|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.
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- Evolution (species in which this domain is found)
Taxonomic distribution of proteins containing RICIN domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with RICIN domain is also avaliable.
Click on the protein counts, or double click on taxonomic names to display all proteins containing RICIN domain in the selected taxonomic class.
- 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)
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% 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 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 2rst NMR structure of the C-terminal domain of EW29 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 3ah1 HA1 subcomponent of botulinum type C progenitor toxin complexed with N-acetylneuramic acid 3ah2 HA1 subcomponent of botulinum type C progenitor toxin complexed with N-acetylgalactosamine 3ah4 HA1 subcomponent of botulinum type C progenitor toxin complexed with galactose 3aj5 HA1 (HA33) subcomponent of botulinum type C progenitor toxin complexed with N-acetylgalactosamine, bound at site II 3aj6 HA1 (HA33) mutant F179I of botulinum type C progenitor toxin complexed with N-acetylgalactosamine, bound at site II 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 3o44 Crystal Structure of the Vibrio cholerae Cytolysin (HlyA) Heptameric Pore 3o5w Binding of kinetin in the active site of mistletoe lectin I 3pg0 Crystal structure of designed 3-fold symmetric protein, ThreeFoil 3rti Crystal structure of ricin bound with formycin monophosphate 3rtj Crystal structure of ricin bound with dinucleotide ApG 3vsf Crystal structure of 1,3Gal43A, an exo-beta-1,3-Galactanase from Clostridium thermocellum 3vsz Crystal structure of Ct1,3Gal43A in complex with galactan 3vt0 Crystal structure of Ct1,3Gal43A in complex with lactose 3vt1 Crystal structure of Ct1,3Gal43A in complex with galactose 3vt2 Crystal structure of Ct1,3Gal43A in complex with isopropy-beta-D-thiogalactoside 3w9t pore-forming CEL-III 3win Clostridium botulinum Hemagglutinin 3wmy Crystal Structure of Streptomyces coelicolor alpha-L-arabinofuranosidase 3wmz Crystal Structure of Streptomyces coelicolor alpha-L-arabinofuranosidase ethylmercury derivative 3wn0 Crystal Structure of Streptomyces coelicolor alpha-L-arabinofuranosidase in complex with L-arabinose 3wn1 Crystal Structure of Streptomyces coelicolor alpha-L-arabinofuranosidase in complex with xylotriose 3wn2 Crystal Structure of Streptomyces coelicolor alpha-L-arabinofuranosidase in complex with xylohexaose 4den Structural insightsinto potent, specific anti-HIV property of actinohivin; Crystal structure of actinohivin in complex with alpha(1-2) mannobiose moiety of high-mannose type glycan of gp120 4eb2 Crystal structure Mistletoe Lectin I from Viscum album in complex with n-acetyl-d-glucosamine at 1.94 A resolution. 4end Crystal structure of anti-HIV actinohivin in complex with alpha-1,2-mannobiose (P 2 21 21 form) 4g1r Crystal structure of anti-HIV actinohivin in complex with alphs-1,2-mannobiose (Form II) 4g1s Crystal structure of a potent anti-HIV lectin actinohivin in complex with alpha-1,2-mannotriose 4hr6 Crystal structure of snake gourd (Trichosanthes anguina) seed lectin, a three chain homologue of type II RIPs 4ion Macrolepiota procera ricin B-like lectin (MPL) 4iyb Macrolepiota procera ricin B-like lectin (MPL) in complex with galactose 4izx Macrolepiota procera ricin B-like lectin (MPL) in complex with lactose 4j2s Macrolepiota procera ricin B-like lectin (MPL) in complex with Di-LacNAc 4jkx Crystal structure Mistletoe Lectin I from Viscum album in complex with kinetin at 2.35 A resolution. 4jp0 Crystal structure of Cry35Ab1 4lo0 Apo HA17-HA33 4lo1 HA17-HA33-Gal 4lo2 HA17-HA33-Lac 4lo3 HA17-HA33-LacNac 4lo7 HA70(D3)-HA17-HA33
- Links (links to other resources describing this domain)
PFAM Ricin_B_lectin INTERPRO IPR000772 PROSITE SHIGA_RICIN