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28  structures 11812  species 2  interactions 24419  sequences 10  architectures

Family: PFL-like (PF02901)

Summary: Pyruvate formate lyase-like

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Pyruvate formate lyase-like Provide feedback

This family of enzymes includes pyruvate formate lyase [1] choline trimethylamine lyase [2] glycerol dehydratase [3] 4-hydroxyphenylacetate decarboxylase [4] and benzylsuccinate synthase [5].

Literature references

  1. Becker A, Fritz-Wolf K, Kabsch W, Knappe J, Schultz S, Volker Wagner AF; , Nat Struct Biol 1999;6:969-975.: Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase. PUBMED:10504733 EPMC:10504733

  2. Craciun S, Balskus EP;, Proc Natl Acad Sci U S A. 2012;109:21307-21312.: Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme. PUBMED:23151509 EPMC:23151509

  3. O'Brien JR, Raynaud C, Croux C, Girbal L, Soucaille P, Lanzilotta WN;, Biochemistry. 2004;43:4635-4645.: Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization. PUBMED:15096031 EPMC:15096031

  4. Selmer T, Andrei PI;, Eur J Biochem. 2001;268:1363-1372.: p-Hydroxyphenylacetate decarboxylase from Clostridium difficile. A novel glycyl radical enzyme catalysing the formation of p-cresol. PUBMED:11231288 EPMC:11231288

  5. Leuthner B, Leutwein C, Schulz H, Horth P, Haehnel W, Schiltz E, Schagger H, Heider J; , Mol Microbiol 1998;28:615-628.: Biochemical and genetic characterization of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism. PUBMED:9632263 EPMC:9632263

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004184

Pyruvate formate lyase (PFL) catalyzes the non-oxidative conversion of pyruvate and CoA to formate and acetyl-CoA. Several other enzymes have been identified in the pyruvate formate lyase family: ketoacid formate lyase, glycerol dehydratase (GD), benzyl succinate synthetase and p-hydroxyphenylacetate decarboxylase [PUBMED:10425676, PUBMED:16414072].

The PFL domain has a unique alpha/beta barrel arrangement, with five 'up' strands and three 'down' strands; the up and down strands are linked by a unique beta finger that carries a key thiyl radical [PUBMED:10425676, PUBMED:16414072].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PFL-like (CL0339), which has the following description:

The N- and C-terminal halves of the structure have similar topologies but in some cases only one is represented by the members here, viz; the C-terminal domain of the R1 subunit of ribonucleotide reductase, and the N-terminal of PFL. The full-length structure is modelled by NRDD.

The clan contains the following 6 members:

DUF3029 DUF711 Gly_radical NRDD PFL-like Ribonuc_red_lgC


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Structural domain
Previous IDs: PFL;
Type: Family
Author: Griffiths-Jones SR
Number in seed: 126
Number in full: 24419
Average length of the domain: 582.90 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 80.10 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.3 24.3
Trusted cut-off 24.3 24.4
Noise cut-off 24.0 24.0
Model length: 648
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
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Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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There are 2 interactions for this family. More...

Gly_radical PFL-like


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PFL-like domain has been found. There are 28 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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