Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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RICIN Ricin-type beta-trefoil

SMART accession number:	SM00458
Description:	Carbohydrate-binding domain formed from presumed gene triplication.
Interpro abstract (IPR000772):	Ricin is a legume lectin from the seeds of the castor bean plant, Ricinus communis. The seeds are poisonous to people, animals and insects and just one milligram of ricin can kill an adult. Primary structure analysis has shown the presence of a similar domain in many carbohydrate-recognition proteins like plant and bacterial AB-toxins, glycosidases or proteases [(PUBMED:9603958), (PUBMED:7664090), (PUBMED:8844840)]. This domain, known as the ricin B lectin domain, can be present in one or more copies and has been shown in some instance to bind simple sugars, such as galactose or lactose. The ricin B lectin domain is composed of three homologous subdomains of 40 amino acids (alpha, beta and gamma) and a linker peptide of around 15 residues (lambda). It has been proposed that the ricin B lectin domain arose by gene triplication from a primitive 40 residue galactoside-binding peptide [(PUBMED:3561502), (PUBMED:1881882)]. The most characteristic, though not completely conserved, sequence feature is the presence of a Q-W pattern. Consequently, the ricin B lectin domain as also been refered as the (QxW)3 domain and the three homologous regions as the QxW repeats [(PUBMED:7664090), (PUBMED:8844840)]. A disulphide bond is also conserved in some of the QxW repeats [(PUBMED:7664090)]. The 3D structure of the ricin B chain has shown that the three QxW repeats pack around a pseudo threefold axis that is stabilised by the lambda linker [(PUBMED:3561502)]. The ricin B lectin domain has no major segments of a helix or beta sheet but each of the QxW repeats contains an omega loop [(PUBMED:1881882)]. An idealized omega-loop is a compact, contiguous segment of polypeptide that traces a 'loop-shaped' path in three-dimensional space; the main chain resembles a Greek omega.
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 2458 RICIN domains in 2231 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a RICIN domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with RICIN domain is also avaliable.

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  Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Takifugu rubripes

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Hazes B
  • The (QxW)3 domain: a flexible lectin scaffold.
  • Protein Sci. 1996; 5: 1490-501
  • Display abstract

  • Lectins form a class of proteins that have evolved a specialized carbohydrate-binding function. Based on amino acid sequence analysis, several lectin families have been described and a lectin domain, the (QxW)3 domain, was discussed recently based on 11 family members. In this paper, the (QxW)3 domain family is extended to 45 sequences, several of which have very low sequence identity with the previously known members of the family. A hidden Markov model was used to identify the most divergent members of the family. The expanded set of sequences gives us a more complete appreciation of the conserved features, and the lack thereof, in this lectin family. This, in turn, provides new insights in the structural and functional properties of the individual family members.

  • Smith PD, Moss SE
  • Structural evolution of the annexin supergene family.
  • Trends Genet. 1994; 10: 241-6
  • Display abstract

  • The annexin family of calcium-binding proteins is comprised of at least ten mammalian genes, with additional representatives in lower eukaryotes. Recent structural analyses of several annexin genes have provided insights into the relationship between exon organization and functional domains. We discuss the implications of these findings and speculate on the evolutionary origins of the annexin supergene family.

  • Robertus J
  • The structure and action of ricin, a cytotoxic N-glycosidase.
  • Semin Cell Biol. 1991; 2: 23-30
  • Display abstract

  • The X-ray structure of the heterodimeric plant cytotoxin ricin has been elucidated. The A chain, known to be a specific N-glycosidase, has a prominent active site cleft. The B chain is a two domain lectin, which arose from the replication of a primitive sugar binding peptide. The molecular model reveals residues which are likely to be important in the action of the protein. Site directed mutagenesis reveals the relative importance of a number of these groups. A model for the mechanism of the A chain, including steric strain of the scissile bond and carboxonium ion transition state stabilization is proposed.

  • Rutenber E, Ready M, Robertus JD
  • Structure and evolution of ricin B chain.
  • Nature. 1987; 326: 624-6
  • Display abstract

  • Ricin is a dimeric toxin from the castor bean Ricinus communis, which is composed of a sugar-binding subunit (B) that attaches to receptors on the surfaces of target cells and a subunit (A) with enzymatic activity that attacks and inactivates ribosomes. We report here that comparison of amino-acid sequence data with high-resolution structure analysis of the ricin B subunit shows it to be the product of a series of gene duplications. The modern protein has two sugar-binding domains, each of which is composed of three copies of a more ancient galactose-binding peptide of about 40 residues.

