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Information on EC 3.2.2.22 - rRNA N-glycosylase and Organism(s) Trichosanthes kirilowii and UniProt Accession P09989
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3.2.2.22 rRNA N-glycosylaseIUBMB Comments
Ricin A-chain and related toxins show this activity. Naked rRNA is attacked more slowly than rRNA in intact ribosomes. Naked rRNA from Escherichia coli is cleaved at a corresponding position.
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The taxonomic range for the selected organisms is: Trichosanthes kirilowii
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
pd-l1, ricin, shiga toxin, saporin, abrin, ricinus communis agglutinin, gelonin, ricin a chain, trichosanthin, ribosome-inactivating proteins, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
gelonin
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-
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karasurin-A
KRN recombinantly combined with pokeweed antiviral protein (PAP)
Mirabilis antiviral protein
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-
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momorcochin-S
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-
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nigrin b
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ribosomal ribonucleate N-glycosidase
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-
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ribosome-inactivating protein
ricin
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-
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RIP
RNA N-glycosidase
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-
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rRNA N-glycosidase
saporins
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trichosanthin
rRNA N-glycosidase
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-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes
catalytic mechanism
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of N-glycosyl bond
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-
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SYSTEMATIC NAME
IUBMB Comments
rRNA N-glycohydrolase
Ricin A-chain and related toxins show this activity. Naked rRNA is attacked more slowly than rRNA in intact ribosomes. Naked rRNA from Escherichia coli is cleaved at a corresponding position.
CAS REGISTRY NUMBER
COMMENTARY
113756-12-0
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
28Sdelta rRNA + H2O
?
-
depurination of the A51 residue of Trypanosoma cruzi 28Sdelta rRNA, the C-terminal end of ribosomal P proteins is required for full activity of trichosanthin
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?
rRNA + H2O
?
depurination of A-4324 of 28S rRNA, inhibition of protein synthesis in a nuclease-untreated rabbit reticulocyte lysate
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-
?
RNA + H2O
?
ribosomes from rat liver (eukaryotic) and Escherichia coli JM109 (prokaryotic), 37°C, 25 mM Tris-HCl buffer, pH 7.6 with 50 mM KCl and 5 mM MgCl2
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-
?
additional information
?
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depurination of specific adenine at sarcin-ricin loop of 28S rRNA, preventing the binding of elongation factors to the GTPase activation centre of the ribosome
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?
additional information
?
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trichosanthin is immunogenic and leads to IgE production in humans, Trichosanthes kirilowii root tubers containing trichosanthin causes abortion, overview
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-
?
additional information
?
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the enzyme shows polynucleotide:adenosine glycosidase, PAGase, activity
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-
?
additional information
?
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in a cell-free rabbit reticulocyte lysate system, enzyme inhibits protein synthesis with an IC50 of about 5 nM. Enzyme is cytotoxic to leukemia U937 and choriocarcinoma JAR cells
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-
?
additional information
?
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karasurin-A shows RNA N-glycosidase activity only towards eukaryotic ribosomes while pokeweed antiviral protein is active towards eukaryotic and prokaryotic ribosomes, removal of specific adenine from alpha-sarcin/ricin loop of the large rRNA, substrate specificity (eukaryotic/prokaryotic) determined by C-terminus residues 209-225
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?
additional information
?
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Trichosanthrip acts on 28S rRNA, and inhibits protein synthesis in rabbit reticulocyte lysates, overview
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?
additional information
?
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the enzyme can depurinate hybrid ribosomes carrying P1-P2 heterodimer but not Escherichia coli 50 S ribosomes or 50 S coreribosomes
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
depurination of specific adenine at sarcin-ricin loop of 28S rRNA, preventing the binding of elongation factors to the GTPase activation centre of the ribosome
-
-
?
additional information
?
-
-
trichosanthin is immunogenic and leads to IgE production in humans, Trichosanthes kirilowii root tubers containing trichosanthin causes abortion, overview
-
-
?
additional information
?
