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724  structures 320  species 1  interaction 1651  sequences 73  architectures

Family: Lectin_legB (PF00139)

Summary: Legume lectin domain

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This is the Wikipedia entry entitled "Leguminous lectin family". More...

Leguminous lectin family Edit Wikipedia article

Lectin_legB
PDB 1rin EBI.jpg
x-ray crystal structure of a pea lectin-trimannoside complex at 2.6 angstroms resolution
Identifiers
Symbol Lectin_legB
Pfam PF00139
Pfam clan CL0004
InterPro IPR001220
PROSITE PDOC00278
SCOP 1lem
SUPERFAMILY 1lem

In molecular biology, the leguminous lectin family is a family of lectin proteins.

It is one of the largest lectin families with more than 70 lectins reported in a review in 1990.[1] Leguminous lectins consist of two or four subunits, each containing one carbohydrate-binding site. The interaction with sugars requires tightly bound calcium and manganese ions. The structural similarities of these lectins are reported by the primary structural analyses and X-ray crystallographic studies.[2][3] X-ray studies have shown that the folding of the polypeptide chains in the region of the carbohydrate-binding sites is also similar, despite differences in the primary sequences. The carbohydrate-binding sites of these lectins consist of two conserved amino acids on beta pleated sheets. One of these loops contains transition metals, calcium and manganese, which keep the amino acid residues of the sugar-binding site at the required positions. Amino acid sequences of this loop play an important role in the carbohydrate-binding specificities of these lectins. These lectins bind either glucose, mannose or galactose. The exact function of legume lectins is not known but they may be involved in the attachment of nitrogen-fixing bacteria to legumes and in the protection against pathogens.[4][5]

Some legume lectins are proteolytically processed to produce two chains, beta (which corresponds to the N-terminal) and alpha (C-terminal). The lectin concanavalin A (conA) from jack bean is exceptional in that the two chains are transposed and ligated (by formation of a new peptide bond). The N terminus of mature conA thus corresponds to that of the alpha chain and the C terminus to the beta chain.[6]

References[edit]

  1. ^ Sharon N, Lis H (1990). "Legume lectins--a large family of homologous proteins.". FASEB J 4 (14): 3198–208. PMID 2227211. 
  2. ^ de Oliveira TM, Delatorre P, da Rocha BA, de Souza EP, Nascimento KS, Bezerra GA et al. (2008). "Crystal structure of Dioclea rostrata lectin: insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins.". J Struct Biol 164 (2): 177–82. doi:10.1016/j.jsb.2008.05.012. PMID 18682294. 
  3. ^ Rozwarski DA, Swami BM, Brewer CF, Sacchettini JC (1998). "Crystal structure of the lectin from Dioclea grandiflora complexed with core trimannoside of asparagine-linked carbohydrates.". J Biol Chem 273 (49): 32818–25. PMID 9830028. 
  4. ^ Roopashree S, Singh SA, Gowda LR, Rao AG (2006). "Dual-function protein in plant defence: seed lectin from Dolichos biflorus (horse gram) exhibits lipoxygenase activity.". Biochem J 395 (3): 629–39. doi:10.1042/BJ20051889. PMC 1462680. PMID 16441240. 
  5. ^ Beringer JE, Brewin N, Johnston AW, Schulman HM, Hopwood DA (1979). "The Rhizobium--legume symbiosis.". Proc R Soc Lond B Biol Sci 204 (1155): 219–33. PMID 36624. 
  6. ^ Carrington DM, Auffret A, Hanke DE (1985). "Polypeptide ligation occurs during post-translational modification of concanavalin A.". Nature 313 (5997): 64–7. doi:10.1038/313064a0. PMID 3965973. 

This article incorporates text from the public domain Pfam and InterPro IPR001220

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

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Legume lectin domain Provide feedback

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001220

Lectins are carbohydrate-binding proteins. Leguminous lectins form one of the largest lectin families and resemble each other in their physicochemical properties, though they differ in their carbohydrate specificities. They bind either glucose/mannose or galactose [PUBMED:2227211]. Carbohydrate-binding activity depends on the simultaneous presence of both a calcium and a transition metal ion [PUBMED:9546043]. The exact function of legume lectins is not known, but they may be involved in the attachment of nitrogen-fixing bacteria to legumes and in the protection against pathogens [PUBMED:16441240, PUBMED:36624].

Some legume lectins are proteolytically processed to produce two chains, beta (which corresponds to the N-terminal) and alpha (C-terminal) [PUBMED:8373823]. The lectin concanavalin A (conA) from jack bean is exceptional in that the two chains are transposed and ligated (by formation of a new peptide bond). The N terminus of mature conA thus corresponds to that of the alpha chain and the C terminus to the beta chain [PUBMED:3965973]. Though the legume lectins monomer is structurally well conserved, their quaternary structures vary widely [PUBMED:9546043].

Gene Ontology

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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 Concanavalin (CL0004), which has the following description:

This superfamily includes a diverse range of carbohydrate binding domains and glycosyl hydrolase enzymes that share a common structure.

The clan contains the following 16 members:

DUF1080 DUF2401 Gal-bind_lectin Glyco_hydro_11 Glyco_hydro_12 Glyco_hydro_16 Glyco_hydro_7 Laminin_G_1 Laminin_G_2 Laminin_G_3 Lectin_leg-like Lectin_legB Pentaxin Sialidase SKN1 Toxin_R_bind_N

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...

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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.

  Seed
(47)
Full
(1651)
Representative proteomes NCBI
(1765)
Meta
(72)
RP15
(114)
RP35
(409)
RP55
(591)
RP75
(782)
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Format an alignment

  Seed
(47)
Full
(1651)
Representative proteomes NCBI
(1765)
Meta
(72)
RP15
(114)
RP35
(409)
RP55
(591)
RP75
(782)
Alignment:
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Sequence:
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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
(47)
Full
(1651)
Representative proteomes NCBI
(1765)
Meta
(72)
RP15
(114)
RP35
(409)
RP55
(591)
RP75
(782)
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.

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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: lectin_legB;
Type: Domain
Author: Sonnhammer ELL, Bateman A
Number in seed: 47
Number in full: 1651
Average length of the domain: 204.20 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 39.67 %

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 20.2 20.2
Trusted cut-off 20.2 20.2
Noise cut-off 20.1 20.1
Model length: 237
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Lectin_legB

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 Lectin_legB domain has been found. There are 724 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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