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Oxidoreductase PDB-id
3c8f
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Description
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Protein chain
245 a.a. *
Ligands
SF4
MT2
PGE
Waters ×60

* Residue conservation analysis
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PDB id: 3c8f
Name: Oxidoreductase
Title: 4fe-4s-pyruvate formate-lyase activating enzyme with partially disordered adomet

Structure:
Pyruvate formate-lyase 1-activating enzyme. Chain: a. Synonym: pfl-activating enzyme, formatE-C- acetyltransferase-activating enzyme 1. Engineered: yes

Source:
Escherichia coli. Gene: pfla. Expressed in: escherichia coli.

UniProt:
P0A9N4 (PFLA_ECOLI) Pfam   ArchSchema ?
Seq: 246 a.a.
Struc: 245 a.a.
Key:    PfamA domain  Secondary structure

Enzyme class:
E.C.1.97.1.4   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:
S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical (see diagram below)

Cofactor:
Iron-sulfur

Resolution:
2.25Å

R-factor:
0.224

R-free:
0.298

Authors:
J.L.Vey,C.L.Drennan

Key ref:
J.L.Vey et al. (2008). Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.. Proc Natl Acad Sci U S A, 105, 16137-16141. [PubMed id: 18852451] [DOI: 10.1073/pnas.0806640105]

Date:
11-Feb-08

Release date:
28-Oct-08
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Enzyme reaction for E.C.1.97.1.4


S-adenosyl-L-methionine
+ dihydroflavodoxin
+ [formate acetyltransferase]-glycine
=
5'-deoxyadenosine
+
methionine
+ flavodoxin
+ [formate acetyltransferase]-glycine-2-yl radical
Cofactor


Iron-sulfur
Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

 
    Key reference    
 
 
DOI no: 10.1073/pnas.0806640105 Proc Natl Acad Sci U S A 105:16137-16141 (2008)
PubMed id: 18852451  
 
 
Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme.
J.L.Vey, J.Yang, M.Li, W.E.Broderick, J.B.Broderick, C.L.Drennan.
 
  ABSTRACT  
 
Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G(734) of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G(734). Our structures provide fundamental insights into the interactions between the activase and the G(734) loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G(734) of pyruvate formate-lyase.
 
  Selected figure(s)  
 
Figure 1.
Stereoview of PFL-AE with secondary structural elements assigned numerically (helices in cyan, strands in yellow). The loops after strands β1′, β1, and β6 are labeled A (red, residues 10–20), B (purple, residues 27–47), and C (orange, residues 201–225). The 4Fe-4S cluster (ruby and gold), AdoMet (green carbons), and peptide (teal carbons) are depicted in sticks with oxygens colored red and nitrogens colored blue.
Figure 2.
Substrate and cofactor binding. Colors are as in Fig. 1, with protein side chain carbons in gray. Conserved motifs (33) are labeled in blue. Composite omit maps are shown as a blue mesh and are contoured at 1σ. Hydrogen bond lengths and other distances are represented as dashed lines. (A) Detail of cluster–AdoMet interaction with composite omit map contoured around the AdoMet. Distances of interest between the unique iron of the 4Fe-4S cluster and AdoMet atoms are shown. (B) AdoMet–protein interactions. (C) Peptide–protein interactions. (D) Omit map contoured around the peptide.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19752030 H.Yesilkaya, F.Spissu, S.M.Carvalho, V.S.Terra, K.A.Homer, R.Benisty, N.Porat, A.R.Neves, and P.W.Andrew (2009).
Pyruvate formate lyase is required for pneumococcal fermentative metabolism and virulence.
  Infect Immun, 77, 5418-5427.  
19706452 Y.Nicolet, P.Amara, J.M.Mouesca, and J.C.Fontecilla-Camps (2009).
Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins.
  Proc Natl Acad Sci U S A, 106, 14867-14871.
PDB codes: 3iix 3iiz
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