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52  structures 243  species 1  interaction 1632  sequences 6  architectures

Family: Tryp_alpha_amyl (PF00234)

Summary: Protease inhibitor/seed storage/LTP family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Plant lipid transfer proteins". More...

Plant lipid transfer proteins Edit Wikipedia article

Plant lipid transfer protein/seed storage/trypsin-alpha amylase inhibitor
Identifiers
Symbol LTP/seed_store/tryp_amyl_inhib
Pfam PF00234
InterPro IPR003612
SMART SM00499

Plant lipid transfer proteins, also known as plant LTPs or PLTPs, are a group of highly-conserved proteins of about 9kDa found in higher plant tissues.[1] As its name implies, lipid transfer proteins are responsible for the shuttling of phospholipids and other fatty acid groups between cell membranes.[2] LTPs are also able to bind acyl groups.[2]

Other related proteins

Plant lipid transfer proteins share the same structural domain[3] with seed storage proteins[4] and trypsin-alpha amylase inhibitors.[5][6] The domain forms a four-helical bundle in a right-handed superhelix with a folded leaf topology, which is stabilised by disulfide bonds, and which has 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, [7] [8] 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. [9]

They are used as antioxidants and prevent diseases.[citation needed]

Commercial importance

Lipid transfer protein 1 (from barley) is responsible, when denatured by the mashing process, for the bulk of foam which forms on top of beer.[10]

Role in plant biology

These proteins in plants may be involved in:

  • cutin biosynthesis
  • surface wax formation
  • pathogen defense reactions
  • for adaptation of plants to environmental changes[11]

See also

References

  1. ^ http://content.karger.com/ProdukteDB/produkte.asp?Doi=53671
  2. ^ a b http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.47.1.627?cookieSet=1&journalCode=arplant.2
  3. ^ Bonvin AM, Lyu PC, Samuel D, Cheng CS, Lin KF, Liu YN, Hsu ST (2005). "Characterization and structural analyses of nonspecific lipid transfer protein 1 from mung bean". Biochemistry 44 (15): –. doi:10.1021/bi047608v. PMID 15823028. 
  4. ^ Bruix M, Santoro J, Rico M, Gimenez-Gallego G, Pantoja-Uceda D (2003). "Solution structure of RicC3, a 2S albumin storage protein from Ricinus communis". Biochemistry 42 (47): –. doi:10.1021/bi0352217. PMID 14636051. 
  5. ^ Fukuyama K, Oda Y, Morimoto T, Matsunaga T, Miyazaki T (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): –. doi:10.1021/bi971307m. PMID 9354618. 
  6. ^ Betzel C, Srinivasan A, Singh TP, Gourinath S, Alam N (2000). "Structure of the bifunctional inhibitor of trypsin and alpha-amylase from ragi seeds at 2.2 A resolution". Acta Crystallogr. D 56: –. doi:10.1107/s0907444999016601. PMID 10713515. 
  7. ^ http://www.allergy-clinic.co.uk/food-allergy/food-allergy-guide/
  8. ^ http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000528
  9. ^ http://www.food-allergens.de/symposium-2-4/peach/peach-allergens.htm Peach allergy, M.Besler et al.
  10. ^ http://www.crc.dk/flab/foam.htm
  11. ^ "Science Direct". 


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Literature references

  1. 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

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:

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Prolamin (CL0482), which has the following description:

This superfamily is characterised by families with only slightly differing disulfide-bonding patterning.

The clan contains the following 5 members:

Gliadin Hydrophob_seed LTP_2 Prolamin_like Tryp_alpha_amyl

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...

View options

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
(187)
Full
(1632)
Representative proteomes NCBI
(4676)
Meta
(6)
RP15
(29)
RP35
(95)
RP55
(159)
RP75
(214)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(187)
Full
(1632)
Representative proteomes NCBI
(4676)
Meta
(6)
RP15
(29)
RP35
(95)
RP55
(159)
RP75
(214)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(187)
Full
(1632)
Representative proteomes NCBI
(4676)
Meta
(6)
RP15
(29)
RP35
(95)
RP55
(159)
RP75
(214)
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: Prosite
Previous IDs: tryp_alpha_amyl;
Type: Family
Author: Bateman A, Finn RD, Griffiths-Jones SR
Number in seed: 187
Number in full: 1632
Average length of the domain: 103.10 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 68.27 %

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 21.7 21.7
Trusted cut-off 21.7 21.7
Noise cut-off 21.6 21.6
Model length: 90
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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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 adjacent tab. More...

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Interactions

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

Tryp_alpha_amyl

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 Tryp_alpha_amyl domain has been found. There are 52 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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