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242  structures 331  species 1  interaction 3003  sequences 115  architectures

Family: Jacalin (PF01419)

Summary: Jacalin-like lectin domain

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This is the Wikipedia entry entitled "Jacalin-like lectin domain". More...

Jacalin-like lectin domain Edit Wikipedia article

Jacalin-like lectin domain
PDB 1c3n EBI.jpg
crystal structure of helianthus tuberosus lectin complexed to man(1-2)man
Identifiers
Symbol Jacalin
Pfam PF01419
InterPro IPR001229
SCOP 1jac
SUPERFAMILY 1jac

In molecular biology, the jacalin-like lectin domain is a mannose-binding lectin domain with a beta-prism fold consisting of three 4-stranded beta-sheets, with an internal pseudo 3-fold symmetry. Some lectins in this group stimulate distinct T- and B-cell functions, such as Jacalin, which binds to the T-antigen and acts as an agglutinin. This domain is found in 1 to 6 copies in lectins. The domain is also found in the salt-stress induced protein from rice and an animal prostatic spermine-binding protein.

Database of jacalin like lectins and structure function relations.[1] Proteins containing this domain include:

References

  1. ^ Raval et al, "A database analysis of jacalin-like lectins: sequence–structure–function relationships" Glycobiology vol. 14 no. 12 pp. 1247–1263, 2004 http://glycob.oxfordjournals.org/content/14/12/1247.full.pdf
  2. ^ Jeyaprakash AA, Geetha Rani P, Banuprakash Reddy G, Banumathi S, Betzel C, Sekar K, Surolia A, Vijayan M (August 2002). "Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexes". J. Mol. Biol. 321 (4): 637–45. doi:10.1016/S0022-2836(02)00674-5. PMID 12206779. 
  3. ^ Jeyaprakash AA, Srivastav A, Surolia A, Vijayan M (May 2004). "Structural basis for the carbohydrate specificities of artocarpin: variation in the length of a loop as a strategy for generating ligand specificity". J. Mol. Biol. 338 (4): 757–70. doi:10.1016/j.jmb.2004.03.040. PMID 15099743. 
  4. ^ Lee X, Thompson A, Zhang Z, Ton-that H, Biesterfeldt J, Ogata C, Xu L, Johnston RA, Young NM (March 1998). "Structure of the complex of Maclura pomifera agglutinin and the T-antigen disaccharide, Galbeta1,3GalNAc". J. Biol. Chem. 273 (11): 6312–8. doi:10.1074/jbc.273.11.6312. PMID 9497359. 
  5. ^ Bourne Y, Zamboni V, Barre A, Peumans WJ, Van Damme EJ, Rouge P (December 1999). "Helianthus tuberosus lectin reveals a widespread scaffold for mannose-binding lectins". Structure. 7 (12): 1473–82. doi:10.1016/s0969-2126(00)88338-0. PMID 10647178. 
  6. ^ Bourne Y, Roig-Zamboni V, Barre A, Peumans WJ, Astoul CH, Van Damme EJ, Rouge P (January 2004). "The crystal structure of the Calystegia sepium agglutinin reveals a novel quaternary arrangement of lectin subunits with a beta-prism fold". J. Biol. Chem. 279 (1): 527–33. doi:10.1074/jbc.M308218200. PMID 14561768. 
  7. ^ Ziolkowska NE, O'Keefe BR, Mori T, Zhu C, Giomarelli B, Vojdani F, Palmer KE, McMahon JB, Wlodawer A (July 2006). "Domain-swapped structure of the potent antiviral protein griffithsin and its mode of carbohydrate binding". Structure. 14 (7): 1127–35. doi:10.1016/j.str.2006.05.017. PMID 16843894. 

This article incorporates text from the public domain Pfam and InterPro IPR001229

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

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Jacalin-like lectin domain Provide feedback

Proteins containing this domain are lectins. It is found in 1 to 6 copies in these proteins. The domain is also found in the animal prostatic spermine-binding protein (P15501).

Literature references

  1. Sankaranarayanan R, Sekar K, Banerjee R, Sharma V, Surolia A, Vijayan M; , Nat Struct Biol 1996;3:596-603.: A novel mode of carbohydrate recognition in jacalin, a Moraceae plant lectin with a beta-prism fold. PUBMED:8673603 EPMC:8673603


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001229

The jacalin-like mannose-binding lectin domain has a beta-prism fold consisting of three 4-stranded beta-sheets, with an internal pseudo 3-fold symmetry. Some proteins with this domain stimulate distinct T- and B- cell functions, such as the plant lectin jacalin, which binds to the T-antigen and acts as an agglutinin. The domain can occur in tandem-repeat arrangements with up to six copies, and in architectures combined with a variety of other functional domains. While the family was initially named after an abundant protein found in the jackfruit seed, taxonomic distribution is not restricted to plants. The domain is also found in the salt-stress induced protein from rice and an animal prostatic spermine-binding protein. Proteins containing this domain include:

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 Man_lectin (CL0568), which has the following description:

This familu of lectins has a beta-prism fold [1-2].

The clan contains the following 5 members:

Beta-prism_lec Endotoxin_M Endotoxin_mid Jacalin VOMI

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 (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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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
(36)
Full
(3003)
Representative proteomes UniProt
(4274)
NCBI
(6016)
Meta
(2)
RP15
(318)
RP35
(1004)
RP55
(2181)
RP75
(3033)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(36)
Full
(3003)
Representative proteomes UniProt
(4274)
NCBI
(6016)
Meta
(2)
RP15
(318)
RP35
(1004)
RP55
(2181)
RP75
(3033)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(36)
Full
(3003)
Representative proteomes UniProt
(4274)
NCBI
(6016)
Meta
(2)
RP15
(318)
RP35
(1004)
RP55
(2181)
RP75
(3033)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Bateman A
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 36
Number in full: 3003
Average length of the domain: 120.90 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 44.87 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -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: 135
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Selections

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Interactions

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

Jacalin

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 Jacalin domain has been found. There are 242 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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