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35  structures 280  species 1  interaction 783  sequences 10  architectures

Family: Lectin_leg-like (PF03388)

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
PDB 1r1z EBI.jpg
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
Identifiers
Symbol Lectin_leg-like
Pfam PF03388
Pfam clan CL0004
InterPro IPR005052
SCOP 1gv9
SUPERFAMILY 1gv9

In molecular biology the L-type 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[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.[2][3]

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.[4][5][6][7]

References

  1. ^ 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. doi:10.1016/0092-8674(94)90047-7. PMID 8205612. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ 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. 
  6. ^ 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. 
  7. ^ 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. 

This article incorporates text from the public domain Pfam and InterPro IPR005052

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.

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

  1. 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

  2. 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

  3. 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].

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.

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(8)
Full
(783)
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(811)
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(29)
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(158)
RP35
(234)
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RP75
(470)
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  Seed
(8)
Full
(783)
Representative proteomes NCBI
(811)
Meta
(29)
RP15
(158)
RP35
(234)
RP55
(362)
RP75
(470)
Alignment:
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  Seed
(8)
Full
(783)
Representative proteomes NCBI
(811)
Meta
(29)
RP15
(158)
RP35
(234)
RP55
(362)
RP75
(470)
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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: Pfam-B_2789 (release 6.6)
Previous IDs: none
Type: Family
Author: Mifsud W
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 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 20.1 20.1
Trusted cut-off 20.1 20.1
Noise cut-off 20.0 20.0
Model length: 230
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Lectin_leg-like

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 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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