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PDBsum entry 2pfl

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protein metals Protein-protein interface(s) links
Lyase PDB id
2pfl
Jmol
Contents
Protein chains
759 a.a. *
Metals
_NA ×2
_CL ×2
Waters ×742
* Residue conservation analysis
PDB id:
2pfl
Name: Lyase
Title: Crystal structure of pfl from e.Coli
Structure: Protein (pyruvate formate-lyase). Chain: a, b. Synonym: pfl. Ec: 2.3.1.54
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.90Å     R-factor:   0.202     R-free:   0.242
Authors: A.Becker,K.Fritz-Wolf,W.Kabsch,J.Knappe,S.Schultz,A.F.V.Wagn
Key ref:
A.Becker et al. (1999). Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase. Nat Struct Biol, 6, 969-975. PubMed id: 10504733 DOI: 10.1038/13341
Date:
26-May-99     Release date:   15-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P09373  (PFLB_ECOLI) -  Formate acetyltransferase 1
Seq:
Struc:
 
Seq:
Struc:
760 a.a.
759 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.54  - Formate C-acetyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acetyl-CoA + formate = CoA + pyruvate
Acetyl-CoA
+ formate
= CoA
+ pyruvate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1038/13341 Nat Struct Biol 6:969-975 (1999)
PubMed id: 10504733  
 
 
Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase.
A.Becker, K.Fritz-Wolf, W.Kabsch, J.Knappe, S.Schultz, A.F.Volker Wagner.
 
