Top Level Name

  ⌊ Superfamily (core) Radical SAM

    ⌊ Subgroup organic radical-activating enzymes

  activating enzymes, group 2

     ⌊ Family pyruvate formate-lyase activase

Total 100% <100%
Functional domains 3653 3612 41
UniProtKB 21042 20982 60
GI 37239 37095 144
Structures 3
Reactions 1
Functional domains of this family were last updated on June 28, 2017
New functional domains were last added to this family on June 22, 2014

Pyruvate formate lyase activating enzyme (PFL-AE) is a member of the Radical SAM superfamily that functions by catalyzing the formation of the Gly734 radical of PFL.

Characterization using rapid freeze-quenching to trap a catalytically competent intermediate and characterization of the intermediate by electron paramagnetic resonance, (13)C, and (57)Fe electron nuclear double-resonance spectroscopies reveals that the intermediate contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster.

Vey JL, Yang J, Li M, Broderick WE, Broderick JB, Drennan CL

Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme

▸ Abstract

Proc Natl Acad Sci U S A 2008;105(42):16137-16141 | PubMed ID: 18852451

Buis JM, Broderick JB

Pyruvate formate-lyase activating enzyme: elucidation of a novel mechanism for glycyl radical formation

▸ Abstract

Arch Biochem Biophys 2005;433(1):288-296 | PubMed ID: 15581584

Peng Y, Veneziano SE, Gillispie GD, Broderick JB

Pyruvate formate-lyase, evidence for an open conformation favored in the presence of its activating enzyme

▸ Abstract

J Biol Chem 2010;285(35):27224-27231 | PubMed ID: 20571026

Crain AV, Broderick JB

Pyruvate formate-lyase and its activation by pyruvate formate-lyase activating enzyme

▸ Abstract

J Biol Chem 2014;289(9):5723-5729 | PubMed ID: 24338017

Horitani M, Shisler K, Broderick WE, Hutcheson RU, Duschene KS, Marts AR, Hoffman BM, Broderick JB

Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond

▸ Abstract

Science 2016;352(6287):822-825 | PubMed ID: 27174986

No notes.

Sequence Similarity Networks

Download a Sequence Similarity Network of this family (XGMML format ).

Network downloads are XGMML files that are readable by program such as Cytoscape. In these networks, nodes represent proteins and edges represent pairwise similarities better than a given edge-score cutoff. The edge score is either a bit score for full networks or mean E values for a Repnet. Additionally, these networks contain several attributes with data from the SFLD.

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Full sequence similarity network is not available for this superfamily due to its size.
Repnet: 50% ID (21-May-2017)

List of files included in the download. A detailed list of included node attributes, their definitions, and their uses [revised: 1/24/2014].

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Multiple Sequence Alignment

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Multiple Sequence Alignment

Align one or multiple sequences to the alignment of a representative set of sequences of this family.
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Downloads

Data Type All (#) Known (#)
Full length FASTA (3653) ()
Complete annotation (.tsv) (3653) ()
Annotation suitable for Excel ® (.tsv) (3653) ()
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Cutoff Value
The least significant edge-score at which pairwise similarities are included in the network. A bit score for the full network, or a mean E value for the Repnet.
XGMML format
Open in Cytoscape via:
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Download the annotation of all sequences as shown in the table below as a ͟Tab ͟Separated ͟Value (TSV) file. This file can be imported into a spreadsheet application.
Full length FASTA
Full length sequences in FASTA format.
Functional Domain FASTA
Sequences of the Functional Domain in FASTA format.
Complete annotation
Download complete annotation of sequences sets of this superfamily as a ͟Tab ͟Separated ͟Value (TSV) file. This file has all data but cell size can exceed the maximum supported by spreadsheet programs (such as Microsoft Excel ®).
Spreadsheet ready annotation
Annotation of sequences sets of this superfamily in a ͟Tab ͟Separated ͟Value (TSV) file. This file can be imported into a spreadsheet application. Cells which exceed the allowed spreadsheet maximum (32.5K) are preceded by the word "Truncated" and clipped short.
Total number of functional domains in this group.
Number of Functional Domains that have been manually or automatically been assigned to a family.
Number of Functional Domains that have not been assigned to a family.
Number of structures available from the PDB for members of this group.
Number of Functional Domains with 100% of Conserved Residues
Number of Functional Domains with less than 100% Conserved Residues

Active Site

Click on the picture to download the Chimera session file for the generated image above.

Catalyzed Reaction(s)

[formate-C-acetyltransferase]-activating enzyme

+ + + + +
S-adenosyl-L-methioninate
67040
Pyruvate Formate-Lyase (inactive)
2pfl
1,5-dihydroflavin
62787
L-methionine zwitterion
57844
5'-deoxyadenosine
17319
semiquinone
15817
Pyruvate Formate-Lyase (active)
2pfl

EC: 1.97.1.4 | IntEnz: 1.97.1.4 | Kegg: 1.97.1.4 | BioCyc: 1.97.1.4 | BRENDA: 1.97.1.4