SUPERFAMILY 1.75 HMM library and genome assignments server

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 (811) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,210 12,603 49
Proteins 6,525 11,268 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) biosynthetic process 0.0000000004078 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.000000175 Least Informative Direct
Biological Process (BP) protein metabolic process 0.00002826 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.6801 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.006132 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) localization 0.8893 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.2042 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9626 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
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 0.0000000000001254 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0003486 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.0009284 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.001978 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.6588 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.0072 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.01645 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.4855 Moderately Informative Inherited
Biological Process (BP) positive regulation of transport 0.0000000004179 Informative Direct
Biological Process (BP) response to oxidative stress 0.0000001647 Informative Direct
Biological Process (BP) positive regulation of intracellular signal transduction 0.0000004077 Informative Direct
Biological Process (BP) regulation of ion transport 0.000003331 Informative Direct
Biological Process (BP) regulation of secretion 0.000005647 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00004439 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.00009514 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.3534 Informative Inherited
Biological Process (BP) protein glycosylation 0 Highly Informative Direct
Biological Process (BP) post-translational protein modification 0.000000000000001913 Highly Informative Direct
Biological Process (BP) aging 0.00000000004915 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.000000003339 Highly Informative Direct
Biological Process (BP) positive regulation of ion transport 0.000000005658 Highly Informative Direct
Biological Process (BP) response to salt stress 0.00004707 Highly Informative Direct
Biological Process (BP) oligosaccharide metabolic process 0.002153 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.000000000000001593 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) cation binding 0.01065 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring glycosyl groups 0 Informative Direct
Molecular Function (MF) enzyme binding 0.0000007764 Informative Direct
Molecular Function (MF) receptor activity 0.0000117 Informative Direct
Molecular Function (MF) UDP-glycosyltransferase activity 0.0000000000006042 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.000000000003834 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring hexosyl groups 0.00001361 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.02193 Least Informative Inherited
Cellular Component (CC) membrane 0.001246 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.01894 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.312 Least Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0.00000002803 Moderately Informative Direct
Cellular Component (CC) Golgi apparatus 0 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

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.01149Least InformativeInherited
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Glycosylases0Moderately InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0InformativeDirect
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0.004625Highly InformativeInherited

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 componentSecreted0.0000001989Moderately InformativeDirect
DomainTransmembrane0.0000000005108Least InformativeDirect
DomainSignal-anchor0InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionLectin0InformativeDirect
Post-translational modificationTransferase0.0000000000002204Least InformativeDirect
Post-translational modificationHydrolase0.1505Least InformativeInherited
Post-translational modificationReceptor0.000002223Moderately InformativeDirect
Post-translational modificationGlycosyltransferase0InformativeDirect
Post-translational modificationToxin0InformativeDirect
Post-translational modificationGlycosidase0.00000000006971InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationPalmitate0.00008083Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)glycan metabolism0.2467Moderately InformativeInherited
UniPathway (UP)protein glycosylation0InformativeDirect
UniPathway (UP)glycan degradation0.003406InformativeInherited
UniPathway (UP)xylan degradation0.00001993Highly InformativeDirect

Document: UP 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]