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12  structures 46  species 1  interaction 190  sequences 32  architectures

Family: Pacifastin_I (PF05375)

Summary: Pacifastin inhibitor (LCMII)

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Pacifastin inhibitor (LCMII) Provide feedback

Structures of members of this family show that they are comprised of a triple-stranded antiparallel beta-sheet connected by three disulfide bridges, which defines this as a novel family of serine protease inhibitors [1,2].

Literature references

  1. Simonet G, Claeys I, Broeck JV; , Comp Biochem Physiol B Biochem Mol Biol 2002;132:247-255.: Structural and functional properties of a novel serine protease inhibiting peptide family in arthropods. PUBMED:11997226 EPMC:11997226

  2. Roussel A, Mathieu M, Dobbs A, Luu B, Cambillau C, Kellenberger C; , J Biol Chem 2001;276:38893-38898.: Complexation of two proteic insect inhibitors to the active site of chymotrypsin suggests decoupled roles for binding and selectivity. PUBMED:11495915 EPMC:11495915


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008037

Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties.

This family of serine protease inhibitors belong to MEROPS inhibitor family I19, clan IW. They inhibit chymotrpsin, a peptidase belong to the S1 family (INTERPRO) [PUBMED:14705960].

They were first isolated from Locusta migratoria migratoria(migratory locust). These were HI, LMCI-1 (PMP-D2) and LMCI-2 (PMP-C) [PUBMED:1472051, PUBMED:1740125, PUBMED:10696590]; five additional members SGPI-1 to 5 were identified in Schistocerca gregaria (desert locust) [PUBMED:9475173, PUBMED:11856311], and a heterodimeric serine protease inhibitor (pacifastin) was isolated from the hemolymph of Pacifastacus leniusculus (Signal crayfish) [PUBMED:9192625].

Pacifastin is a 155kDa composed of two covalently linked subunits, which are separately encoded. The heavy chain of pacifastin (105 kDa) is related to transferrins, containing three transferrin lobes, two of which seem to be active for iron binding [PUBMED:9192625]. A number of the members of the transferrin family are also serine peptidases belong to MEROPS peptidase family S60 (INTERPRO). The light chain of pacifastin (44 kDa) is the proteinase inhibitory subunit, and has nine cysteine-rich inhibitory domains that are homologous to each other. The locust inhibitors share a conserved array of six cysteine residues with the pacifastin light chain. The structure of members of this family reveal that they are comprised of a triple-stranded antiparallel beta-sheet connected by three disulphide bridges [PUBMED:9192625].

The biological function(s) of the locust inhibitors is (are) not fully understood. LMCI-1 and LMCI-2 were shown to inhibit the endogenous proteolytic activating cascade of prophenoloxidase [PUBMED:11997226]. Expression analysis shows that the genes encoding the SGPI precursors are differentially expressed in a time-, stage- and hormone-dependent manner.

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
(36)
Full
(190)
Representative proteomes NCBI
(244)
Meta
(4)
RP15
(66)
RP35
(91)
RP55
(112)
RP75
(121)
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Format an alignment

  Seed
(36)
Full
(190)
Representative proteomes NCBI
(244)
Meta
(4)
RP15
(66)
RP35
(91)
RP55
(112)
RP75
(121)
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
(36)
Full
(190)
Representative proteomes NCBI
(244)
Meta
(4)
RP15
(66)
RP35
(91)
RP55
(112)
RP75
(121)
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.

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: Pfam-B_35181 (release 7.8)
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 36
Number in full: 190
Average length of the domain: 37.20 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 11.86 %

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 26.4 26.4
Trusted cut-off 26.4 26.4
Noise cut-off 26.3 26.3
Model length: 40
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

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 Pacifastin_I domain has been found. There are 12 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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