Summary: outer membrane porin, OprD family
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outer membrane porin, OprD family Provide feedback
This family includes outer membrane proteins related to OprD. OprD has been described as a serine type peptidase . However the proposed catalytic residues are not conserved suggesting that many of these proteins are not peptidases.
Yoshihara E, Yoneyama H, Ono T, Nakae T; , Biochem Biophys Res Commun 1998;247:142-145.: Identification of the catalytic triad of the protein D2 protease in Pseudomonas aeruginosa. PUBMED:9636669 EPMC:9636669
Ochs MM, Bains M, Hancock RE; , Antimicrob Agents Chemother 2000;44:1983-1985.: Role of putative loops 2 and 3 in imipenem passage through the specific porin OprD of Pseudomonas aeruginosa. PUBMED:10858367 EPMC:10858367
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005318
This family contains bacterial outer membrane porins with serine protease activity [PUBMED:9636669]. The serine peptidase domain belongs to MEROPS peptidase family S43 (clan PA(S)).
However many of these proteins are not peptidases and are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the S43 family. The putative role of these protein could be to bind ligands and to facilitate the diffusion through the outer membrane.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||integral to membrane (GO:0016021)|
|Molecular function||porin activity (GO:0015288)|
|Biological process||transport (GO:0006810)|
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This clan gathers together a large set of beta barrel membrane proteins.Although these proteins have different numbers of beta strands in the barrel they have significant sequence similarity between families.
The clan contains the following 54 members:Ail_Lom Autotransporter Bac_surface_Ag Campylo_MOMP Channel_Tsx CopB DUF1302 DUF1597 DUF2320 DUF2490 DUF2860 DUF3078 DUF3138 DUF3187 DUF3308 DUF3374 DUF3575 DUF4289 DUF481 DUF560 Gcw_chp HP_OMP HP_OMP_2 KdgM LamB Legionella_OMP MipA OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF OstA_C PagL Phenol_MetA_deg Porin_1 Porin_2 Porin_4 Porin_O_P Porin_OmpG ShlB Surface_Ag_2 Toluene_X TonB_dep_Rec TraF_2 TSA Usher YfaZ
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Number in seed:||47|
|Number in full:||2107|
|Average length of the domain:||371.00 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||90.15 %|
|HMM build commands:||
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|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 OprD domain has been found. There are 29 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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