Summary

Serpin (serine protease inhibitor)

Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.

Literature references

Wright HT; , Bioessays 1996;18:453-464.: The structural puzzle of how serpin serine proteinase inhibitors work. PUBMED:8787534

InterPro entry IPR000215

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.

Serpins (SERine Proteinase INhibitors) PUBMED:14705960, PUBMED:2690952, PUBMED:8417965 belong to MEROPS inhibitor family I4, clan ID. Serpins are proteins that are primarily known as irreversible serine protease inhibitors active against S1 (), S8 () and C14 () peptidases. There are both extra- and intra-cellular serpins, which are found in all groups of organisms with the notable exception of fungi PUBMED:11116082, PUBMED:12411597. In contrast to "rigid" proteinase inhibitors, such as those of the Kunitz or Kazal families, the serpins are metastable proteins (active-state proteins) which interact with their substrate and irreversibly trap the acyl intermediate as a result of a major conformational change PUBMED:11116079; they are best described as suicide substrate inhibitors. The common structure of these proteins is a multi-domain fold containing a bundle of 8 or 9 alpha helices and a beta sandwich formed by 3 beta sheets. The reactive centre loop (RCL) is found in the C-terminal part of these proteins.

Serpins and their homologues are a group of high molecular weight (40 to 50 kDa) structurally related proteins involved in a number of fundamental biological processes such as blood coagulation, complement activation, fibrinolysis, angiogenesis, inflammation, tumour suppression and hormone transport. All known serpins have been classified into 16 clades and 10 orphan sequences; the vertebrate serpins can be conveniently classified into six sub-groups PUBMED:11116082. In human plasma they represent approximately 2% of the total protein, of which 70% is alpha-1-antitrypsin. On the basis of strong sequence similarities, a number of proteins with no known inhibitory activity also belong to this family, these include: angiotensinogen, corticosteroid-binding globulin and thyroxin-binding globulin PUBMED:12824063.

Gene Ontology

Molecular function

serine-type endopeptidase inhibitor activity (GO:0004867)

External database links

HOMSTRAD:	serpin
PANDIT:	PF00079
PROSITE:	PDOC00256
SCOP:	1hle
SYSTERS:	Serpin

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

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

Alignment:	Seed (181) Full (2454) NCBI (4876) Metagenomics (68)
Viewer:

Formatting options

Alignment:	Seed (181) Full (2454)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

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

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (181) Full (2454) NCBI (4876) Metagenomics (68)
Full length sequences	Full-sequences (2454)

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 HMMER2.

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. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

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:

Overington and HMM_iterative_training

Previous IDs:

serpin;

Type:

Domain

Author:

Eddy SR

Number in seed:

181

Number in full:

2454

Average length of the domain:

303.00 aa

Average identity of full alignment:

23 %

Average coverage of the sequence by the domain:

82.01 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.3	20.3
Trusted cut-off	20.4	20.3
Noise cut-off	20.1	20.1

Model length:

369

Family (HMM) version:

13

Download:

download the raw HMM for this family

Species distribution

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Interactions

There are 3 interactions for this family. More...

Serpin Somatomedin_B 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 Serpin domain has been found.

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Family: Serpin (PF00079)

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