SERPIN

SERine Proteinase INhibitors

• SMART accession number: SM00093
• Interpro abstract (IPR023796):

  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 (IPR001254), S8 (IPR000209) and C14 (IPR002398) 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)].

  This entry represents the structural domain of serpins. It consists of a cluster of helices and a beta-sandwich.

There are 2594 SERPIN domains in 2585 proteins in SMART's nrdb database.

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Osterwalder T, Contartese J, Stoeckli ET, Kuhn TB, Sonderegger P
• Neuroserpin, an axonally secreted serine protease inhibitor.
• EMBO J. 1996; 15: 2944-53

We have identified and chromatographically purified an axonally secreted glycoprotein of CNS and PNS neurons. Several peptides derived from it were microsequenced. Based on these sequences, a fragment of the corresponding cDNA was amplified and used as a probe to isolate a full length cDNA from a chicken brain cDNA library. Because the deduced amino acid sequence qualified the protein as a novel member of the serpin family of serine protease inhibitors, we called it neuroserpin. Analysis of the primary structural features further characterized neuroserpin as a heparin-independent, functional inhibitor of a trypsin-like serine protease. In situ hybridization revealed a predominantly neuronal expression during the late stages of neurogenesis and in the adult brain in regions which exhibit synaptic plasticity. Thus, neuroserpin might function as an axonally secreted regulator of the local extracellular proteolysis involved in the reorganization of the synaptic connectivity during development and synapse plasticity in the adult.

• Komiyama T et al.
• Inhibition of interleukin-1 beta converting enzyme by the cowpox virus serpin CrmA. An example of cross-class inhibition.
• J Biol Chem. 1994; 269: 19331-7

We reported previously that human interleukin-1 beta converting enzyme (ICE) is regulated by the CrmA serpin encoded by cowpox virus. We now report the mechanism and kinetics of this unusual inhibition of a cysteine proteinase by a member of the serpin superfamily previously thought to inhibit serine proteinase only. CrmA possesses several characteristics typical of a number of inhibitory serpins. It is conformationally unstable, unfolding around 3 M urea, and stable to denaturation in 8 M urea upon complex formation with ICE. CrmA rapidly inhibits ICE with an association rate constant (kon) of 1.7 x 10(7) M-1 s-1, forming a tight complex with an equilibrium constant for inhibition (Ki) of less than 4 x 10(-12) M. These data indicate that CrmA is a potent inhibitor of ICE, consistent with the dramatic effects of CrmA on modifying host responses to virus infection. The inhibition of ICE by CrmA is an example of a "cross-class" interaction, in which a serpin inhibits a non-serine proteinase. Since CrmA possesses characteristics shared by inhibitors of serine proteinases, we presume that ICE, though it is a cysteine proteinase, has a substrate binding geometry strikingly close to that of serine proteinases. We reason that it is the substrate binding geometry, not the catalytic mechanism of a proteinase, that dictates its reactivity with protein inhibitors.

• Zou Z et al.
• Maspin, a serpin with tumor-suppressing activity in human mammary epithelial cells.
• Science. 1994; 263: 526-9

A gene encoding a protein related to the serpin family of protease inhibitors was identified as a candidate tumor suppressor gene that may play a role in human breast cancer. The gene product, called maspin, is expressed in normal mammary epithelial cells but not in most mammary carcinoma cell lines. Transfection of MDA-MB-435 mammary carcinoma cells with the maspin gene did not alter the cells' growth properties in vitro, but reduced the cells' ability to induce tumors and metastasize in nude mice and to invade through a basement membrane matrix in vitro. Analysis of human breast cancer specimens revealed that loss of maspin expression occurred most frequently in advanced cancers. These results support the hypothesis that maspin functions as a tumor suppressor.

