Summary: Omptin family
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Omptin Edit Wikipedia article
These are aspartate proteases, which cleave peptides with the use of a water molecule. Found in the outer membrane of gram-negative enterobacteria such as Shigella, Yersenia, E. coli, and Salmonella. Consist of a widely conserved beta barrel spanning the membrane with 5 extra-cellular loops. These loops are responsible for the various substrate specificities. These proteases rely upon binding of LPS for activity.
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Omptin family Provide feedback
The omptin family is a family of serine proteases.
Internal database links
SCOOP: | Pom |
External database links
MEROPS: | A26 |
PROSITE: | PDOC00657 |
SCOP: | 1i78 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000036
Aspartic peptidases, also known as aspartyl proteases ([intenz:3.4.23.-]), are widely distributed proteolytic enzymes [ PUBMED:6795036 , PUBMED:2194475 , PUBMED:1851433 ] known to exist in vertebrates, fungi, plants, protozoa, bacteria, archaea, retroviruses and some plant viruses. All known aspartic peptidases are endopeptidases. A water molecule, activated by two aspartic acid residues, acts as the nucleophile in catalysis. Aspartic peptidases can be grouped into five clans, each of which shows a unique structural fold [ PUBMED:8439290 ].
- Peptidases in clan AA are either bilobed (family A1 or the pepsin family) or are a homodimer (all other families in the clan, including retropepsin from HIV-1/AIDS) [ PUBMED:2682266 ]. Each lobe consists of a single domain with a closed beta-barrel and each lobe contributes one Asp to form the active site. Most peptidases in the clan are inhibited by the naturally occurring small-molecule inhibitor pepstatin [ PUBMED:4912600 ].
- Clan AC contains the single family A8: the signal peptidase 2 family. Members of the family are found in all bacteria. Signal peptidase 2 processes the premurein precursor, removing the signal peptide. The peptidase has four transmembrane domains and the active site is on the periplasmic side of the cell membrane. Cleavage occurs on the amino side of a cysteine where the thiol group has been substituted by a diacylglyceryl group. Site-directed mutagenesis has identified two essential aspartic acid residues which occur in the motifs GNXXDRX and FNXAD (where X is a hydrophobic residue) [ PUBMED:10497172 ]. No tertiary structures have been solved for any member of the family, but because of the intramembrane location, the structure is assumed not to be pepsin-like.
- Clan AD contains two families of transmembrane endopeptidases: A22 and A24. These are also known as "GXGD peptidases" because of a common GXGD motif which includes one of the pair of catalytic aspartic acid residues. Structures are known for members of both families and show a unique, common fold with up to nine transmembrane regions [ PUBMED:21765428 ]. The active site aspartic acids are located within a large cavity in the membrane into which water can gain access [ PUBMED:23254940 ].
- Clan AE contains two families, A25 and A31. Tertiary structures have been solved for members of both families and show a common fold consisting of an alpha-beta-alpha sandwich, in which the beta sheet is five stranded [ PUBMED:10331925 , PUBMED:10864493 ].
- Clan AF contains the single family A26. Members of the clan are membrane-proteins with a unique fold. Homologues are known only from bacteria. The structure of omptin (also known as OmpT) shows a cylindrical barrel containing ten beta strands inserted in the membrane with the active site residues on the outer surface [ PUBMED:11566868 ].
- There are two families of aspartic peptidases for which neither structure nor active site residues are known and these are not assigned to clans. Family A5 includes thermopsin, an endopeptidase found only in thermophilic archaea. Family A36 contains sporulation factor SpoIIGA, which is known to process and activate sigma factor E, one of the transcription factors that controls sporulation in bacteria [ PUBMED:21751400 ].
This group of aspartic peptidases belongs to the MEROPS family A26 (clan AF). Members of the family are transmembrane proteins. The type example for the family is omptin (also known as protease VII) from Escherichia coli, the product of the ompT gene. Omptin preferentially cleaves polypeptides between two basically-charged amino acids [ PUBMED:3056908 ]. The tertiary structure has been solved and shows a ten-stranded beta barrel, and because the strands are amphipathic, hydrolphilic rsidue point into the barrel with the hydrophobic residue on the outside. The active site residues, two pairs of aspartic acids and a histidine, are on opposite sides of the active site groove and at the periplasmic surface [ PUBMED:11566868 ]. Because the enzyme is sensitive to the serine protease inhibitor diisopropylfluoro-phosphate [ PUBMED:3056908 ], omptin was incorrectly identified as a serine peptidase.
The family also includes the surface protease Pla from the plague organism Yersinia pestis, which is an important virulence factor. Pla can activate plasminogen and inactivate plasmin inhibitor, which may lead to uncontrolled proteolysis and aid entry of the bacterium into the circulation [ PUBMED:11401715 ]. Pla is temperature sensitive, with proteolytic activity changing with temperature. At temperatures below 30 C, Pla acts as a coagulase, but at temperatures above 30 C it is fibrolytic [ PUBMED:2526282 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | cell outer membrane (GO:0009279) |
Molecular function | endopeptidase activity (GO:0004175) |
Biological process | proteolysis (GO:0006508) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan MBB (CL0193), which has the following description:
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 117 members:
Ail_Lom Alginate_exp Attacin_C Attacin_N Autotransporter BBP2 BBP2_2 BBP7 BCSC_C Campylo_MOMP Caps_assemb_Wzi CBP_BcsS Channel_Tsx Chlam_OMP CopB CymA DcaP DUF1207 DUF1302 DUF1842 DUF2219 DUF2490 DUF2715 DUF2860 DUF3034 DUF3078 DUF3138 DUF3187 DUF3373 DUF3570 DUF3573 DUF3575 DUF3769 DUF3996 DUF4421 DUF4595 DUF481 DUF4840 DUF5020 DUF5686 DUF5723 DUF5777 DUF5916 DUF6048 DUF6089 DUF6268 Gcw_chp GrlR HP_OMP HP_OMP_2 HpuA IAT_beta KdgM LamB Legionella_OMP Lipoprot_C LptD LptD_2 MDM10 MipA MOSP_C MSP MtrB_PioB NfrA_C Omp85 Omp85_2 Omp_AT OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_like OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF PagL PagP Phenol_MetA_deg PLA1 Pom Porin_1 Porin_10 Porin_2 Porin_3 Porin_4 Porin_5 Porin_6 Porin_7 Porin_8 Porin_O_P Porin_OmpG Porin_OmpG_1_2 Porin_OmpL1 PorP_SprF PorV Serpulina_VSP ShlB SlipAM Surface_Ag_2 TbpB_B_D Toluene_X TonB_dep_Rec TraF_2 TraO TSA UPF0164 UPF0257 Usher Usher_TcfC YadA_anchor YaiO YfaZ YjbHAlignments
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...
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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 (11) |
Full (200) |
Representative proteomes | UniProt (2317) |
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RP15 (44) |
RP35 (109) |
RP55 (196) |
RP75 (443) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (11) |
Full (200) |
Representative proteomes | UniProt (2317) |
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RP15 (44) |
RP35 (109) |
RP55 (196) |
RP75 (443) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Prosite |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Finn RD |
Number in seed: | 11 |
Number in full: | 200 |
Average length of the domain: | 255.1 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 79.94 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 283 | ||||||||||||
Family (HMM) version: | 23 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 Omptin domain has been found. There are 9 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 |
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O33641 | View 3D Structure | Click here |
P06185 | View 3D Structure | Click here |
P09169 | View 3D Structure | Click here |
P17811 | View 3D Structure | Click here |
P58603 | View 3D Structure | Click here |
Q326M1 | View 3D Structure | Click here |