-
karasurin-A shows RNA N-glycosidase activity only towards eukaryotic ribosomes while pokeweed antiviral protein is active towards eukaryotic and prokaryotic ribosomes, removal of specific adenine from alpha-sarcin/ricin loop of the large rRNA, substrate specificity (eukaryotic/prokaryotic) determined by C-terminus residues 209-225
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-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
scFvC5
single chain fragment variable antibody, blocks interaction between trichosanthin K173, R174, and K177 residues and ribosomal P proteins protecting ribosomes from inactivation
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
medicinal plant with anti-tumor and anti-HIV properties
Uniprot
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
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trichosanthin is highly toxic to trophoblasts and choriocarcinoma cells. Low-density lipoprotein receptor-related protein 1 is an essential receptor for trichosanthin in 2-choriocarcinoma cell lines
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). RIPT_TRIKI
289
0
31676
Swiss-Prot
Secretory Pathway (Reliability: 1)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
trichosanthin interacts with the C-terminal tail of eukaryotic ribosomal protein P2, involving residues K173, R174, and K177 of trichosanthin
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D176A
1.5fold increase in enzyme concentration required for 50% inhibition of protein synthesis
K173A
weakened binding to eukaryotic ribosomal protein P2, 7.5fold increase in enzyme concentration required for 50% inhibition of protein synthesis
K173A/R174A/K177A
K177A
weakened binding to eukaryotic ribosomal protein P2, 3fold increase in enzyme concentration required for 50% inhibition of protein synthesis
R174A
weakened binding to eukaryotic ribosomal protein P2, 6fold increase in enzyme concentration required for 50% inhibition of protein synthesis
V232K/N236D
17-fold reduced activity compared to wild-type, no ribosome interaction, V232K is at mouth of hydrophobic pocket, where the LF motif of c11-P binds, expected to block the access of the P-protein to the pocket, N236D substitution removes hydrogen bond between the amide of Asn236 and the backbone carbonyl of Leu9 of c11-P
additional information
chimera proteins of 3 domains of pokeweed antiviral protein and karasurin-A (N-terminal 1-74, central 75-177, C-terminal 178-262), C-terminal end determines determines specificity to eukaryotic or eukaryotic and prokaryotic ribosomes, PAP-region 209-225 is required for activity towards prokaryotic ribosomes
K173A/R174A/K177A
mutant unable to bind to eucaryotic ribosomal protein P2 and to ribosomal stalk in vitro, 18fold less active in inhibition of translation than wild-type
K173A/R174A/K177A
no ribosome interaction, drastically reduced N-glycosidase acitivity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Hi-Trap CM-Sepharose column followed by Hi-Trap SP-Sepharose column with 20 mM phosphate buffer, pH 6.7
cell centrifugation, washing, lysozyme application, sonication, centrifugation, supernatants applied to GSTrap FF column, elution with sonication buffer and 10 mM reduced glutathione, desalted, concentrated and glutathione S-transferase (GST) cleaved off with PreScission Protease
native enzyme from mature seeds by ammonium sulfate fractionation, cation exchange chromatography and gel filtration to 96.6% purity
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
plasmid pMAL-c2 to amplify pokeweed antiviral protein and karasurin-A by PCR, expression in Escherichia coli XL1-Blue cells with expression plasmid pGEX-6P-1
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
medicine
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trichosanthin is immunogenic and leads to IgE production in humans, Trichosanthes kirilowii is a traditional chinese medicine plant, root tubers containing trichosanthin cause abortion, overview
medicine
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injection of trichosanthin into rat eyes causes distinct retinal changes at 1 nM. Toxic effects are most pronounced in the cells of the outer nuclear layer, less pronounced on those of the inner nuclear layer, and little on the ganglion cells. Apoptosis is the predominant type of cell death induced by trichosanthin
medicine
the enzyme is used in the official Chinese medicine to induce abortion and to treat hydatidiform mol
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Peumans, W.J.; Hao, Q.; Van Damme, E.J.
Ribosome-inactivating proteins from plants: more than RNA N-glycosidases?
FASEB J.
15
1493-1506
2001
Abrus precatorius, Ricinus communis, Eranthis hyemalis, Suregada multiflora, Hordeum vulgare, Momordica charantia, no activity in Arabidopsis thaliana, Phytolacca americana, Phytolacca insularis, Saponaria officinalis, Trichosanthes kirilowii, Trichosanthes sp.
Hartley, M.R.; Lord, J.M.
