PDBsum entry: 3cb8

Oxidoreductase

PDB id: 3cb8

Contents

Protein chain

244 a.a. *

Ligands

VAL-SER-GLY-TYR-ALA-VAL

SF4-SAM

FMT ×4

Metals

_NA

Waters ×12

* Residue conservation analysis

PDB id:

3cb8

Name:

Oxidoreductase

Title:

4fe-4s-pyruvate formate-lyase activating enzyme in complex with adomet and a peptide substrate

Structure:

Pyruvate formate-lyase 1-activating enzyme. Chain: a. Synonym: pfl-activating enzyme, formatE-C- acetyltransferase-activating enzyme 1. Engineered: yes. Peptide substrate vsgyav. Chain: b. Engineered: yes

Source:

Escherichia coli. Gene: pfla. Expressed in: escherichia coli. Synthetic: yes. Other_details: the peptide was synthesized by celtek peptides

Resolution:

2.77Å R-factor: 0.229 R-free: 0.254

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:

21-Feb-08 Release date: 28-Oct-08

Protein chain

P0A9N4  (PFLA_ECOLI) -  Pyruvate formate-lyase 1-activating enzyme

Seq: 246 a.a.

Struc: 244 a.a.

Enzyme reactions

• Enzyme class: E.C.1.97.1.4 - [Formate-C-acetyltransferase]-activating enzyme.
• Reaction: S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical

S-adenosyl-L-methionine (Bound ligand (Het Group name = SAM) corresponds exactly) + dihydroflavodoxin + [formate C-acetyltransferase]-glycine (Bound ligand (Het Group name = GLY) matches with 44.00% similarity) = 5'-deoxyadenosine + L-methionine (Bound ligand (Het Group name = VAL) matches with 70.00% similarity) + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical

• Cofactor: Iron-sulfur

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: oxidation reduction (4 terms)
• Biochemical function: catalytic activity (6 terms)

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.