  • Villafranca JE, Robertus JD
  • Ricin B chain is a product of gene duplication.
  • J Biol Chem. 1981; 256: 554-6
  • Display abstract

  • The cytotoxin ricin is a heterodimer composed of an A chain which enzymatically inhibits protein synthesis on eukaryotic ribosomes and a lectin B chain which binds to cell surfaces and triggers uptake of the toxin. A low resolution (4 A) x-ray structure revealed that the B chain is a bilobal structure and that each domain binds a galactose sugar. These apparent structural similarities suggested that the protein might have internal symmetry and might have arisen by gene duplication. A subsequent search of the amino acid sequence provided strong evidence for homology between th NH2- and COOH-terminal halves of the B chain and suggested that they may have arisen from a common ancestor. There is no strong relationship between the halves of the A chain and little, if any, significant sequence homology between the A and B chains of ricin.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 48.20 map00512 O-Glycan biosynthesis 48.20 map01030 Glycan structures - biosynthesis 1 0.90 map00600 Sphingolipid metabolism 0.45 map00520 Nucleotide sugars metabolism 0.45 map00530 Aminosugars metabolism 0.45 map00603 Glycosphingolipid biosynthesis - globoseries 0.45 map00561 Glycerolipid metabolism 0.45 map00052 Galactose metabolism 0.45 map01032 Glycan structures - degradation This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with RICIN domain which could be assigned to a KEGG orthologous group, and not all proteins containing RICIN domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of RICIN domains in PDB

