| PF00188 |
Cysteine-rich secretory protein family |
This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes and non-vertebrate eukaryotes, The nine subfamilies of the mammalian CAP 'super'family include: the human glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis related-1 (GAPR1) proteins, peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), cysteine-rich secretory proteins (CRISPs), CRISP LCCL domain containing 1 (CRISPLD1), CRISP LCCL domain containing 2 (CRISPLD2), mannose receptor like and the R3H domain containing like proteins. Members are most often secreted and have an extracellular endocrine or paracrine function and are involved in processes including the regulation of extracellular matrix and branching morphogenesis, potentially as either proteases or protease inhibitors; in ion channel regulation in fertility; as tumour suppressor or pro-oncogenic genes in tissues including the prostate; and in cell-cell adhesion during fertilisation. The overall protein structural conservation within the CAP 'super'family results in fundamentally similar functions for the CAP domain in all members, yet the diversity outside of this core region dramatically alters the target specificity and, thus, the biological consequences. The Ca++-chelating function would fit with the various signalling processes (e.g. the CRISP proteins) that members of this family are involved in, and also the sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how Q91055 blocks the Ca++ transporting ryanodine receptors. |
| PF00332 |
Glycosyl hydrolases family 17 |
O-Glycosyl hydrolases (3.2.1.) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families. This classification is available on the CAZy (CArbohydrate-Active EnZymes) website. Glycoside hydrolase family 17 GH17 comprises enzymes with several known activities; endo-1,3-beta-glucosidase (3.2.1.39); lichenase (3.2.1.73); exo-1,3-glucanase (3.2.1.58). Currently these enzymes have only been found in plants and in fungi. |
| PF00182 |
Chitinase class I |
Chitinases are enzymes that catalyse the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Chitinases belong to glycoside hydrolase families 18 or 19. Chitinases of family 19 (also known as classes I, II and IV) are enzymes from plants that function in the defence against fungal and insect pathogens by destroying their chitin-containing cell wall. Some family 19 chitinases are found in bacteria. Class I and II chitinases are similar in their catalytic domains. Class I chitinases have an N-terminal cysteine-rich, chitin-binding domain which is separated from the catalytic domain by a proline and glycine-rich hinge region. Class II chitinases lack both the chitin-binding domain and the hinge region. Class IV chitinases are similar to class I, but they are smaller in size due to certain deletions. |
| PF00967 |
Barwin family |
Barwin is a basic protein isolated from aqueous extracts of barley seeds. It is 125 amino acids in length, and contains six cysteine residues that combine to form three disulphide bridges. Comparative analysis shows the sequence to be highly similar to a 122 amino acid stretch in the C-terminal of the products of two wound-induced genes (win1 and win2) from potato, the product of the hevein gene of rubber trees, and pathogenesis-related protein 4 from tobacco. The high levels of similarity to these proteins, and their ability to bind saccharides, suggest that the barwin domain may be involved in a common defence mechanism in plants. |
| PF00314 |
Thaumatin family |
This family is also referred to as pathogenesis-related group 5 (PR5), as many thaumatin-like proteins accumulate in plants in response to infection by a pathogen and possess antifungal activity. The proteins are involved in systemically acquired resistance and stress response in plants, although their precise role is unknown. The PR5K receptor protein kinase from Arabidopsis comprises an extracellular domain related to the PR5 proteins, and an intracellular protein-serine/threonine kinase domain. |
| PF00280 |
Potato inhibitor I family |
This family of proteinase inhibitors belong to MEROPS inhibitor family I13, clan IG. They inhibit peptidases of the S1 (IPR001254) and S8 (IPR000209) families. Potato inhibitor type I sequences are not solely restricted to potatoes but are found in other plant species for example: barley endosperm chymotrypsin inhibitor, and pumpkin trypsin inhibitor. Apart from leeches, e.g.Hirudo medicinalis (Medicinal leech), homologues are not found in metazoa. In general, the proteins have retained a specificity towards chymotrypsin-like and elastase-like proteases. Structurally these inhibitors are small (60 to 90 residues) and in contrast with other families of protease inhibitors, they lack disulphide bonds. The inhibitor is a wedge-shaped molecule, its pointed edge formed by the protease-binding loop, which contains the scissile bond. The loop binds tightly to the protease active site, subsequent cleavage of the scissile bond causing inhibition of the enzyme. |
| PF00082 |
Subtilase family |
The glycosyl hydrolases family 18 (GH18) GH18 is widely distributed in all kingdoms and contains hydrolytic enzymes with chitinase or endo-N-acetyl-beta-D-glucosaminidase (ENGase) activity as well as chitinase-like lectins (chi-lectins/proteins (CLPs). Chitinases (3.2.1.14) are hydrolytic enzymes that cleave the beta-1,4-bond releasing oligomeric, dimeric (chitobiose) or monomeric (N-actetylglucosamine, GlcNAc) products. ENGases (3.2.1.96) hydrolyze the beta-1,4 linkage in the chitobiose core of N-linked glycans from glycoproteins leaving one GlcNAc residue on the substrate. CLPs do not display chitinase activity but some of them have been reported to have specific functions and carbohydrate binding property. This family also includes glycoproteins from mammals, such as oviduct-specific glycoproteins. |
