Summary: Legume-like lectin family
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This is the Wikipedia entry entitled "L-type lectin domain". More...
L-type lectin domain Edit Wikipedia article
| Lectin_leg-like | |||||||||
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the crystal structure of the carbohydrate recognition domain of the glycoprotein sorting receptor p58/ergic-53 reveals a novel metal binding site and conformational changes associated with calcium ion binding
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| Identifiers | |||||||||
| Symbol | Lectin_leg-like | ||||||||
| Pfam | PF03388 | ||||||||
| Pfam clan | CL0004 | ||||||||
| InterPro | IPR005052 | ||||||||
| SCOP | 1gv9 | ||||||||
| SUPERFAMILY | 1gv9 | ||||||||
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In molecular biology the L-like lectin domain is a protein domain found in lectins which are similar to the leguminous plant lectins.
Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 and ERGIC-53 lectins.[1] Although proteins containging this domain were originally identified as a family of animal lectins, there are also yeast representatives.[1]
ERGIC-53 is a 53kDa protein, localised to the intermediate region between the endoplasmic reticulum and the Golgi apparatus (ER-Golgi-Intermediate Compartment, ERGIC). It was identified as a calcium-dependent, mannose-specific lectin.[2] Its dysfunction has been associated with combined factors V and VIII deficiency, suggesting an important and substrate-specific role for ERGIC-53 in the glycoprotein-secreting pathway.[2][3]
The L-like lectin domain has an overall globular shape composed of a beta-sandwich of two major twisted antiparallel beta-sheets. The beta-sandwich comprises a major concave beta-sheet and a minor convex beta-sheet, in a variation of the jelly roll fold.[4][5][6][7]
References
- ^ a b Fiedler K, Simons K (June 1994). "A putative novel class of animal lectins in the secretory pathway homologous to leguminous lectins". Cell. 77 (5): 625–6. PMID 8205612. doi:10.1016/0092-8674(94)90047-7.
- ^ a b Itin C, Roche AC, Monsigny M, Hauri HP (March 1996). "ERGIC-53 is a functional mannose-selective and calcium-dependent human homologue of leguminous lectins". Mol. Biol. Cell. 7 (3): 483–93. PMC 275899
. PMID 8868475. doi:10.1091/mbc.7.3.483. - ^ Nichols WC, Terry VH, Wheatley MA, Yang A, Zivelin A, Ciavarella N, Stefanile C, Matsushita T, Saito H, de Bosch NB, Ruiz-Saez A, Torres A, Thompson AR, Feinstein DI, White GC, Negrier C, Vinciguerra C, Aktan M, Kaufman RJ, Ginsburg D, Seligsohn U (April 1999). "ERGIC-53 gene structure and mutation analysis in 19 combined factors V and VIII deficiency families". Blood. 93 (7): 2261–6. PMID 10090935.
- ^ Velloso LM, Svensson K, Schneider G, Pettersson RF, Lindqvist Y (May 2002). "Crystal structure of the carbohydrate recognition domain of p58/ERGIC-53, a protein involved in glycoprotein export from the endoplasmic reticulum". J. Biol. Chem. 277 (18): 15979–84. PMID 11850423. doi:10.1074/jbc.M112098200.
- ^ Velloso LM, Svensson K, Pettersson RF, Lindqvist Y (December 2003). "The crystal structure of the carbohydrate-recognition domain of the glycoprotein sorting receptor p58/ERGIC-53 reveals an unpredicted metal-binding site and conformational changes associated with calcium ion binding". J. Mol. Biol. 334 (5): 845–51. PMID 14643651. doi:10.1016/j.jmb.2003.10.031.
- ^ Satoh T, Sato K, Kanoh A, Yamashita K, Yamada Y, Igarashi N, Kato R, Nakano A, Wakatsuki S (April 2006). "Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p". J. Biol. Chem. 281 (15): 10410–9. PMID 16439369. doi:10.1074/jbc.M512258200.
- ^ Satoh T, Cowieson NP, Hakamata W, Ideo H, Fukushima K, Kurihara M, Kato R, Yamashita K, Wakatsuki S (September 2007). "Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36". J. Biol. Chem. 282 (38): 28246–55. PMID 17652092. doi:10.1074/jbc.M703064200.
This article incorporates text from the public domain Pfam and InterPro IPR005052
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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.
Legume-like lectin family Provide feedback
Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 P49256 and ERGIC-53 P49257 lectins. These two proteins were the first recognised members of a family of animal lectins similar (19-24%) to the leguminous plant lectins [1]. The alignment for this family aligns residues lying towards the N-terminus, where the similarity of VIP36 and ERGIC-53 is greatest. However, while Fiedler and Simons [1] identified these proteins as a new family of animal lectins, our alignment also includes yeast sequences. ERGIC-53 is a 53kD protein, localised to the intermediate region between the endoplasmic reticulum and the Golgi apparatus (ER-Golgi-Intermediate Compartment, ERGIC). It was identified as a calcium-dependent, mannose-specific lectin [2]. Its dysfunction has been associated with combined factors V and VIII deficiency OMIM:227300 OMIM:601567 suggesting an important and substrate-specific role for ERGIC-53 in the glycoprotein- secreting pathway [2,3].