Cytotoxic ribosome-inactivating lectins from plants
Biochim. Biophys. Acta
1701
1-14
2004
Abrus precatorius, Cucurbita pepo, Dianthus caryophyllus, Escherichia coli, Mirabilis jalapa, Momordica charantia, Phytolacca americana, Sambucus nigra, Saponaria officinalis, Shigella dysenteriae, Trichosanthes kirilowii, Triticum aestivum, Viscum album, Adenia volkensii, Sambucus ebulus, Ricinus communis (P02879)
Stirpe, F.
Ribosome-inactivating proteins
Toxicon
44
371-383
2004
Abrus precatorius, Ricinus communis, Suregada multiflora, Hordeum vulgare, Phytolacca americana, Sambucus nigra, Saponaria officinalis, Shigella dysenteriae, Trichosanthes kirilowii, Viscum album, Zea mays, Phoradendron californicum, Adenia volkensii, Adenia digitata, Mirabilis expansa
Ayub, M.J.; Smulski, C.R.; Ma, K.W.; Levin, M.J.; Shaw, P.C.; Wong, K.B.
The C-terminal end of P proteins mediates ribosome inactivation by trichosanthin but does not affect the pokeweed antiviral protein activity
Biochem. Biophys. Res. Commun.
369
314-319
2008
Trichosanthes kirilowii (P09989), Phytolacca americana (P10297)
Xu, L.; Wang, Y.; Wang, L.; Gao, Y.; An, C.
TYchi, a novel chitinase with RNA N-glycosidase and anti-tumor activities
Front. Biosci.
13
3127-3135
2008
Trichosanthes kirilowii
Chan, D.S.; Chu, L.O.; Lee, K.M.; Too, P.H.; Ma, K.W.; Sze, K.H.; Zhu, G.; Shaw, P.C.; Wong, K.B.
Interaction between trichosanthin, a ribosome-inactivating protein, and the ribosomal stalk protein P2 by chemical shift perturbation and mutagenesis analyses
Nucleic Acids Res.
35
1660-1672
2007
Trichosanthes kirilowii (P09989)
Sha, O.; Kwong, W.H.; Pang Cho, E.Y.; Wai Yew, D.T.; Ng, T.B.
Different neuronal toxicity of single-chain ribosome-inactivating proteins on the rat retina
Toxicon
51
45-53
2008
Ricinus communis, Trichosanthes kirilowii
Too, P.H.; Ma, M.K.; Mak, A.N.; Wong, Y.T.; Tung, C.K.; Zhu, G.; Au, S.W.; Wong, K.B.; Shaw, P.C.
The C-terminal fragment of the ribosomal P protein complexed to trichosanthin reveals the interaction between the ribosome-inactivating protein and the ribosome
Nucleic Acids Res.
37
602-610
2009
Trichosanthes kirilowii (P09989)
Nagasawa, Y.; Fujii, K.; Yoshikawa, T.; Kobayashi, Y.; Kondo, T.
Pokeweed antiviral protein region Gly209-Lys225 is critical for RNA N-glycosidase activity of the prokaryotic ribosome
Phytochemistry
69
1653-1660
2008
Phytolacca americana, Trichosanthes kirilowii (P24478)
Shu, S.H.; Xie, G.Z.; Guo, X.L.; Wang, M.
Purification and characterization of a novel ribosome-inactivating protein from seeds of Trichosanthes kirilowii Maxim
Protein Expr. Purif.
67
120-125
2009
Trichosanthes kirilowii
Lee, K.M.; Yusa, K.; Chu, L.O.; Yu, C.W.; Oono, M.; Miyoshi, T.; Ito, K.; Shaw, P.C.; Wong, K.B.; Uchiumi, T.
Solution structure of human P1?P2 heterodimer provides insights into the role of eukaryotic stalk in recruiting the ribosome-inactivating protein trichosanthin to the ribosome
Nucleic Acids Res.
41
8776-8787
2013
Trichosanthes kirilowii
Stirpe, F.
Ribosome-inactivating proteins: from toxins to useful proteins
Toxicon
67
12-16
2013
Suregada multiflora, Hordeum vulgare, Phytolacca americana, Bougainvillea spectabilis, Trichosanthes kirilowii (Q8W4U4)
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