  PDB code	Main view	Title
  1abr		Crystal structure of abrin-a
  1ce7		Mistletoe lectin i from viscum album
  1dqg		Crystal structure of the cysteine rich domain of mannose receptor
  1dqo		Crystal structure of the cysteine rich domain of mannose receptor complexed with acetylgalactosamine-4-sulfate
  1fwu		Crystal structure of the cysteine-rich domain of mannose receptor complexed with 3-so4-lewis(x)
  1fwv		Crystal structure of the cysteine-rich domain of mannose receptor complexed with 3-so4-lewis(a)
  1ggp		Crystal structure of trichosanthes kirilowii lectin-1 and its relation to the type 2 ribosome inactivating proteins
  1hwm		Ebulin,orthorhombic crystal form model
  1hwn		Ebulin complexed with galactose, trigonal crystal form
  1hwo		Ebulin complexed with lactose, trigonal crystal form
  1hwp		Ebulin complexed with pteroic acid, trigonal crystal form
  1isv		Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with xylose
  1isw		Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with xylobiose
  1isx		Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with xylotriose
  1isy		Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with glucose
  1isz		Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with galactose
  1it0		Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with lactose
  1knl		Streptomyces lividans xylan binding domain cbm13
  1knm		Streptomyces lividans xylan binding domain cbm13 in complex with lactose
  1m2t		Mistletoe lectin i from viscum album in complex with adenine monophosphate. crystal structure at 1.9 a resolution
  1mc9		Strepromyces lividans xylan binding domain cbm13 in complex with xylopentaose
  1onk		Mistletoe lectin i from viscum album
  1oql		Mistletoe lectin i from viscum album complexed with galactose
  1pc8		Crystal structure of a novel form of mistletoe lectin from himalayan viscum album l. at 3.8a resolution
  1pum		Mistletoe lectin i in complex with galactose
  1puu		Mistletoe lectin i in complex with lactose
  1qxm		Crystal structure of a hemagglutinin component (ha1) from type c clostridium botulinum
  1rzo		Agglutinin from ricinus communis with galactoaza
  1sz6		Mistletoe lectin i from viscum album. crystal structure at 2.05 a resolution
  1tfm		Crystal structure of a ribosome inactivating protein in its naturally inhibited form
  1v6u		Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with 2(2)-alpha-l- arabinofuranosyl-xylobiose
  1v6v		Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with 3(2)-alpha-l- arabinofuranosyl-xylotriose
  1v6w		Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with 2(2)-4-o-methyl-alpha- d-glucuronosyl-xylobiose
  1v6x		Crystal structure of xylanase from streptomyces olivaceoviridis e-86 complexed with 3(3)-4-o-methyl-alpha- d-glucuronosyl-xylotriose
  1vcl		Crystal structure of hemolytic lectin cel-iii
  1xez		Crystal structure of the vibrio cholerae cytolysin (hlya) pro-toxin with octylglucoside bound
  1xhb		The crystal structure of udp-galnac: polypeptide alpha-n- acetylgalactosaminyltransferase-t1
  1xyf		Endo-1,4-beta-xylanase from streptomyces olivaceoviridis
  1ybi		Crystal structure of ha33a, a neurotoxin-associated protein from clostridium botulinum type a
  1yf8		Crystal structure of himalayan mistletoe rip reveals the presence of a natural inhibitor and a new functionally active sugar-binding site
  2aai		Crystallographic refinement of ricin to 2.5 angstroms
  2d1z		Crystal structure of catalytic-site mutant xylanase from streptomyces olivaceoviridis e-86
  2d20		Crystal structure of michaelis complex of catalytic-site mutant xylanase from streptomyces olivaceoviridis e-86
  2d22		Crystal structure of covalent glycosyl-enzyme intermediate of catalytic-site mutant xylanase from streptomyces olivaceoviridis e-86
  2d23		Crystal structure of ep complex of catalytic-site mutant xylanase from streptomyces olivaceoviridis e-86
  2d24		Crystal structure of es complex of catalytic-site mutant xylanase from streptomyces olivaceoviridis e-86
  2d7i		Crsytal structure of pp-galnac-t10 with udp, galnac and mn2+
  2d7r		Crystal structure of pp-galnac-t10 complexed with galnac- ser on lectin domain
  2dry		Crystal structure of the earthworm lectin c-terminal domain mutant
  2drz		Crystal structure of the earthworm lectin c-terminal domain mutant in complex with lactose
  2ds0		Crystal structure of the earthworm lectin c-terminal domain mutant in complex with 6'-sialyllactose
  2e4m		Crystal structure of hemagglutinin subcomponent complex (ha- 33/ha-17) from clostridium botulinum serotype d strain 4947
  2ehi		Ha1 subcomponent of botulinum type c progenitor toxin complexed with n-acetylneuramic acid
  2ehm		Ha1 subcomponent of botulinum type c progenitor toxin complexed with n-acetylgalactosamine
  2ehn		Ha1 subcomponent of botulinum type c progenitor toxin complexed with galactose
  2ffu		Crystal structure of human ppgalnact-2 complexed with udp and ea2
  2ffv		Human ppgalnact-2 complexed with manganese and udp
  2mll		Mistletoe lectin i from viscum album
  2q3n		Agglutinin from abrus precatorius (apa-i)
  2r9k		Crystal structure of misteltoe lectin i in complex with phloretamide
  2rg9		Crystal structure of viscum album mistletoe lectin i in native state at 1.95 a resolution, comparison of structure active site conformation in ricin and in viscumin
  2vlc		Crystal structure of natural cinnamomin (isoform iii)
  2vsa		Structure and mode of action of a mosquitocidal holotoxin
  2vse		Structure and mode of action of a mosquitocidal holotoxin
  2z48		Crystal structure of hemolytic lectin cel-iii complexed with galnac
  2z49		Crystal structure of hemolytic lectin cel-iii complexed with methyl-alpha-d-galactopylanoside
  2zqn		Crystal structure of the earthworm r-type lectin c-half in complex with lactose
  2zqo		Crystal structure of the earthworm r-type lectin c-half in complex with galnac
  2zr1		Agglutinin from abrus precatorius
  3a07		Crystal structure of actinohivin; potent anti-hiv protein
  3a21		Crystal structure of streptomyces avermitilis beta-l- arabinopyranosidase
  3a22		Crystal structure of beta-l-arabinopyranosidase complexed with l-arabinose
  3a23		Crystal structure of beta-l-arabinopyranosidase complexed with d-galactose
  3c9z		Sambucus nigra agglutinin ii (sna-ii), tetragonal crystal form
  3ca0		Sambucus nigra agglutinin ii (sna-ii), hexagonal crystal form
  3ca1		Sambucus nigra agglutinin ii (sna-ii)- tetragonal crystal form- complexed to galactose
  3ca3		Crystal structure of sambucus nigra agglutinin ii (sna-ii)- tetragonal crystal form- complexed to n-acetylgalactosamine
  3ca4		Sambucus nigra agglutinin ii, tetragonal crystal form- complexed to lactose
  3ca5		Crystal structure of sambucus nigra agglutinin ii (sna-ii)- tetragonal crystal form- complexed to alpha1 methylgalactose
  3ca6		Sambucus nigra agglutinin ii (sna-ii)- tetragonal crystal form- complexed to tn antigen
  3cah		Sambucus nigra aggutinin ii. tetragonal crystal form- complexed to fucose
  3d7w		Mistletoe lectin i in complex with zeatin

• Links (links to other resources describing this domain)

• PFAM	Ricin_B_lectin
  INTERPRO	IPR000772
  PROSITE	SHIGA_RICIN

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