• Steele FR, Chader GJ, Johnson LV, Tombran-Tink J
• Pigment epithelium-derived factor: neurotrophic activity and identification as a member of the serine protease inhibitor gene family.
• Proc Natl Acad Sci U S A. 1993; 90: 1526-30

Cultured pigment epithelial cells of the fetal human retina secrete a protein, pigment epithelium-derived factor (PEDF), that induces a neuronal phenotype in cultured human retinoblastoma cells. Morphological changes include the induction of an extensive neurite meshwork and the establishment of corona-like cellular aggregates surrounding a central lumen. The differentiated cells also show increases in the expression of neuron-specific enolase and the 200-kDa neurofilament subunit. Amino acid and DNA sequence data demonstrate that PEDF belongs to the serine protease inhibitor (serpin) family. The PEDF gene contains a typical signal-peptide sequence, initiator methionine codon, and polyadenylylation signal and matches the size of other members of the serpin superfamily (e.g., alpha 1-antitrypsin). It lacks homology, however, at the putative serpin reactive center. Thus, PEDF could exert a paracrine effect in the embryonic retina, influencing neuronal differentiation by a mechanism that does not involve classic inhibition of serine protease activity.

• Clarke EP, Sanwal BD
• Cloning of a human collagen-binding protein, and its homology with rat gp46, chick hsp47 and mouse J6 proteins.
• Biochim Biophys Acta. 1992; 1129: 246-8

Several cDNA clones encoding a collagen-binding protein were isolated from human fibroblasts. The cDNA encoded a 417 amino acid protein, containing two potential N-linked oligosaccharide binding sites and a C-terminal RDEL sequence, which has been shown to act as an endoplasmic retention signal in other systems. The derived amino acid sequence of the protein shows close homology with gp46 from rat skeletal myoblasts, J6 protein from mouse F9 embryonal carcinoma cells and hsp47 from chick embryo fibroblasts. It also shows sequence similarity with members of the serpin family.

• Holland LJ, Suksang C, Wall AA, Roberts LR, Moser DR, Bhattacharya A
• A major estrogen-regulated protein secreted from the liver of Xenopus laevis is a member of the serpin superfamily. Nucleotide sequence of cDNA and hormonal induction of mRNA.
• J Biol Chem. 1992; 267: 7053-9

Estrogen treatment of Xenopus frogs causes four mRNAs to become highly abundant in the liver. Three of these mRNAs have been previously identified as coding for vitellogenin, ferritin, and serum retinol binding protein. We show here that the fourth abundant liver messenger RNA comprises about 1500 nucleotides and codes for a 45-kDa secreted protein, designated Ep45. A clone complementary to Ep45 mRNA was isolated, and its identity was confirmed by hybridization selection of mRNA that translated in vitro into the Ep45 precursor. Nucleotide sequence analysis of the nearly full length cDNA revealed a total length of 1454 base pairs consisting of: 36 nucleotides of the 5' noncoding region, 1308 base pairs encoding an open reading frame of 436 amino acids, and 110 nucleotides of the 3' untranslated region. Ep45 mRNA may originate from as many as four closely spaced transcription start sites, which are 15 to 21 bases upstream of the first nucleotide of the cDNA clone. The Xenopus laevis genome appears to contain a single Ep45 gene. The deduced amino acid sequence indicates that Ep45 has features typical of a secreted protein, including a signal peptide of 16 amino acids and three potential sites for N-linked glycosylation, and is related to the serine protease inhibitors, a large family of proteins with very diverse physiological functions. Ep45 mRNA was absent in the liver of normal male frogs and increased at least 100-fold in response to estradiol-17 beta. Thus, both Ep45 and vitellogenin mRNAs are switched from undetectable to very high levels, a pattern of expression not found for any other mRNAs in Xenopus liver.

