Summary: Omptin family
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Omptin Edit Wikipedia article
Omptins (EC 220.127.116.11, protease VII, protease A, gene ompT proteins, ompT protease, protein a, Pla, OmpT) are a family of bacterial proteases. They 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 flexneri, Yersinia pestis, Escherichia coli, and Salmonella enterica. Omptins 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 lipopolysaccharide for activity.
- Hritonenko V, Stathopoulos C (2007). "Omptin proteins: an expanding family of outer membrane proteases in Gram-negative Enterobacteriaceae". Mol. Membr. Biol. 24 (5-6): 395–406. doi:10.1080/09687680701443822. PMID 17710644.
- Kukkonen M, Korhonen TK (July 2004). "The omptin family of enterobacterial surface proteases/adhesins: from housekeeping in Escherichia coli to systemic spread of Yersinia pestis". Int. J. Med. Microbiol. 294 (1): 7–14. doi:10.1016/j.ijmm.2004.01.003. PMID 15293449.
- Haiko J, Laakkonen L, Juuti K, Kalkkinen N, Korhonen TK (September 2010). "The omptins of Yersinia pestis and Salmonella enterica cleave the reactive center loop of plasminogen activator inhibitor 1". J. Bacteriol. 192 (18): 4553–61. doi:10.1128/JB.00458-10. PMC 2937412. PMID 20639337. Retrieved 2011-04-10.
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Omptin family Provide feedback
The omptin family is a family of serine proteases.
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External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000036
In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
- Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
- Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases.
In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding.
Aspartic endopeptidases EC of vertebrate, fungal and retroviral origin have been characterised [PUBMED:1455179]. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [PUBMED:10625704] and archaean preflagellin have been described [PUBMED:16983194, PUBMED:14622420].
Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure.
This group of aspartic peptidases belongs to the MEROPS family A26 (clan AF). The omptin family, comprises a number of novel outer membrane-associated serine proteases that are distinct from trypsin-like proteases in that they cleave polypeptides between two basically-charged amino acids [PUBMED:3056908]. The enzyme is sensitive to the serine protease inhibitor diisopropylfluoro-phosphate, to divalent cations such as Cu2+, Zn2+ and Fe2+ [PUBMED:3056908], and is temperature regulated, activity decreasing at lower temperatures [PUBMED:3056908, PUBMED:8288530]. Temperature regulation is most prominently shown in the Yersinia pestis coagulase/fibrinolysin protein, where coagulase activity is prevalent below 30 degrees Celsius, and fibrinolysin (protease) activity is prevalent above this point, the optimum temperature being 37 degrees [PUBMED:2526282]. It is possible that this assists in 'flea blockage' and transmission of the bacteria to animals [PUBMED:2526282].
The Escherichia coli OmpT has previously been classified as a serine protease with Ser(99) and His(212) as active site residues. The X-ray structure of the enzyme is inconsistent with this classification, and the involvement of a nucleophilic water molecule that is activated by the Asp(210)/His(212) catalytic dyad classifies this as a aspartic endopeptidase where activity is also strongly dependent on Asp(83) and Asp(85). Both may function in binding of the water molecule and/or oxyanion stabilisation. The proposed mechanism implies a novel proteolytic catalytic site [PUBMED:11576541, PUBMED:11566868].
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)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
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EGFdomains, and finally a single
- the UniProt description of the protein sequence
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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 59 members:Ail_Lom Autotransporter Bac_surface_Ag BBP2 BBP2_2 Campylo_MOMP Channel_Tsx CopB DUF2490 DUF2860 DUF3078 DUF3138 DUF3187 DUF3308 DUF3575 DUF481 DUF560 Gcw_chp HP_OMP HP_OMP_2 KdgM LamB Legionella_OMP MipA MtrB_PioB Omp_AT OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_like OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF OstA_C PagL PagP Phenol_MetA_deg Porin_1 Porin_10 Porin_2 Porin_4 Porin_7 Porin_8 Porin_O_P Porin_OmpG ShlB Surface_Ag_2 TcfC Toluene_X TonB_dep_Rec TraF_2 TSA Usher YfaZ
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Author:||Finn RD, Bateman A|
|Number in seed:||15|
|Number in full:||2919|
|Average length of the domain:||272.00 aa|
|Average identity of full alignment:||62 %|
|Average coverage of the sequence by the domain:||90.47 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|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 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 seqence.
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