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Information on EC 3.2.2.22 - rRNA N-glycosylase and Organism(s) Phytolacca americana and UniProt Accession P10297

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     3 Hydrolases
         3.2 Glycosylases
             3.2.2 Hydrolysing N-glycosyl compounds
                3.2.2.22 rRNA N-glycosylase
IUBMB 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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Select one or more organisms in this record: ?
This record set is specific for:
Phytolacca americana
UNIPROT: P10297
Word Map
The taxonomic range for the selected organisms is: Phytolacca americana
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
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
gelonin
-
-
-
0
Mirabilis antiviral protein
-
-
-
0
momorcochin-S
-
-
-
0
nigrin b
-
-
-
0
PAGase
257893
-
PAP-I
257893
-
PAP-II
PAP-III
257893
-
PAP-R
278266
-
PAP-S
pokeweed anti-viral protein
pokeweed antiviral protein
polynucleotide:adenosine glycosidase
257893
-
ribosomal ribonucleate N-glycosidase
-
-
-
0
ribosome inactivating protein
257893
-
ribosome-inactivating protein
257893
-
ribosome-specific N-glycosidase
278264, 278265, 278266, 278267
-
ricin
-
-
-
0
RNA N-glycosidase
-
-
-
0
rRNA N-glycosidase
-
-
-
0
saporins
-
-
-
0
type 1 RIP
257893
-
type I ribosome-inactivating protein
type I RIP
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes
show the reaction diagram
N70 of PAP is required for depurination catalytic activity, N70 facilitates depurination in trans
hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of N-glycosyl bond
-
-
-
0
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 hide
113756-12-0
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
28Sdelta rRNA + H2O
?
show the reaction diagram
-
depurination of the A51 residue of Trypanosoma cruzi 28Sdelta rRNA, the C-terminal end of ribosomal P proteins is not required for full activity
-
?
rRNA + H2O
?
show the reaction diagram
2'-anthraniloyl 7-methylguanosine triphosphate + H2O
?
show the reaction diagram
-
depurination downstream of cap structure, 2.4-fold enhanced binding to m7GTP upon the addition of translation initiation factor G4 (elFiso4G)
-
-
?
25S rNA + H2O
?
show the reaction diagram
-
-
enzyme depurinates the sarcin/ricin loop when the A-site of the ribosomal peptidyl-transferase center is unoccupied
-
?
8-vinyl-2'-deoxyadenosine containing 10-mer stem-tetraloop RNA + H2O
8-vinyladenine + ?
show the reaction diagram
-
-
slow
-
?
brome mosaic virus RNA + H2O
?
show the reaction diagram
large RNA + H2O
?
show the reaction diagram
removal of a single adenine
-
-
?
RNA + H2O
?
show the reaction diagram
rRNA + H2O
?
show the reaction diagram
supercoiled double-stranded DNA + H2O
nicked and linear forms of DNA
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
rRNA + H2O
?
show the reaction diagram
PAP causes translation arrest and is cytotoxic in targeted cells
-
-
?
brome mosaic virus RNA + H2O
?
show the reaction diagram
-
depurination of the viral RNA, anti-viral activity of PAP by inhbition of accumulation of viral RNA and viral proliferation in barley protoplasts, overview
-
-
?
RNA + H2O
?
show the reaction diagram
-
the enzyme is active on viral RNA, e.g. from Human immunodeficiency virus-1 and Brome mosaic virus, RNA accession mechanism via interaction with translation initiation factors 4G and iso4G, overview
-
-
?
rRNA + H2O
?
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
puromycin
-
prior incubation of ribosomes with puromycin inhibits both the binding and depurination by the enzyme
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
PAP-S: increase in cells that show DNA damage in both species, reduced weight gain of Spodoptera frugiperda (not Anticarsia gemmatalis) on day 4 with 40 microg, increased weight gain with 20 microg in Spodoptera frugiperda, not significant increase in weight gain in Anticarsia gemmatalis fed with 40 microg, reduced weight in Anticarsia gemmatalis and Spodoptera frugiperda at day 10 with 40 microg, 57.1% mortality in Anticarsia gemmatalis, in Anticarsia gemmatalis 30-40% reduced level of lipid peroxidation with 40 microg, in Spodoptera frugiperda superoxide dismutase inhibition to 20% and catalase activity increase with 40 microg
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4
-
polynucleotide:adenosine glycosidase
7.5
-
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
the enzyme is synthesized as inactive precursor protein, accumulated in the endoplasmic reticulum associated to membranes, and needs to cleaved to the mature active form in the endoplasmic reticulum of the targeted cell, the mature form is retro-translocated from the ER to the cytosol where it is accumulated and escapes degradation, residues E176 and N70 are essential for catalytic activity
-
Manually annotated by BRENDA team
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
RIP1_PHYAM
313
1
35219
Swiss-Prot
Secretory Pathway (Reliability: 1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
29000
-
isoform PAP
30000
-
isoform PAP II
31000
-
isoform PAP-S
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
-
subunit A
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
proteolytic modification
