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9  structures 418  species 0  interactions 512  sequences 3  architectures

Family: Omptin (PF01278)

Summary: Omptin family

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This is the Wikipedia entry entitled "Omptin". More...

Omptin Edit Wikipedia article

Omptin
Identifiers
Symbol Omptin
Pfam PF01278
Pfam clan CL0193
PROSITE PDOC00657
MEROPS A26
SCOP 1i78
SUPERFAMILY 1i78
OPM superfamily 27
OPM protein 2x55

Omptins (EC 3.4.23.49, protease VII, protease A, gene ompT proteins, ompT protease, protein a, Pla, OmpT) are a family of bacterial proteases.[1] 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.[2]

Omptins have been linked with pathogenesis in several bacteria.[1]

References[edit]

  1. ^ a b 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. 
  2. ^ 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. 

Further reading[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Omptin family Provide feedback

The omptin family is a family of serine proteases.

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].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(7)
Full
(512)
Representative proteomes NCBI
(269)
Meta
(1)
RP15
(10)
RP35
(21)
RP55
(29)
RP75
(44)
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Format an alignment

  Seed
(7)
Full
(512)
Representative proteomes NCBI
(269)
Meta
(1)
RP15
(10)
RP35
(21)
RP55
(29)
RP75
(44)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(7)
Full
(512)
Representative proteomes NCBI
(269)
Meta
(1)
RP15
(10)
RP35
(21)
RP55
(29)
RP75
(44)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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 View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Family
Author: Finn RD, Bateman A
Number in seed: 7
Number in full: 512
Average length of the domain: 275.50 aa
Average identity of full alignment: 56 %
Average coverage of the sequence by the domain: 92.86 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.1 20.1
Trusted cut-off 20.4 20.4
Noise cut-off 19.6 19.3
Model length: 295
Family (HMM) version: 15
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 seqence.

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