Summary: Legume-like lectin family
This is the Wikipedia entry entitled "L-type lectin domain". More...
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L-type lectin domain Edit Wikipedia article
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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
Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 and ERGIC-53 lectins. Although proteins containging this domain were originally identified as a family of animal lectins, there are also yeast representatives.
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. Its dysfunction[disambiguation needed] 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.
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.
- 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. doi:10.1016/0092-8674(94)90047-7. PMID 8205612.
- 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. doi:10.1091/mbc.7.3.483. PMC 275899. PMID 8868475.
- 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. doi:10.1074/jbc.M112098200. PMID 11850423.
- 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. doi:10.1016/j.jmb.2003.10.031. PMID 14643651.
- 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. doi:10.1074/jbc.M512258200. PMID 16439369.
- 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. doi:10.1074/jbc.M703064200. PMID 17652092.
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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 . 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  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 . 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].
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
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
External database links
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].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
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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
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Curation and family details
|Seed source:||Pfam-B_2789 (release 6.6)|
|Number in seed:||8|
|Number in full:||783|
|Average length of the domain:||200.80 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||52.53 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
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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 35 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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