pyruvate synthase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1232 a.a.
1231 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
DOI no: 10.1126/science.1066198 Science 294:2559-2563 (2001)
PubMed id: 11752578  
 
 
Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase.
E.Chabrière, X.Vernède, B.Guigliarelli, M.H.Charon, E.C.Hatchikian, J.C.Fontecilla-Camps.
 
  ABSTRACT  
 
In anaerobic organisms, the decarboxylation of pyruvate, a crucial component of intermediary metabolism, is catalyzed by the metalloenzyme pyruvate: ferredoxin oxidoreductase (PFOR) resulting in the generation of low potential electrons and the subsequent acetylation of coenzyme A (CoA). PFOR is the only enzyme for which a stable acetyl thiamine diphosphate (ThDP)-based free radical reaction intermediate has been identified. The 1.87 A-resolution structure of the radical form of PFOR from Desulfovibrio africanus shows that, despite currently accepted ideas, the thiazole ring of the ThDP cofactor is markedly bent, indicating a drastic reduction of its aromaticity. In addition, the bond connecting the acetyl group to ThDP is unusually long, probably of the one-electron type already described for several cation radicals but not yet found in a biological system. Taken together, our data, along with evidence from the literature, suggest that acetyl-CoA synthesis by PFOR proceeds via a condensation mechanism involving acetyl (PFOR-based) and thiyl (CoA-based) radicals.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. (A) Stereo pair of the acetyl-ThDP moiety and the bound CO[2 ]molecule of PFOR and their protein environment. (B) Stereo pair of the superposition of a part of the active site of PFOR in the uncomplexed (green), and radical forms. The movements of the thiazole ring and the side chains of Asn996 and Tyr994 are concerted, and the S1 atom from the thiazole ring keeps its hydrogen bond to Asn996 in the two conformations. Part (A) was prepared using Molscript (39) and Raster3d (40); (B) was prepared with Turbo-Frodo (38).
Figure 4.
Fig. 4. Postulated mechanism of acetyl-CoA synthesis by PFOR. Only the thiazolium ring moiety of ThDP is fully depicted (R and R' as in Fig. 1, B and C). (A) Deprotonated carbanion species (see Fig. 1A). The proton is putatively bound to 4'-iminopyridimine (not shown). (B) Pyruvate decarboxylation and hypothetical enamine formation; the CO[2] reaction product stays in the active site. (C) One electron transfer from the active site to one of the [4Fe4S] clusters. Hypothetical n cation radical formation. (D) Observed /n cation radical with a long C2-C2 bond (27) and a bent thiazole ring (Fig. 2). Note that (i) ketonization of the enamine (B) upon radical formation (C) and (ii) tautomerization of the C5-C4 double bond to a C4-C4 double bond, in going from (B) to (C), are required to explain the observed stereochemistry of the adduct. The net result of these two rearrangements is a significant reduction in the aromaticity of the thiazole ring. Because this process is generally considered to be unfavorable, the protein environment is thought to play a key role in the stabilization of (C) and (D). The loss of one electron from the active site and the bending of the thiazole ring are shown here as a single step because we do not know the detailed sequence of events. (E) Hypothetical fragmented C-C bond resulting in carbocation and acetyl radical species (28, 29). Upon fragmentation, the aromaticity of the thiazole ring is thought to be restored (A), closing the cycle. (F) Acetyl-CoA synthesis through condensation of a thiyl CoA radical with the acetyl radical. Although the reaction is shown in the direction of acetyl-CoA synthesis, PFORs are capable of catalyzing the reverse reaction.
 
  The above figures are reprinted by permission from the AAAs: Science (2001, 294, 2559-2563) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20414806 R.S.Gupta (2010).
Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups.
  Photosynth Res, 104, 357-372.  
20015072 T.Ikeda, M.Yamamoto, H.Arai, D.Ohmori, M.Ishii, and Y.Igarashi (2010).
Enzymatic and electron paramagnetic resonance studies of anabolic pyruvate synthesis by pyruvate: ferredoxin oxidoreductase from Hydrogenobacter thermophilus.
  FEBS J, 277, 501-510.  
  20885930 T.Iwasaki (2010).
Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus.
  Archaea, 2010, 0.  
19805340 B.G.Han, M.Dong, H.Liu, L.Camp, J.Geller, M.Singer, T.C.Hazen, M.Choi, H.E.Witkowska, D.A.Ball, D.Typke, K.H.Downing, M.Shatsky, S.E.Brenner, J.M.Chandonia, M.D.Biggin, and R.M.Glaeser (2009).
Survey of large protein complexes in D. vulgaris reveals great structural diversity.
  Proc Natl Acad Sci U S A, 106, 16580-16585.  
19476487 K.Tittmann (2009).
Reaction mechanisms of thiamin diphosphate enzymes: redox reactions.
  FEBS J, 276, 2454-2468.  
18066702 S.M.da Silva, S.S.Venceslau, C.L.Fernandes, F.M.Valente, and I.A.Pereira (2008).
Hydrogen as an energy source for the human pathogen Bilophila wadsworthia.
  Antonie Van Leeuwenhoek, 93, 381-390.  
18378591 S.W.Ragsdale (2008).
Enzymology of the wood-Ljungdahl pathway of acetogenesis.
  Ann N Y Acad Sci, 1125, 129-136.  
18801467 S.W.Ragsdale, and E.Pierce (2008).
Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation.
  Biochim Biophys Acta, 1784, 1873-1898.  
17475535 J.J.Cotelesage, J.Puttick, H.Goldie, B.Rajabi, B.Novakovski, and L.T.Delbaere (2007).
How does an enzyme recognize CO2?
  Int J Biochem Cell Biol, 39, 1204-1210.
PDB codes: 2olq 2olr
17158936 P.S.Hoffman, G.Sisson, M.A.Croxen, K.Welch, W.D.Harman, N.Cremades, and M.G.Morash (2007).
Antiparasitic drug nitazoxanide inhibits the pyruvate oxidoreductases of Helicobacter pylori, selected anaerobic bacteria and parasites, and Campylobacter jejuni.
  Antimicrob Agents Chemother, 51, 868-876.  
16680160 G.Wille, D.Meyer, A.Steinmetz, E.Hinze, R.Golbik, and K.Tittmann (2006).
The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.
  Nat Chem Biol, 2, 324-328.
PDB codes: 2ez4 2ez8 2ez9 2ezt 2ezu
16752902 S.O.Mansoorabadi, J.Seravalli, C.Furdui, V.Krymov, G.J.Gerfen, T.P.Begley, J.Melnick, S.W.Ragsdale, and G.H.Reed (2006).
EPR spectroscopic and computational characterization of the hydroxyethylidene-thiamine pyrophosphate radical intermediate of pyruvate:ferredoxin oxidoreductase.
  Biochemistry, 45, 7122-7131.  
16704345 W.Buckel, and B.T.Golding (2006).
Radical enzymes in anaerobes.
  Annu Rev Microbiol, 60, 27-49.  
12146957 C.Furdui, and S.W.Ragsdale (2002).
The roles of coenzyme A in the pyruvate:ferredoxin oxidoreductase reaction mechanism: rate enhancement of electron transfer from a radical intermediate to an iron-sulfur cluster.
  Biochemistry, 41, 9921-9937.  
12383259 V.I.Bunik, and C.Sievers (2002).
Inactivation of the 2-oxo acid dehydrogenase complexes upon generation of intrinsic radical species.
  Eur J Biochem, 269, 5004-5015.  
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.