| PF00704 |
Glycosyl hydrolases family 18 |
PR-8 proteins are glycosyl hydrolases family 18 members, including chitinases that hydrolyze chitin polymers. They play important roles in plant defense against fungal pathogens by degrading chitin in fungal cell walls and are induced during pathogen infection. |
| PF00141 |
Peroxidase |
This entry represents the first type of haem peroxidases found predominantly in bacteria, fungi, plants. |
| PF00407 |
Pathogenesis-related protein Bet v 1 family |
This family is named after Bet v 1, the major birch pollen allergen. This protein belongs to family 10 of plant pathogenesis-related proteins (PR-10), cytoplasmic proteins of 15-17 kd that are wide-spread among dicotyledonous plants. In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. A classification by sequence similarity yielded several subfamilies related to PR-10: - Pathogenesis-related proteins PR-10: These proteins were identified as major tree pollen allergens in birch and related species (hazel, alder), as plant food allergens expressed in high levels in fruits, vegetables and seeds (apple, celery, hazelnut), and as pathogenesis-related proteins whose expression is induced by pathogen infection, wounding, or abiotic stress. Hyp-1 (Q8H1L1), an enzyme involved in the synthesis of the bioactive naphthodianthrone hypericin in St. John's wort (Hypericum perforatum) also belongs to this family. Most of these proteins were found in dicotyledonous plants. In addition, related sequences were identified in monocots and conifers. - Cytokinin-specific binding proteins: These legume proteins bind cytokinin plant hormones. - (S)-Norcoclaurine synthases are enzymes catalysing the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine. -Major latex proteins and ripening-related proteins are proteins of unknown biological function that were first discovered in the latex of opium poppy (Papaver somniferum) and later found to be upregulated during ripening of fruits such as strawberry and cucumber. The occurrence of Bet v 1-related proteins is confined to seed plants with the exception of a cytokinin-binding protein from the moss Physcomitrella patens (Q9AXI3). |
| PF00304 |
Gamma-thionin family |
PR-12 proteins are part of the gamma-thionin family, small cysteine-rich peptides with antimicrobial activity. They exhibit broad-spectrum activity against bacteria, fungi, and oomycetes, contributing to plant innate immunity through membrane disruption mechanisms. |
| PF00234 |
Protease inhibitor/seed storage/LTP family |
This family is composed of trypsin-alpha amylase inhibitors, seed storage proteins and lipid transfer proteins from plants. |
| PF00190 |
Cupin |
This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant. |
| PF04450 |
Peptidase of plants and bacteria |
These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens. |
| PF01565 |
FAD binding domain |
This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme 1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan. |
| PF00560 |
Leucine Rich Repeat |
CAUTION: This Pfam may not find all Leucine Rich Repeats in a protein. Leucine Rich Repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains. |
| PF00931 |
NB-ARC domain |
This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals. This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1). It contains the three-layered α-β fold and subsequent short α-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome. |
| PF01030 |
Receptor L domain |
The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain. |
| PF01582 |
TIR domain |
The Toll/interleukin-1 receptor (TIR) homology domain is an intracellular signalling domain found in MyD88, interleukin 1 receptor and the Toll receptor. It contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins thought to be involved in resistance to disease. When activated, TIR domains recruit cytoplasmic adaptor proteins MyD88 (Q99836) and TOLLIP (Toll interacting protein, Q9H0E2). In turn, these associate with various kinases to set off signalling cascades. |
| PF03382 |
Mycoplasma protein of unknown function, DUF285 |
This region appears distantly related to leucine rich repeats. |
| PF05725 |
FNIP Repeat |
This short repeat is predominantly found in proteins from mimivirus and lower eukaryotes, including Calmodulin-binding protein CmbB from Dictyostelium discoideum (Social amoeba). It appears to be related to PF00560 (personal obs:C Yeats). The alignment consists of two tandem repeats. It is termed the FNIP repeat after the pattern of conserved residues. |
| PF07723 |
Leucine Rich Repeat |
This Pfam entry includes some LRRs that fail to be detected with the PF00560 model. |
| PF07725 |
Leucine Rich Repeat |
This Pfam entry includes some LRRs that fail to be detected with the PF00560 model. |
| PF13306 |
BspA type Leucine rich repeat region (6 copies) |
This family includes a number of leucine rich repeats. This family contains a large number of BSPA-like surface antigens from Trichomonas vaginalis. |
| PF13516 |
Leucine Rich repeat |
Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions.Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response. |
| PF13855 |
Leucine rich repeat |
Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions.Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response. |
| PF14580 |
Leucine-rich repeat |
PF14580 corresponds to a Leucine-Rich Repeat domain variant associated with NBS-LRR proteins. This domain is involved in the specific recognition of pathogen effectors, contributing to the plant's ability to distinguish between different pathogens and mount appropriate defenses. |
| PF18052 |
Rx N-terminal domain |
This entry represents the N-terminal domain found in many plant resistance proteins. This domain has been predicted to be a coiled-coil, however the structure shows that it adopts a four helical bundle fold. |
