SUPERFAMILY 1.75 HMM library and genome assignments server


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 process0.00028140.0008426Least InformativeDirect
Biological Process (BP)regulation of cellular process0.0024540.0102Least InformativeInherited
Biological Process (BP)regulation of biosynthetic process1.515e-056.98e-05Moderately InformativeDirect
Biological Process (BP)negative regulation of metabolic process3.074e-061.938e-06Moderately InformativeDirect
Biological Process (BP)regulation of gene expression1.721e-058.743e-05Moderately InformativeDirect
Biological Process (BP)negative regulation of cellular process6.252e-057.036e-05Moderately InformativeDirect
Biological Process (BP)regulation of protein metabolic process3.603e-065.284e-07Moderately InformativeDirect
Biological Process (BP)negative regulation of biosynthetic process2.242e-072.648e-07InformativeDirect
Biological Process (BP)posttranscriptional regulation of gene expression2.232e-081.165e-09InformativeDirect
Biological Process (BP)negative regulation of protein metabolic process1.124e-079.603e-10InformativeDirect
Biological Process (BP)regulation of translation1.46e-092.664e-11Highly InformativeDirect
Molecular Function (MF)hydrolase activity8.743e-061.012e-06Least InformativeDirect
Molecular Function (MF)hydrolase activity, acting on glycosyl bonds9.985e-111.141e-13InformativeDirect
Molecular Function (MF)hydrolase activity, hydrolyzing N-glycosyl compounds3.902e-140Highly 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 0.0008426 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.0102 Least Informative Inherited
Biological Process (BP) regulation of biosynthetic process 6.98e-05 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 1.938e-06 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 8.743e-05 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 7.036e-05 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 5.284e-07 Moderately Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 2.648e-07 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 1.165e-09 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 9.603e-10 Informative Direct
Biological Process (BP) regulation of translation 2.664e-11 Highly Informative Direct
Molecular Function (MF) hydrolase activity 1.012e-06 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 1.141e-13 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
DomainSignal3.104e-16Least InformativeDirect
Molecular functionLectin0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationToxin0InformativeDirect
Post-translational modificationGlycoprotein1.867e-06Least InformativeDirect
Post-translational modificationDisulfide bond5.562e-06Least InformativeDirect
Post-translational modificationPyrrolidone carboxylic acid1.32e-05InformativeDirect

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

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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 ]