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9  structures 67  species 2  interactions 81  sequences 4  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

  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


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

Aspartic peptidases, also known as aspartyl proteases (EC), 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 amnd 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

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Domain organisation

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Alignments

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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.

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(14)
Full
(81)
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(803)
NCBI
(1281)
Meta
(1)
RP15
(20)
RP35
(59)
RP55
(101)
RP75
(243)
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  Seed
(14)
Full
(81)
Representative proteomes UniProt
(803)
NCBI
(1281)
Meta
(1)
RP15
(20)
RP35
(59)
RP55
(101)
RP75
(243)
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  Seed
(14)
Full
(81)
Representative proteomes UniProt
(803)
NCBI
(1281)
Meta
(1)
RP15
(20)
RP35
(59)
RP55
(101)
RP75
(243)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

HMM logo

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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.

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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: 14
Number in full: 81
Average length of the domain: 263.90 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 80.32 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.1 20.1
Trusted cut-off 20.1 21.7
Noise cut-off 19.2 17.4
Model length: 283
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 2 interactions for this family. More...

Omptin Trypsin

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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