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176  structures 239  species 2  interactions 945  sequences 12  architectures

Family: RIP (PF00161)

Summary: Ribosome inactivating protein

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This is the Wikipedia entry entitled "Ribosome inactivating protein". More...

Ribosome inactivating protein Edit Wikipedia article

Ribosome-inactivating protein
PDB 1paf EBI.jpg
Structure of pokeweed antiviral protein.[1]
Identifiers
Symbol RIP
Pfam PF00161
InterPro IPR001574
PROSITE PDOC00248
SCOP 1paf
SUPERFAMILY 1paf

A ribosome-inactivating protein is a protein synthesis inhibitor that acts at the ribosome.[2]

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.[3][4][5] 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.[6] 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;[7] this lies near a conserved arginine, which also plays a role in catalysis.[8]

Examples include:

They exist in bacteria and plants.[9]

References

  1. ^ Monzingo AF, Collins EJ, Ernst SR, Irvin JD, Robertus JD (October 1993). "The 2.5 A structure of pokeweed antiviral protein". J. Mol. Biol. 233 (4): 705–15. doi:10.1006/jmbi.1993.1547. PMID 8411176. 
  2. ^ Ribosome Inactivating Proteins at the US National Library of Medicine Medical Subject Headings (MeSH)
  3. ^ Igarashi K, Endo Y, Tsurugi K, Takeda Y, Ogasawara T, Yutsudo T (1988). "Site of action of a Vero toxin (VT2) from Escherichia coli O157:H7 and of Shiga toxin on eukaryotic ribosomes. RNA N-glycosidase activity of the toxins". Eur. J. Biochem. 171 (1): 45–50. doi:10.1111/j.1432-1033.1988.tb13756.x. PMID 3276522. 
  4. ^ May MJ, Hartley MR, Roberts LM, Krieg PA, Osborn RW, Lord JM (1989). "Ribosome inactivation by ricin A chain: a sensitive method to assess the activity of wild-type and mutant polypeptides". EMBO J. 8 (1): 301–308. PMC 400803. PMID 2714255. 
  5. ^ Funatsu G, Islam MR, Minami Y, Sung-Sil K, Kimura M (1991). "Conserved amino acid residues in ribosome-inactivating proteins from plants". Biochimie 73 (7): 1157–1161. doi:10.1016/0300-9084(91)90160-3. PMID 1742358. 
  6. ^ Zhou K, Fu Z, Chen M, Lin Y, Pan K (1994). "Structure of trichosanthin at 1.88 A resolution". Proteins 19 (1): 4–13. doi:10.1002/prot.340190103. PMID 8066085. 
  7. ^ Collier RJ, Calderwood SB, Mekalanos JJ, Hovde CJ (1988). "Evidence that glutamic acid 167 is an active-site residue of Shiga-like toxin I". Proc. Natl. Acad. Sci. U.S.A. 85 (8): 2568–2572. doi:10.1073/pnas.85.8.2568. PMC 280038. PMID 3357883. 
  8. ^ Monzingo AF, Collins EJ, Ernst SR, Irvin JD, Robertus JD (1993). "The 2.5 A structure of pokeweed antiviral protein". J. Mol. Biol. 233 (4): 705–715. doi:10.1006/jmbi.1993.1547. PMID 8411176. 
  9. ^ Mak AN, Wong YT, An YJ, et al. (2007). "Structure-function study of maize ribosome-inactivating protein: implications for the internal inactivation region and the sole glutamate in the active site". Nucleic Acids Res. 35 (18): 6259–67. doi:10.1093/nar/gkm687. PMC 2094058. PMID 17855394. 

This article incorporates text from the public domain Pfam and InterPro IPR001574


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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001574

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 [PUBMED:3276522, PUBMED:2714255, PUBMED:1742358]. 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 [PUBMED:8066085]. 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 [PUBMED:3357883]; this lies near a conserved arginine, which also plays a role in catalysis [PUBMED:8411176].

Gene Ontology

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Domain organisation

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Alignments

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(73)
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(945)
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(936)
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RP35
(17)
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RP75
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  Seed
(73)
Full
(945)
Representative proteomes NCBI
(936)
Meta
(0)
RP15
(2)
RP35
(17)
RP55
(64)
RP75
(103)
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  Seed
(73)
Full
(945)
Representative proteomes NCBI
(936)
Meta
(0)
RP15
(2)
RP35
(17)
RP55
(64)
RP75
(103)
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Gzipped Download   Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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Curation and family details

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Seed source: Prosite
Previous IDs: none
Type: Domain
Author: Sonnhammer ELL, Griffiths-Jones SR
Number in seed: 73
Number in full: 945
Average length of the domain: 197.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 61.64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.1 20.1
Trusted cut-off 20.7 20.7
Noise cut-off 19.9 19.5
Model length: 206
Family (HMM) version: 14
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Species distribution

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Interactions

There are 2 interactions for this family. More...

RIP Ricin_B_lectin

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the RIP domain has been found. There are 176 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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