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318  structures 7687  species 0  interactions 14442  sequences 42  architectures

Family: Pep_deformylase (PF01327)

Summary: Polypeptide deformylase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Polypeptide deformylase Provide feedback

No Pfam abstract.

Literature references

  1. Meinnel T, Blanquet S, Dardel F; , J Mol Biol 1996;262:375-386.: A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase. PUBMED:8845003 EPMC:8845003

  2. Dardel F, Ragusa S, Lazennec C, Blanquet S, Meinnel T; , J Mol Biol 1998;280:501-513.: Solution structure of nickel-peptide deformylase. PUBMED:9665852 EPMC:9665852


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR023635

Peptide deformylase (PDF) is an essential metalloenzyme required for the removal of the formyl group at the N terminus of nascent polypeptide chains in eubacteria: EC [ PUBMED:9846875 ]. The enzyme acts as a monomer and binds a single metal ion, catalysing the reaction: N-formyl-L-methionine + H 2 O = formate + methionyl peptide Catalytic efficiency strongly depends on the identity of the bound metal [ PUBMED:9565550 ].

The structure of these enzymes is known [ PUBMED:8845003 , PUBMED:9665852 ]. PDF, a zinc metalloenzyme from the mitochondrion, comprises an active core domain of 147 residues and a C-terminal tail of 21 residue. The 3D fold of the catalytic core has been determined by X-ray crystallography and NMR. Overall, the structure contains a series of anti-parallel beta-strands that surround two perpendicular alpha-helices. The C-terminal helix contains the characteristic HEXXH motif of metalloenzymes, which is crucial for activity. The helical arrangement, and the way the histidine residues bind the zinc ion, is reminiscent of metalloproteases such as thermolysin or metzincins. However, the arrangement of secondary and tertiary structures of PDF, and the positioning of its third zinc ligand (a cysteine residue), are quite different. These discrepancies, together with notable biochemical differences, suggest that PDF constitutes a new class of zinc-metalloenzymes [ PUBMED:8845003 ].

These enzymes utilize Fe(II) as the catalytic metal ion, which can be replaced with a nickel or cobalt ion with no loss of activity. There are two types of peptide deformylases, types I and II, which differ in structure only in the outer surface of the domain. Because these enzymes are essential only in prokaryotes (although eukaryotic gene sequences have been found), they are a target for a new class of antibacterial agents [ PUBMED:11738381 , PUBMED:10931273 , PUBMED:12126617 , PUBMED:12823970 ].

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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Alignments

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(75)
Full
(14442)
Representative proteomes UniProt
(65972)
RP15
(1871)
RP35
(7016)
RP55
(14970)
RP75
(25636)
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HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(75)
Full
(14442)
Representative proteomes UniProt
(65972)
RP15
(1871)
RP35
(7016)
RP55
(14970)
RP75
(25636)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(75)
Full
(14442)
Representative proteomes UniProt
(65972)
RP15
(1871)
RP35
(7016)
RP55
(14970)
RP75
(25636)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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

HMM logo

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...

Trees

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: Sarah Teichmann
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Griffiths-Jones SR
Number in seed: 75
Number in full: 14442
Average length of the domain: 154.2 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 82.8 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.8 22.8
Trusted cut-off 23.0 22.9
Noise cut-off 22.6 22.7
Model length: 159
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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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Structures

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 Pep_deformylase domain has been found. There are 318 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A077ZG17 View 3D Structure Click here
A0A0D2G1T7 View 3D Structure Click here
A0A0H3H3U3 View 3D Structure Click here
A0A0H3KB98 View 3D Structure Click here
A0A0P0V5Q2 View 3D Structure Click here
A0A0R0ELH1 View 3D Structure Click here
A0A0R0HSP6 View 3D Structure Click here
A0A1C1C6E2 View 3D Structure Click here
A0LEJ7 View 3D Structure Click here
A0LUE1 View 3D Structure Click here
A0QQP8 View 3D Structure Click here
A1A2Z1 View 3D Structure Click here
A1BHK0 View 3D Structure Click here
A1T320 View 3D Structure Click here
A1UAD9 View 3D Structure Click here
A1UUB4 View 3D Structure Click here
A3DCX4 View 3D Structure Click here
A4HS79 View 3D Structure Click here
A4I7U7 View 3D Structure Click here
A4SFP2 View 3D Structure Click here
A4VFH8 View 3D Structure Click here
A4VXS1 View 3D Structure Click here
A4XNB3 View 3D Structure Click here
A4YLB9 View 3D Structure Click here
A5CF65 View 3D Structure Click here
A5D1C0 View 3D Structure Click here
A5EWL8 View 3D Structure Click here
A5GQU9 View 3D Structure Click here
A5US58 View 3D Structure Click here
A5VDM3 View 3D Structure Click here
A5VJ71 View 3D Structure Click here
A6H0E7 View 3D Structure Click here
A6L7J9 View 3D Structure Click here
A6L9R8 View 3D Structure Click here
A6TEU0 View 3D Structure Click here
A6TRW8 View 3D Structure Click here
A8AQI1 View 3D Structure Click here
A8AV30 View 3D Structure Click here
A8F524 View 3D Structure Click here
A8LE21 View 3D Structure Click here