• Kirchhoff C, Habben I, Ivell R, Krull N
• A major human epididymis-specific cDNA encodes a protein with sequence homology to extracellular proteinase inhibitors.
• Biol Reprod. 1991; 45: 350-7

The amino acid sequence of a major human epididymis-specific protein was deduced from the nucleotide sequence of its cloned cDNA. The encoded product showed characteristics of a secretory protein, with a signal peptide followed by a small (approximately 10-kDa), acidic (pI 4.3), and cysteine-rich polypeptide. The positions of half-cysteines suggested that it was a two-domain member of the family of 'four-disulfide core' proteins to which a number of proteinase inhibitors belong. Southern blot analyses of human genomic DNA showed that the transcripts originated from a single copy gene. Northern blot and in situ transcript hybridization specifically localized the HE4 (human epididymis gene product) mRNA to the epithelial cells of the epididymal duct, predominantly within the distal sections. A possible function in sperm maturation as indicated by amino acid similarities to extracellular proteinase inhibitors of genital tract mucous secretions is discussed in the context of its tissue-specific transcription.

• Huber R, Carrell RW
• Implications of the three-dimensional structure of alpha 1-antitrypsin for structure and function of serpins.
• Biochemistry. 1989; 28: 8951-66

• Carrell RW, Pemberton PA, Boswell DR
• The serpins: evolution and adaptation in a family of protease inhibitors.
• Cold Spring Harb Symp Quant Biol. 1987; 52: 527-35

Disease (disease genes where sequence variants are found in this domain)

SwissProt sequences and OMIM curated human diseases associated with missense mutations within the SERPIN domain.

Protein	Disease
Angiotensin-3 (P01019) (SMART)	OMIM:106150: {Hypertension, essential, susceptibility to} ; {Preeclampsia, susceptibility to}
Neuroserpin (Q99574) (SMART)	OMIM:602445: Encephalopathy, familial, with neuroserpin inclusion bodies OMIM:604218:
Alpha-1-antichymotrypsin His-Pro-less (P01011) (SMART)	OMIM:107280: Alpha-1-antichymotrypsin deficiency ; Cerebrovascular disease, occlusive
Plasma serine protease inhibitor (P05154) (SMART)	OMIM:601841: Protein C inhibitor deficiency
Thyroxine-binding globulin (P05543) (SMART)	OMIM:314200: THYROXINE-BINDING GLOBULIN OF SERUM; TBG
Short peptide from AAT (P01009) (SMART)	OMIM:107400: Emphysema-cirrhosis ; Hemorrhagic diathesis due to `antithrombin' Pittsburgh ; Emphysema
Heparin cofactor 2 (P05546) (SMART)	OMIM:142360: Thrombophilia due to heparin cofactor II deficiency
Antithrombin-III (P01008) (SMART)	OMIM:107300: Antithrombin III deficiency
Plasma protease C1 inhibitor (P05155) (SMART)	OMIM:106100: Angioedema, hereditary

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
64.71	map04610	Complement and coagulation cascades
22.06	map04115	p53 signaling pathway
13.24	map04614	Renin-angiotensin system

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with SERPIN domain which could be assigned to a KEGG orthologous group, and not all proteins containing SERPIN domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

Structure (3D structures containing this domain)

