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Peptide deformylase superfamily
SCOP classification
Superfamily statistics
Functional annotation
General category | Metabolism |
Detailed category | Coenzyme metabolism and transport |
Document: Function annotation of SCOP domain superfamilies
Enzyme Commission (EC) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: EC annotation of SCOP domains
Enzyme Commission (EC) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: EC annotation of SCOP domains
UniProtKB KeyWords (KW) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: KW 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 [ 9846875] . 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 [ 9565550].
The structure
of these enzymes is known [ 8845003, 9665852]. 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.
[ 8845003]. |
InterPro database
PDBeMotif information about ligands, sequence and structure motifs
PDBeMotif resource
Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]
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.
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Alignments of sequences to 9 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.
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Browse and view proteins in genomes which have
different domain combinations including a Peptide deformylase domain.
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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.
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Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.
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There are 9 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.
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Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]
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