Summary: Protease inhibitor/seed storage/LTP family
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This is the Wikipedia entry entitled "Plant lipid transfer proteins". More...
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Plant lipid transfer proteins Edit Wikipedia article
|Plant lipid transfer protein|
Plant lipid transfer proteins, also known as plant LTPs or PLTPs, are a group of highly-conserved proteins of about 7-9kDa found in higher plant tissues. As its name implies, lipid transfer proteins are responsible for the shuttling of phospholipids and other fatty acid groups between cell membranes. LTPs are divided into two structurallyrelated subfamilies according to their molecular masses: LTP1s (9 kDa) and LTP2s (7 kDa). Various LTPs bind a wide range of ligands, including fatty acids (FAs) with a C10â€“C18 chain length, acyl derivatives of coenzyme A (CoA), phospho- and galactolipids, prostaglandin B2, sterols, molecules of organic solvents, and some drugs. LTP2
LTPs constitute one of the classes of defense PRPs, many of which have antimicrobial and enzymatic activities or are enzyme inhibitors. Different proteins of this class can exhibit the following activities:
and inhibit some enzymes.
Ordinarily, most lipids do not spontaneously exit membranes because their hydrophobicity makes them poorly soluble in water. LTPs facilitate the movement of lipids between membranes by binding, and solubilising them. LTPs typically have broad substrate specificity and so can interact with a variety of different lipids.
LTPs in plants may be involved in:
- cutin biosynthesis
- surface wax formation
- mitochondrial growth
- pathogen defense reactions
- adaptation to environmental changes
- lipid metabolism
- fertilization of flowering plants
- adaptation of plants under stress conditions
- activation and regulation of signaling cascades
- fruit ripening
Plant lipid transfer proteins consist of 4 alpha-helices in a right-handed superhelix with a folded leaf topology. The structure is stabilised by disulfide bonds linking the helices to each other.
The structure forms an internal hydrophobic cavity in which 1-2 lipids can be bound. The outer surface of the protein is hydrophilic allowing the complex to be soluble. The use of hydrophobic interactions, with very few charged interactions, allows the protein to have broad specificity for a range of lipids.
Plant lipid transfer proteins share the same structural domain with seed storage proteins and trypsin-alpha amylase inhibitors. These proteins share the same superhelical, disulphide-stabilised four-helix bundle containing an internal cavity.
There is no sequence similarity between animal and plant LTPs. In animals, cholesterylester transfer protein (CETP), also called plasma lipid transfer protein, is a plasma protein that facilitates the transport of cholesteryl esters and triglycerides between the lipoproteins.
Role in human health
PLTPs are pan-allergens,   and may be directly responsible for cases of food allergy. Pru p 3, the major allergen from peach, is a 9-kDa allergen belonging to the family of lipid-transfer proteins.  Allergic properties are closely linked with high thermal stability and resistance to gastrointestinal proteolysis of the proteins. Many of the LTP allergens are able to cause not only manifestation of allergic reactions but also sensitization via the gastrointestinal tract, being thus class I food allergens. In contrast, class II food allergens are able only to elicit allergic symptoms due to its cross-reactivity with major sensitizer.
They are used as antioxidants and prevent diseases.
- Asero R, Mistrello G, Roncarolo D, de Vries SC, Gautier MF, Ciurana CL, Verbeek E, Mohammadi T, Knul-Brettlova V, Akkerdaas JH, Bulder I, Aalberse RC, van Ree R (2001). "Lipid transfer protein: a pan-allergen in plant-derived foods that is highly resistant to pepsin digestion". International Archives of Allergy and Immunology. 124 (1â€“3): 67â€“9. doi:10.1159/000053671. PMID 11306929.
- Finkina EI, Melnikova DN, Bogdanov IV, Ovchinnikova TV (2016). "Lipid Transfer Proteins As Components of the Plant Innate Immune System: Structure, Functions, and Applications". Acta Naturae. 8 (2): 47â€“61. doi:10.32607/20758251-2016-8-2-47-61. PMC 4947988. PMID 27437139.
- Kader JC (June 1996). "Lipid-Transfer Protein in Plants". Annual Review of Plant Physiology and Plant Molecular Biology. 47: 627â€“654. doi:10.1146/annurev.arplant.47.1.627. PMID 15012303.
- Finkina EI, Melnikova DN, Bogdanov IV, Ovchinnikova TV (2017-07-04). "Plant Pathogenesis-Related Proteins PR-10 and PR-14 as Components of Innate Immunity System and Ubiquitous Allergens". Current Medicinal Chemistry. 24 (17): 1772â€“1787. doi:10.2174/0929867323666161026154111. PMID 27784212.
