SUPERFAMILY 1.75 HMM library and genome assignments server

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Peptide deformylase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Peptide deformylase [ 56419]
Superfamily:   Peptide deformylase [ 56420]
Families:   Peptide deformylase [ 56421]


Superfamily statistics
Genomes (2,781) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 4,419 35,072 19
Proteins 4,408 35,047 19


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)In linear amides0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)In linear amides0InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR000181 SSF56420 Protein matches
Abstract

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 [PubMed9846875] . The enzyme acts as a monomer and binds a single zinc ion, catalysing the reaction:: N-formyl-L-methionine + H2O = formate + methionyl peptide Catalytic efficiency strongly depends on the identity of the bound metal [PubMed9565550].

The structure of these enzymes is known [PubMed8845003, PubMed9665852]. PDF, a member of the zinc metalloproteases family, 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 other 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-metalloproteases. [PubMed8845003].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

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Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 30 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Peptide deformylase domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 30 hidden Markov models representing the Peptide deformylase superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) · Internal database links ]