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Ribosome inactivating proteins (RIP) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ribosome inactivating proteins (RIP) [ 56370]
Superfamily:   Ribosome inactivating proteins (RIP) [ 56371] (2)
Families:   Plant cytotoxins [ 56372] (17)
  Shiga toxin, A-chain [ 56395]


Superfamily statistics
Genomes (72) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 618 1,650 45
Proteins 606 1,647 45


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)regulation of metabolic process0.0003010.000934Least InformativeDirect
Biological Process (BP)regulation of cellular process0.0026290.01109Least InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.0000034260.00000233Moderately InformativeDirect
Biological Process (BP)regulation of gene expression0.000019170.00009708Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process0.0000097770.00005122Moderately InformativeDirect
Biological Process (BP)regulation of cellular biosynthetic process0.000014460.00006893Moderately InformativeDirect
Biological Process (BP)negative regulation of cellular process0.000068450.000082Moderately InformativeDirect
Biological Process (BP)regulation of protein metabolic process0.0000039630.0000006013Moderately InformativeDirect
Biological Process (BP)negative regulation of biosynthetic process0.00000023610.0000002944InformativeDirect
Biological Process (BP)posttranscriptional regulation of gene expression0.000000023750.000000001258InformativeDirect
Biological Process (BP)negative regulation of protein metabolic process0.00000011790.0000000009962InformativeDirect
Biological Process (BP)regulation of translation0.0000000016390.00000000002816Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.0000094680.000001107Least InformativeDirect
Molecular Function (MF)hydrolase activity, acting on glycosyl bonds0.00000000010630.0000000000001218InformativeDirect
Molecular Function (MF)hydrolase activity, hydrolyzing N-glycosyl compounds0.000000000000049860Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) regulation of metabolic process 0.000934 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.01109 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00000233 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00009708 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.00005122 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00006893 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.000082 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0000006013 Moderately Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.0000002944 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.000000001258 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.0000000009962 Informative Direct
Biological Process (BP) regulation of translation 0.00000000002816 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.000001107 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 0.0000000000001218 Informative Direct
Molecular Function (MF) hydrolase activity, hydrolyzing N-glycosyl compounds 0 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)Hydrolyzing N-glycosyl compounds0InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Glycosylases0Moderately InformativeDirect
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processPlant defense0InformativeDirect
Biological processAntiviral defense0Highly InformativeDirect
DomainSignal3.091e-16Least InformativeDirect
Molecular functionLectin0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationToxin0InformativeDirect
Post-translational modificationGlycoprotein0.000001948Least InformativeDirect
Post-translational modificationDisulfide bond0.000005522Least InformativeDirect
Post-translational modificationPyrrolidone carboxylic acid0.00001308InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001574 SSF56371 Protein matches
Abstract A number of bacterial and plant toxins act by inhibiting protein synthesis in eukaryotic cells. The toxins of the Shiga and ricin family inactivate 60S ribosomal subunits by an N-glycosidic cleavage which releases a specific adenine base from the sugar-phosphate backbone of 28S rRNA [PubMed3276522, PubMed2714255, PubMed1742358]. Members of the family include shiga and shiga-like toxins, and type I (e.g. trichosanthin and luffin) and type II (e.g. ricin, agglutinin and abrin) ribosome inactivating proteins (RIPs). All these toxins are structurally related. RIPs have been of considerable interest because of their potential use, conjugated with monoclonal antibodies, as immunotoxins to treat cancers. Further, trichosanthin has been shown to have potent activity against HIV-1-infected T cells and macrophages [PubMed8066085]. Elucidation of the structure-function relationships of RIPs has therefore become a major research effort. It is now known that RIPs are structurally related. A conserved glutamic residue has been implicated in the catalytic mechanism [PubMed3357883]; this lies near a conserved arginine, which also plays a role in catalysis [PubMed8411176].

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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · 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 25 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 Ribosome inactivating proteins (RIP) 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 25 hidden Markov models representing the Ribosome inactivating proteins (RIP) 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]