Literature references
-
Fiedler K, Simons K; , Cell 1994;77:625-626.: A putative novel class of animal lectins in the secretory pathway homologous to leguminous lectins. PUBMED:8205612 EPMC:8205612
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Itin C, Roche AC, Monsigny M, Hauri HP; , Mol Biol Cell 1996;7:483-493.: ERGIC-53 is a functional mannose-selective and calcium-dependent human homologue of leguminous lectins. PUBMED:8868475 EPMC:8868475
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Nichols WC, Terry VH, Wheatley MA, Yang A, Zivelin A, Ciavarella N, Stefanile C, Matsushita T, Saito H, de Bosch NB, Ruiz-Saez A, Torres A, Thompson AR, Feinstein DI, White GC, Negrier C, Vinciguerra C, Aktan M, Kaufman RJ, Ginsburg D, Seligsohn U; , Blood 1999;93:2261-2266.: ERGIC-53 gene structure and mutation analysis in 19 combined factors V and VIII deficiency families. PUBMED:10090935 EPMC:10090935
Internal database links
| SCOOP: | Bact_lectin Lectin_legB |
| Similarity to PfamA using HHSearch: | Lectin_legB Bact_lectin |
External database links
| SCOP: | 1gv9 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR005052
Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 and ERGIC-53 lectins. These two proteins were the first members of the family of animal lectins similar to the leguminous plant lectins [PUBMED:8205612]. The alignment for this family is towards the N terminus, where the similarity of VIP36 and ERGIC-53 is greatest. Although they have been identified as a family of animal lectins, this alignment also includes yeast sequences[PUBMED:8205612].
ERGIC-53 is a 53kDa protein, localised to the intermediate region between the endoplasmic reticulum and the Golgi apparatus (ER-Golgi-Intermediate Compartment, ERGIC). It was identified as a calcium-dependent, mannose-specific lectin [PUBMED:8868475]. Its dysfunction has been associated with combined factors V and VIII deficiency, suggesting an important and substrate-specific role for ERGIC-53 in the glycoprotein-secreting pathway [PUBMED:8868475,PUBMED:10090935].
The L-type lectin-like domain has an overall globular shape composed of a beta-sandwich of two major twisted antiparallel beta-sheets. The beta-sandwich comprises a major concave beta-sheet and a minor convex beta-sheet, in a variation of the jelly roll fold [PUBMED:11850423, PUBMED:14643651, PUBMED:16439369, PUBMED:17652092].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Cellular component | membrane (GO:0016020) |
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 49 members:
Alginate_lyase2 ArabFuran-catal Arabino_trans_N Bac_rhamnosid Bact_lectin Calreticulin Cleaved_Adhesin DUF1080 DUF1349 DUF1583 DUF1961 DUF2401 DUF3472 DUF4975 Exotox-A_bind Gal-bind_lectin GalBD_like GH131_N GH43_C2 Glyco_hydro_11 Glyco_hydro_12 Glyco_hydro_16 Glyco_hydro_32C Glyco_hydro_7 HA1 Laminin_G_1 Laminin_G_2 Laminin_G_3 Lectin_leg-like Lectin_legB MAM Methyltransf_FA Neuralized Pentaxin Peptidase_A4 Polysacc_lyase PRY Reoviridae_Vp9 Sial-lect-inser Sialidase SKN1 Spike_NTD SPRY TgMIC1 Toxin_R_bind_N TSP_C VP4_haemagglut XET_C YrpDAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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| Seed (8) |
Full (2264) |
Representative proteomes | UniProt (3406) |
NCBI (4861) |
Meta (29) |
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| RP15 (619) |
RP35 (1161) |
RP55 (1719) |
RP75 (2177) |
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| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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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 (8) |
Full (2264) |
Representative proteomes | UniProt (3406) |
NCBI (4861) |
Meta (29) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (619) |
RP35 (1161) |
RP55 (1719) |
RP75 (2177) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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
| Seed source: | Pfam-B_2789 (release 6.6) |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Mifsud W 
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| Number in seed: | 8 |
| Number in full: | 2264 |
| Average length of the domain: | 202.70 aa |
| Average identity of full alignment: | 29 % |
| Average coverage of the sequence by the domain: | 50.93 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 230 | ||||||||||||
| Family (HMM) version: | 13 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Interactions
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_leg-like domain has been found. There are 58 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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