  ABSTRACT  
 
Pyruvate formate-lyase (PFL) from Escherichia coli uses a radical mechanism to reversibly cleave the C1-C2 bond of pyruvate using the Gly 734 radical and two cysteine residues (Cys 418, Cys 419). We have determined by X-ray crystallography the structures of PFL (non-radical form), its complex with the substrate analog oxamate, and the C418A,C419A double mutant. The atomic model (a dimer of 759-residue monomers) comprises a 10-stranded beta/alpha barrel assembled in an antiparallel manner from two parallel five-stranded beta-sheets; this architecture resembles that of ribonucleotide reductases. Gly 734 and Cys 419, positioned at the tips of opposing hairpin loops, meet in the apolar barrel center (Calpha-Sgamma = 3.7 A). Oxamate fits into a compact pocket where C2 is juxtaposed with Cys 418Sgamma (3.3 A), which in turn is close to Cys 419Sgamma (3.7 A). Our model of the active site is suggestive of a snapshot of the catalytic cycle, when the pyruvate-carbonyl awaits attack by the Cys 418 thiyl radical. We propose a homolytic radical mechanism for PFL that involves Cys 418 and Cys 419 both as thiyl radicals, with distinct chemical functions.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo view of C traces of the PFL dimer in complex with oxamate. The numbers refer to amino acid residues. The position of Arg 624, the primary site of limited proteolysis by trypsin^8, is indicated by an asterisk. The two oxamates (shown as ball and stick) marking the active sites in the dimer are 60 Å apart. Catalytic residues Cys 418, Cys 419 and Gly 734 are colored in cyan.
Figure 7.
Figure 7. Structure of the active site. a, Stereo view with bound oxamate. The model can be conceived as depicting the stage in the catalytic cycle where Cys 418 thiyl is ready to attack C2 of pyruvate (see Fig. 8b). b, Ensemble of catalytic amino acid residues and the substrate molecule. c, Schematic representation. Distances are in angstrom units; residues Tyr 172, Ala 417, Val 420, Ser 733 and Tyr 735 shown in (a) are omitted for clarity.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 969-975) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20191656 E.N.Marsh, D.P.Patterson, and L.Li (2010).
Adenosyl radical: reagent and catalyst in enzyme reactions.
  Chembiochem, 11, 604-621.  
19159265 L.Li, D.P.Patterson, C.C.Fox, B.Lin, P.W.Coschigano, and E.N.Marsh (2009).
Subunit structure of benzylsuccinate synthase.
  Biochemistry, 48, 1284-1292.  
19309133 S.Naumov, and C.Schöneich (2009).
Intramolecular addition of cysteine thiyl radical to phenylalanine and tyrosine in model peptides, Phe (CysS*) and Tyr(CysS*): a computational study.
  J Phys Chem A, 113, 3560-3565.  
18245276 A.Hemschemeier, J.Jacobs, and T.Happe (2008).
Biochemical and physiological characterization of the pyruvate formate-lyase Pfl1 of Chlamydomonas reinhardtii, a typically bacterial enzyme in a eukaryotic alga.
  Eukaryot Cell, 7, 518-526.  
18356528 A.R.Richardson, S.J.Libby, and F.C.Fang (2008).
A nitric oxide-inducible lactate dehydrogenase enables Staphylococcus aureus to resist innate immunity.
  Science, 319, 1672-1676.  
18852451 J.L.Vey, J.Yang, M.Li, W.E.Broderick, J.B.Broderick, and C.L.Drennan (2008).
Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.
  Proc Natl Acad Sci U S A, 105, 16137-16141.
PDB codes: 3c8f 3cb8
18442083 K.Condić-Jurkić, V.T.Perchyonok, H.Zipse, and D.M.Smith (2008).
On the modeling of arginine-bound carboxylates: a case study with Pyruvate Formate-Lyase.
  J Comput Chem, 29, 2425-2433.  
17961174 O.Grundmann, A.Behrends, R.Rabus, J.Amann, T.Halder, J.Heider, and F.Widdel (2008).
Genes encoding the candidate enzyme for anaerobic activation of n-alkanes in the denitrifying bacterium, strain HxN1.
  Environ Microbiol, 10, 376-385.  
18973367 T.Nauser, G.Casi, W.H.Koppenol, and C.Schöneich (2008).
Reversible intramolecular hydrogen transfer between cysteine thiyl radicals and glycine and alanine in model peptides: absolute rate constants derived from pulse radiolysis and laser flash photolysis.
  J Phys Chem B, 112, 15034-15044.  
17898896 A.Marquet, B.T.Bui, A.G.Smith, and M.J.Warren (2007).
Iron-sulfur proteins as initiators of radical chemistry.
  Nat Prod Rep, 24, 1027-1040.  
17983264 C.H.Yeang, and D.Haussler (2007).
Detecting coevolution in and among protein domains.
  PLoS Comput Biol, 3, e211.  
17954980 D.K.Simanshu, S.Chittori, H.S.Savithri, and M.R.Murthy (2007).
Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate.
  J Biosci, 32, 1195-1206.  
16968710 J.C.Pieck, U.Hennecke, A.J.Pierik, M.G.Friedel, and T.Carell (2006).
Characterization of a new thermophilic spore photoproduct lyase from Geobacillus stearothermophilus (SplG) with defined lesion containing DNA substrates.
  J Biol Chem, 281, 36317-36326.  
16756507 P.Nordlund, and P.Reichard (2006).
Ribonucleotide reductases.
  Annu Rev Biochem, 75, 681-706.  
16704345 W.Buckel, and B.T.Golding (2006).
Radical enzymes in anaerobes.
  Annu Rev Microbiol, 60, 27-49.  
16332871 J.Singh, D.Kumar, N.Ramakrishnan, V.Singhal, J.Jervis, J.F.Garst, S.M.Slaughter, A.M.DeSantis, M.Potts, and R.F.Helm (2005).
Transcriptional response of Saccharomyces cerevisiae to desiccation and rehydration.
  Appl Environ Microbiol, 71, 8752-8763.  
16218870 T.Selmer, A.J.Pierik, and J.Heider (2005).
New glycyl radical enzymes catalysing key metabolic steps in anaerobic bacteria.
  Biol Chem, 386, 981-988.  
15352329 G.Gelius-Dietrich, and K.Henze (2004).
Pyruvate formate lyase (PFL) and PFL activating enzyme in the chytrid fungus Neocallimastix frontalis: a free-radical enzyme system conserved across divergent eukaryotic lineages.
  J Eukaryot Microbiol, 51, 456-463.  
15475969 K.M.Larsson, A.Jordan, R.Eliasson, P.Reichard, D.T.Logan, and P.Nordlund (2004).
Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase.
  Nat Struct Mol Biol, 11, 1142-1149.
PDB codes: 1xje 1xjf 1xjg 1xjj 1xjk 1xjm 1xjn
15289575 Y.Nicolet, and C.L.Drennan (2004).
AdoMet radical proteins--from structure to evolution--alignment of divergent protein sequences reveals strong secondary structure element conservation.
  Nucleic Acids Res, 32, 4015-4025.  
14633981 G.Layer, J.Moser, D.W.Heinz, D.Jahn, and W.D.Schubert (2003).
Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes.
  EMBO J, 22, 6214-6224.
PDB code: 1olt
12714601 N.V.Bykova, A.Stensballe, H.Egsgaard, O.N.Jensen, and I.M.Moller (2003).
Phosphorylation of formate dehydrogenase in potato tuber mitochondria.
  J Biol Chem, 278, 26021-26030.  
12009915 A.Adrait, M.Ohrström, A.L.Barra, L.Thelander, and A.Gräslund (2002).
EPR studies on a stable sulfinyl radical observed in the iron-oxygen-reconstituted Y177F/I263C protein R2 double mutant of ribonucleotide reductase from mouse.
  Biochemistry, 41, 6510-6516.  
12163496 A.Becker, and W.Kabsch (2002).
X-ray structure of pyruvate formate-lyase in complex with pyruvate and CoA. How the enzyme uses the Cys-418 thiyl radical for pyruvate cleavage.
  J Biol Chem, 277, 40036-40042.
PDB codes: 1h16 1h17 1h18
12454503 L.Lehtiö, V.M.Leppänen, J.W.Kozarich, and A.Goldman (2002).
Structure of Escherichia coli pyruvate formate-lyase with pyruvate.
  Acta Crystallogr D Biol Crystallogr, 58, 2209-2212.
PDB code: 1mzo
11404104 F.Widdel, and R.Rabus (2001).
Anaerobic biodegradation of saturated and aromatic hydrocarbons.
  Curr Opin Biotechnol, 12, 259-276.  
11166566 J.Stubbe, J.Ge, and C.S.Yee (2001).
The evolution of ribonucleotide reduction revisited.
  Trends Biochem Sci, 26, 93-99.  
11395404 P.A.Frey (2001).
Radical mechanisms of enzymatic catalysis.
  Annu Rev Biochem, 70, 121-148.  
11160102 R.Rabus, H.Wilkes, A.Behrends, A.Armstroff, T.Fischer, A.J.Pierik, and F.Widdel (2001).
Anaerobic initial reaction of n-alkanes in a denitrifying bacterium: evidence for (1-methylpentyl)succinate as initial product and for involvement of an organic radical in n-hexane metabolism.
  J Bacteriol, 183, 1707-1715.  
11231288 T.Selmer, and P.I.Andrei (2001).
p-Hydroxyphenylacetate decarboxylase from Clostridium difficile. A novel glycyl radical enzyme catalysing the formation of p-cresol.
  Eur J Biochem, 268, 1363-1372.  
11114511 J.Stubbe (2000).
Ribonucleotide reductases: the link between an RNA and a DNA world?
  Curr Opin Struct Biol, 10, 731-736.  
10574800 H.Eklund, and M.Fontecave (1999).
Glycyl radical enzymes: a conservative structural basis for radicals.
  Structure, 7, R257-R262.  
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.