PDBsum entry: 3c8f

Oxidoreductase

PDB-id: 3c8f

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

245 a.a. *

Ligands

SF4

MT2

PGE

Waters ×60

* Residue conservation analysis

Tools

Clefts Calculation

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)

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

Quick_links

Procheck

Clefts

Surface

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.