3D Structures of SERPIN domains in PDB

PDB code	Title
1a7c	Human plasminogen activator inhibitor type-1 in complex with a pentapeptide
1ant	Biological implications of a 3 angstroms structure of dimeric antithrombin
1as4	Cleaved antichymotrypsin a349r
1ath	The intact and cleaved human antithrombin iii complex as a model for serpin-proteinase interactions
1att	Crystal structure of cleaved bovine antithrombin iii at 3.2 angstroms resolution
1atu	Uncleaved alpha-1-antitrypsin
1azx	Antithrombin/pentasaccharide complex
1b3k	Plasminogen activator inhibitor-1
1br8	Implications for function and therapy of a 2.9a structure of binary-complexed antithrombin
1by7	Human plasminogen activator inhibitor-2. loop (66-98) deletion mutant
1c5g	Plasminogen activator inhibitor-1
1c8o	2.9 a structure of cleaved viral serpin crma
1d5s	Crystal structure of cleaved antitrypsin polymer
1db2	Crystal structure of native plasminogen activator inhibitor-
1dvm	Active form of human pai-1
1dvn	Latent form of plasminogen activator inhibitor-1 (pai-1)
1dzg	N135q-s380c-antithrombin-iii
1dzh	P14-fluorescein-n135q-s380c-antithrombin-iii
1e03	Plasma alpha antithrombin-iii and pentasaccharide
1e04	Plasma beta antithrombin-iii
1e05	Plasma alpha antithrombin-iii
1ezx	Crystal structure of a serpin:protease complex
1f0c	Structure of the viral serpin crma
1hle	Crystal structure of cleaved equine leucocyte elastase inhibitor determined at 1.95 angstroms resolution
1hp7	A 2.1 angstrom structure of an uncleaved alpha-1- antitrypsin shows variability of the reactive center and other loops
1imv	2.85 a crystal structure of pedf
1iz2	Interactions causing the kinetic trap in serpin protein folding
1jjo	Crystal structure of mouse neuroserpin (cleaved form)
1jmj	Crystal structure of native heparin cofactor ii
1jmo	Crystal structure of the heparin cofactor ii-s195a thrombin complex
1jrr	Human plasminogen activator inhibitor-2.[loop (66-98) deletionmutant] complexed with peptide mimicking the reactive center loop
1jti	Loop-inserted structure of p1-p1' cleaved ovalbumin mutant r339t
1jvq	Crystal structure at 2.6a of the ternary complex between antithrombin, a p14-p8 reactive loop peptide, and an exogenous tetrapeptide
1k9o	Crystal structure of michaelis serpin-trypsin complex
1kct	Alpha1-antitrypsin
1lj5	1.8a resolution structure of latent plasminogen activator inhibitor-1(pai-1)
1lk6	Structure of dimeric antithrombin complexed with a p14-p9 reactive loop peptide and an exogenous tripeptide
1lq8	Crystal structure of cleaved protein c inhibitor
1m93	1.65 a structure of cleaved viral serpin crma
1mtp	The x-ray crystal structure of a serpin from a thermophilic prokaryote
1nq9	Crystal structure of antithrombin in the pentasaccharide- bound intermediate state
1oc0	Plasminogen activator inhibitor-1 complex with somatomedin b domain of vitronectin
1oo8	Crystal structure of a1pi-pittsburgh in the native conformation
1oph	Non-covalent complex between alpha-1-pi-pittsburgh and s195a trypsin
1ova	Crystal structure of uncleaved ovalbumin at 1.95 angstroms resolution
1oyh	Crystal structure of p13 alanine variant of antithrombin
1psi	Intact recombined alpha1-antitrypsin mutant phe 51 to leu
1qlp	2.0 angstrom structure of intact alpha-1-antitrypsin: a canonical template for active serpins
1qmb	Cleaved alpha-1-antitrypsin polymer
1qmn	Alpha1-antichymotrypsin serpin in the delta conformation (partial loop insertion)
1r1l	Structure of dimeric antithrombin complexed with a p14-p9 reactive loop peptide and an exogenous tripeptide (formyl- norleucine-lf)
1sek	The structure of active serpin k from manduca sexta and a model for serpin-protease complex formation
1sng	Structure of a thermophilic serpin in the native state
1sr5	Antithrombin-anhydrothrombin-heparin ternary complex structure
1t1f	Crystal structure of native antithrombin in its monomeric form
1tb6	2.5a crystal structure of the antithrombin-thrombin-heparin ternary complex
1uhg	Crystal structure of s-ovalbumin at 1.9 angstrom resolution
1wz9	The 2.1 a structure of a tumour suppressing serpin
