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165  structures 224  species 1  interaction 1166  sequences 54  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:

  • Artocarpin, a tetrameric plant seed lectin from A. heterophyllus.[3]
  • Lectin MPA, a tetrameric plant seed lectin and agglutinin from Maclura pomifera (Osage orange).[4]
  • Agglutinin from Calystegia sepium (Hedge bindweed).[6]

References[edit]

  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. 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. 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.

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.

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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001229

This entry represents 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. 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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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
(52)
Full
(1166)
Representative proteomes NCBI
(1119)
Meta
(2)
RP15
(227)
RP35
(342)
RP55
(470)
RP75
(665)
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Format an alignment

  Seed
(52)
Full
(1166)
Representative proteomes NCBI
(1119)
Meta
(2)
RP15
(227)
RP35
(342)
RP55
(470)
RP75
(665)
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
(52)
Full
(1166)
Representative proteomes NCBI
(1119)
Meta
(2)
RP15
(227)
RP35
(342)
RP55
(470)
RP75
(665)
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.

Pfam alignments:

HMM logo

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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: 52
Number in full: 1166
Average length of the domain: 122.50 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 46.35 %

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 21.3 21.3
Trusted cut-off 21.4 21.4
Noise cut-off 21.2 21.1
Model length: 130
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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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 165 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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