SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


Ricin B-like lectins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   beta-Trefoil [ 50352] (8)
Superfamily:   Ricin B-like lectins [ 50370] (3)
Families:   Ricin B-like [ 50371] (10)
  Cysteine rich domain [ 50379]
  GlcNAc-alpha-1,4-Gal-releasing endo-beta-galactosidase, GngC, C-terminal domain [ 117212]


Superfamily statistics
Genomes (819) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 7,360 29,219 49
Proteins 6,671 26,195 31


Functional annotation
General category Metabolism
Detailed category Polysaccharide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 0.0000000000001341 Least Informative Direct
Biological Process (BP) biosynthetic process 0.00000000006286 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.04386 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.8705 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.02647 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.001442 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.00000000000001079 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0000005733 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.006661 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.002056 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.03466 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.003614 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.02866 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.003761 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5118 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.5371 Moderately Informative Inherited
Biological Process (BP) positive regulation of transport 0.00000003698 Informative Direct
Biological Process (BP) response to oxidative stress 0.0000008916 Informative Direct
Biological Process (BP) regulation of ion transport 0.000001972 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.000004296 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0000084 Informative Direct
Biological Process (BP) regulation of secretion 0.00001761 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.001788 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.07273 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.07322 Informative Inherited
Biological Process (BP) glycoprotein metabolic process 0 Highly Informative Direct
Biological Process (BP) oligosaccharide biosynthetic process 0 Highly Informative Direct
Biological Process (BP) macromolecule glycosylation 0 Highly Informative Direct
Biological Process (BP) regulation of lipid localization 0.00000000000002769 Highly Informative Direct
Biological Process (BP) aging 0.000000001247 Highly Informative Direct
Biological Process (BP) positive regulation of ion transport 0.000000008103 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.00000001692 Highly Informative Direct
Biological Process (BP) response to osmotic stress 0.001077 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) metal ion binding 0.01692 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring glycosyl groups 0 Informative Direct
Molecular Function (MF) enzyme binding 0.00002398 Informative Direct
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 0.0001517 Informative Direct
Molecular Function (MF) molecular transducer activity 0.0002752 Informative Direct
Molecular Function (MF) UDP-glycosyltransferase activity 0.0000000000001646 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.00000000001353 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring hexosyl groups 0.000006886 Highly Informative Direct
Cellular Component (CC) membrane 0.02594 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.05544 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.4456 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1142 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.000000001003 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.000000006883 Moderately Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) cytoplasmic region 0.0008064 Informative Direct
Cellular Component (CC) Golgi subcompartment 0.0000000001944 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Glycosidases, i.e. enzymes hydrolyzing O- and S-gl1Moderately InformativeInherited
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0.006563InformativeInherited
Enzyme Commission (EC)Alpha-galactosidase0.0000000000725Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processEndocytosis0InformativeDirect
Biological processPlant defense0InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentSecreted0.0000001774Moderately InformativeDirect
DomainTransmembrane0.000000007031Least InformativeDirect
DomainSignal-anchor0InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionLectin0InformativeDirect
Post-translational modificationTransferase0.000000000002005Least InformativeDirect
Post-translational modificationHydrolase0.02972Least InformativeInherited
Post-translational modificationReceptor0.000002016Moderately InformativeDirect
Post-translational modificationToxin0InformativeDirect
Post-translational modificationGlycosyltransferase0InformativeDirect
Post-translational modificationGlycosidase0.0000000002218InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationPalmitate0.000163Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008997 SSF50370 Protein matches
Abstract

The plant cytotoxin ricin is a heterodimer. 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 B chain subunit of ricin (RTB)1 binds to mammalian cell membranes by recognizing galactose-containing receptors. RTB has two domains each with three subdomains; tripeptide kinks in the loops from subdomains 1alpha, 1beta, 2alpha, and 2gamma may interact with galactosides. Each of these subdomains has aromatic residues that can interact with the nonpolar face of galactose, and three of the four subdomain folds (1alpha, 1beta, and 2gamma) have polar residues for hydrogen bond formation to the sugar hydroxyls [PubMed8950484].

The family 10 xylanase from Streptomyces olivaceoviridis E-86 contains a (beta/alpha)(8)-barrel as a catalytic domain, a family 13 carbohydrate binding module as a xylan binding domain (XBD) and a Gly/Pro-rich linker between them. The crystal structure of this enzyme showed that XBD has three similar subdomains, as indicated by the presence of a triple-repeated sequence, forming a galactose binding lectin fold similar to that found in the ricin toxin B-chain [PubMed11829503].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 34 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Ricin B-like lectins domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 34 hidden Markov models representing the Ricin B-like lectins superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]