1xqg	3.10 a crystal structure of maspin, space group p 4 21 2
1xqj	3.10 a crystal structure of maspin, space group i 4 2 2
1xu8	The 2.8 a structure of a tumour suppressing serpin
1yxa	Serpina3n, a murine orthologue of human antichymotrypsin
2ach	Crystal structure of cleaved human alpha1-antichymotrypsin at 2.7 angstroms resolution and its comparison with other serpins
2ant	The 2.6 a structure of antithrombin indicates a conformational change at the heparin binding site
2arq	Human plasminogen activator inhibitor-2.[loop (66-98) deletion mutant] complexed with peptide n-acetyl- teaaagdggvmtgr-oh
2arr	Human plasminogen activator inhibitor-2.[loop (66-98) deletion mutant] complexed with peptide n-acetyl- teaaagmggvmtgr-oh
2b4x	Crystal structure of antithrombin-iii
2b5t	2.1 angstrom structure of a nonproductive complex between antithrombin, synthetic heparin mimetic sr123781 and two s195a thrombin molecules
2beh	Crystal structure of antithrombin variant s137a/v317c/t401c with plasma latent antithrombin
2ceo	Thyroxine-binding globulin complex with thyroxine
2d26	Active site distortion is sufficient for proteinase inhibit second crystal structure of covalent serpin-proteinase complex
2dut	Crystal structure of a m-loop deletion variant of ment in the native conformation
2gd4	Crystal structure of the antithrombin-s195a factor xa- pentasaccharide complex
2h4p	Crystal structure of wildtype ment in the cleaved conformation
2h4q	Crystal structure of a m-loop deletion variant of ment in the cleaved conformation
2h4r	Crystal structure of wildtype ment in the native conformation
2hi9	Crystal structure of human native protein c inhibitor
2hij	Crystal structure of p14 alanine variant of antithrombin
2oay	Crystal structure of latent human c1-inhibitor
2ol2	High resolution structure of native pci in space group p21
2pee	Crystal structure of a thermophilic serpin, tengpin, in the native state
2pef	Crystal structure of a thermophilic serpin, tengpin, in the latent state
2qug	Crystal structure of alpha-1-antitrypsin, crystal form a
2r9y	Structure of antiplasmin
2riv	Crystal structure of the reactive loop cleaved human thyroxine binding globulin
2riw	The reactive loop cleaved human thyroxine binding globulin complexed with thyroxine
2v95	Struture of corticosteroid-binding globulin in complex with cortisol
2vdx	Crystal structure of the reactive loop cleaved corticosteroid binding globulin
2vdy	Crystal structure of the reactive loop cleaved corticosteroid binding globulin complexed with cortisol
2vh4	Structure of a loop c-sheet serpin polymer
2znh	Crystal structure of a domain-swapped serpin dimer
2zv6	Crystal structure of human squamous cell carcinoma antigen 1
3b9f	1.6 a structure of the pci-thrombin-heparin complex
3caa	Cleaved antichymotrypsin a347r
3cvm	High resolution structure of a stable plasminogen activator inhibitor type-1 in its protease cleaved form
3cwl	Crystal structure of alpha-1-antitrypsin, crystal form b
3cwm	Crystal structure of alpha-1-antitrypsin complexed with citrate
3dlw	Antichymotrypsin
3drm	2.2 angstrom crystal structure of thr114phe alpha1- antitrypsin
3dru	Crystal structure of gly117phe alpha1-antitrypsin
3dy0	Crystal structure of cleaved pci bound to heparin
3eox	High quality structure of cleaved pai-1-stab
3evj	Intermediate structure of antithrombin bound to the natural pentasaccharide
3f02	Cleaved human neuroserpin
3f1s	Crystal structure of protein z complexed with protein z- dependent inhibitor
3f5n	Structure of native human neuroserpin
3fgq	Crystal structure of native human neuroserpin
4caa	Cleaved antichymotrypsin t345r
7api	The s variant of human alpha1-antitrypsin, structure and implications for function and metabolism
8api	The s variant of human alpha1-antitrypsin, structure and implications for function and metabolism
9api	The s variant of human alpha1-antitrypsin, structure and implications for function and metabolism
9pai	Cleaved substrate variant of plasminogen activator inhibitor-1

Links (links to other resources describing this domain)

• INTERPRO: IPR023796
• PROSITE: PS00284