- Cheng HC, Cheng PT, Peng P, Lyu PC, Sun YJ (September 2004). "Lipid binding in rice nonspecific lipid transfer protein-1 complexes from Oryza sativa". Protein Science. 13 (9): 2304â€“15. doi:10.1110/ps.04799704. PMC 2280015. PMID 15295114.
- Kader, Jean-Claude (February 1997). "Science Direct". Trends in Plant Science. 2 (2): 66â€“70. doi:10.1016/S1360-1385(97)82565-4.
- Lin KF, Liu YN, Hsu ST, Samuel D, Cheng CS, Bonvin AM, Lyu PC (April 2005). "Characterization and structural analyses of nonspecific lipid transfer protein 1 from mung bean". Biochemistry. 44 (15): 5703â€“12. doi:10.1021/bi047608v. PMID 15823028.
- Pantoja-Uceda D, Bruix M, GimÃ©nez-Gallego G, Rico M, Santoro J (December 2003). "Solution structure of RicC3, a 2S albumin storage protein from Ricinus communis". Biochemistry. 42 (47): 13839â€“47. doi:10.1021/bi0352217. PMID 14636051.
- Oda Y, Matsunaga T, Fukuyama K, Miyazaki T, Morimoto T (November 1997). "Tertiary and quaternary structures of 0.19 alpha-amylase inhibitor from wheat kernel determined by X-ray analysis at 2.06 A resolution". Biochemistry. 36 (44): 13503â€“11. doi:10.1021/bi971307m. PMID 9354618.
- Gourinath S, Alam N, Srinivasan A, Betzel C, Singh TP (March 2000). "Structure of the bifunctional inhibitor of trypsin and alpha-amylase from ragi seeds at 2.2 A resolution". Acta Crystallographica D. 56 (Pt 3): 287â€“93. doi:10.1107/s0907444999016601. PMID 10713515.
- Morris A. "Food Allergy in Detail". Surrey Allergy Clinic.
- InterPro: IPR000528
- Besler M, Herranz JC, FernÃ¡ndez-Rivas M (2000). "Peach allergy". Internet Symposium on Food Allergens. 2 (4): 185â€“201.
- Bogdanov IV, Shenkarev ZO, Finkina EI, Melnikova DN, Rumynskiy EI, Arseniev AS, Ovchinnikova TV (April 2016). "A novel lipid transfer protein from the pea Pisum sativum: isolation, recombinant expression, solution structure, antifungal activity, lipid binding, and allergenic properties". BMC Plant Biology. 16: 107. doi:10.1186/s12870-016-0792-6. PMC 4852415. PMID 27137920.
- Halliwell B (1996). "Antioxidants in human health and disease". Annual Review of Nutrition. 16: 33â€“50. doi:10.1146/annurev.nu.16.070196.000341. PMID 8839918.
- "Foam". Carlsberg Research Laboratory.
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.
Protease inhibitor/seed storage/LTP family Provide feedback
This family is composed of trypsin-alpha amylase inhibitors, seed storage proteins and lipid transfer proteins from plants.
Rico M, Bruix M, Gonzalez C, Monsalve RI, Rodriguez R; , Biochemistry 1996;35:15672-15682.: 1H NMR assignment and global fold of napin BnIb, a representative 2S albumin seed protein. PUBMED:8961930 EPMC:8961930
Internal database links
|SCOOP:||Gliadin Glutenin_hmw Hydrophob_seed LTP_2 Prolamin_like|
|Similarity to PfamA using HHSearch:||Gliadin LTP_2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR016140
This entry represents a structural domain consisting of 4-helices with a folded leaf topology, and forming a right-handed superhelix. This domain occurs in several proteins, including:
- Plant lipid-transfer proteins, such as the non-specific lipid-transfer proteins ns-LTP1 and ns-LTP2 [ PUBMED:10491104 , PUBMED:12011089 ].
- Proteinase/alpha-amylase inhibitors, such as trypsin/alpha-amylase inhibitor RBI from Eleusine coracana (Indian finger millet) [ PUBMED:9687373 ] and Hageman factor/amylase inhibitor from Zea mays (Maize) [ PUBMED:9799488 ].
- Seed storage proteins, such as napin from Brassica napus (Rape) [ PUBMED:8961930 ] and 2S albumin from Ricinus communis (Castor bean) [ PUBMED:14636051 ].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
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- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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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.
|Author:||Bateman A , Finn RD , Griffiths-Jones SR|
|Number in seed:||183|
|Number in full:||2696|
|Average length of the domain:||94.60 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||67.49 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||25|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
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.
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:
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- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
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 Tryp_alpha_amyl domain has been found. There are 91 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 sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.