Summary: Porphyromonas-type peptidyl-arginine deiminase
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Porphyromonas-type peptidyl-arginine deiminase Provide feedback
Peptidyl-arginine deiminase (PAD) enzymes catalyse the deimination of the guanidino group from carboxy-terminal arginine residues of various peptides to produce ammonia. PAD from Porphyromonas gingivalis (PPAD) appears to be evolutionarily unrelated to mammalian PAD (PF03068), which is a metalloenzyme. PPAD is thought to belong to the same superfamily as aminotransferase and arginine deiminase, and to form an alpha/beta propeller structure. This family has previously been named PPADH (Porphyromonas peptidyl-arginine deiminase homologues) . The predicted catalytic residues in PPAD (Q9RQJ2) are Asp130, Asp187, His236, Asp238 and Cys351 . These are absolutely conserved with the exception of Asp187 which is absent in two family members. PPAD is also able to catalyse the deimination of free L-arginine, but has primarily peptidyl-arginine specificity. It may have a FMN cofactor .
McGraw WT, Potempa J, Farley D, Travis J; , Infect Immun 1999;67:3248-3256.: Purification, characterization, and sequence analysis of a potential virulence factor from Porphyromonas gingivalis, peptidylarginine deiminase. PUBMED:10377098 EPMC:10377098
Internal database links
|Similarity to PfamA using HHSearch:||Amidinotransf|
This tab holds annotation information from the InterPro database.
InterPro entry IPR007466
Peptidyl-arginine deiminase (PAD) enzymes catalyse the deimination of the guanidino group from carboxy-terminal arginine residues of various peptides to produce ammonia. PAD from Porphyromonas gingivalis (Bacteroides gingivalis) (PPAD) appears to be evolutionarily unrelated to mammalian PAD (INTERPRO), which is a metalloenzyme. PPAD is thought to belong to the same superfamily as aminotransferase and arginine deiminase, and to form an alpha/beta propeller structure. This family has previously been named PPADH (Porphyromonas peptidyl-arginine deiminase homologues) [PUBMED:11504612]. The predicted catalytic residues in PPAD (SWISSPROT) are Asp130, Asp187, His236, Asp238 and Cys351 [PUBMED:11504612]. These are absolutely conserved with the exception of Asp187 which is absent in two family members. PPAD is also able to catalyse the deimination of free L-arginine, but has primarily peptidyl-arginine specificity. It may have a FMN cofactor [PUBMED:10377098].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||protein-arginine deiminase activity (GO:0004668)|
|Biological process||putrescine biosynthetic process (GO:0009446)|
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This superfamily contains a number of related enzymes such as AstB, peptidyl-arginine deiminase, arginine deiminase and amidinotransferase [1,2].
The clan contains the following 5 members:Amidinotransf AstB eIF-6 PAD PAD_porph
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Curation and family details
|Number in seed:||442|
|Number in full:||1975|
|Average length of the domain:||325.10 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||91.79 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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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 PAD_porph domain has been found. There are 36 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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