the enzyme is synthesized as inactive precursor protein and needs to cleaved to the mature active form in the endoplasmic reticulum of the targeted cell, the mature form is retro-translocated from the ER to the cytosol where it escapes degradation
proteolytic modification
-
enzyme is synthesized in pokeweed plants as a 313-amino-acid precursor with a 22-amino-acid N-terminal signal sequence and a 29-amino-acid C-terminal extension
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E176V
site-directed mutagenesis, inactive mutant showing no cytotoxicity
N70A
site-directed mutagenesis, the mutation delays the enzyme depurination activity on ribosomes and the onset of translation arrest, N70A PAP shows highly reduced cytotoxicity and destabilizes its own mRNA, but binds to cap and blocks cap-dependent translation
C259A
-
decrease in processing of the C-terminal extension
G75D
-
no maturation of precursor form, localization exclusivelly in the membrane fraction
L252K
-
delayed appearance of mature form in the cytosol
L252stop
-
accumulation of the truncated protein primarily in the membrane fraction, at the lumenal side of microsomal membranes
N253A
-
like wild-type, localization in the cytosol
N253R
-
like wild-type, localization in the cytosol
N253stop
-
reduced accumulation of the protein in the cytosol, appearance of a slightly larger form in the membrane fraction
T262stop
-
present in both the membrane fraction and the cytosol
V73E
-
no maturation of precursor form, reduced stability, localized to the lumenal side of microsomal membranes
Y254stop
-
retains the ability to accumulate in the cytosol
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant PAPs from Escherichia coli strain BL21(DE3) by m7G affinity chromatography
by affinity chromatography on a m7G-resin
-
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
-
homogenized frozen leaves filtered through cheesecloth, centrifuged, saturated with ammonium sulfate to 60%, stirred, all at 4 degrees Celsius, centrifuged, pellet resuspended in 20 mM Tris-HCl, pH 7.5 with 1 mM beta-mercaptoethanol, and 0.2 mM EDTA, dialyzed against buffer, centrifuged, loaded onto HiTrap Q FF column, bound proteins loaded onto HiTrap SP FF column, eluted with NaCl gradient, PAP elutes at about 250 mM NaCl
-
native PAP from spring leaves in four steps, ammonium sulfate fractionation, anion and cation exchange chromatography, and dialysis, to homogeneity
-
recombinant PAP from Escherichia coli strain JM101 by an alkaline method
recombinant PAP-II from Escherichia coli strain JM101 by an alkaline method
recombinant PAP-R from Escherichia coli strain JM101 by an alkaline method
recombinant PAP-S from Escherichia coli strain JM101 by an alkaline method
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of His-tagged wild-type and mutant PAPs in Escherichia coli strain BL21(DE3)
DNA and amino acid sequence determination of PAP, expression in Escherichia coli strain JM101
DNA and amino acid sequence determination of PAP-II, expression in Escherichia coli strain JM101
DNA and amino acid sequence determination of PAP-R, expression in Escherichia coli strain JM101
DNA and amino acid sequence determination of PAP-S, expression in Escherichia coli strain JM101
expression in Saccharomyces cerevisiae strain mak8-1 which is more resistant to the enzyme in vivo due to higher affinity for aminoacyl-tRNA
-
expression of wild-type PAP in yeast, and of mutant PAPs in Escherichia coli
-
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 hide
LITERATURE
agriculture
-
PAP can be useful against plant virus infections
medicine
-
PAP acts as immunotoxin
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Endo, Y.; Tsurugi, K.; Lambert, J.M.
The site of action of six different ribosome-inactivating proteins from plants on eukaryotic ribosomes: the RNA N-glycosidase activity of the proteins
Biochem. Biophys. Res. Commun.
150
1032-1036
1988
Suregada multiflora, Momordica charantia, Phytolacca americana, Saponaria officinalis
Manually annotated by BRENDA team
Barbieri, L.; Valbonesi, P.; Righi, F.; Zuccheri, G.; Monti, F.; Gorini, P.; Samori, B.; Stirpe, F.
Polynucleotide:Adenosine glycosidase is the sole activity of ribosome-inactivating proteins on DNA
J. Biochem.
128
883-889
2000
Suregada multiflora, Momordica charantia, Phytolacca americana, Saponaria officinalis
Manually annotated by BRENDA team
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.
Manually annotated by BRENDA team
Zhao, Y.; Wang, X.; Zhou, G.; Li, H.
A pokeweed antiviral protein gene in roots of Phytolacca americana
Acta Virol.
48
131-132
2004
Phytolacca americana (P93444), Phytolacca americana (Q40772), Phytolacca americana (Q53YN2), Phytolacca americana (Q8RYA4), Phytolacca americana
Manually annotated by BRENDA team
Parikh, B.A.; Baykal, U.; Di, R.; Tumer, N.E.
Evidence for retro-translocation of pokeweed antiviral protein from endoplasmic reticulum into cytosol and separation of its activity on ribosomes from its activity on capped RNA
Biochemistry
44
2478-2490
2005
Phytolacca americana (P10297)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
Uckun, F.M.; Rustamova, L.; Vassilev, A.O.; Tibbles, H.E.; Petkevich, A.S.
CNS activity of pokeweed anti-viral protein (PAP) in mice infected with lymphocytic choriomeningitis virus (LCMV)
BMC Infect. Dis.
5
9
2005
Phytolacca americana
Manually annotated by BRENDA team
Picard, D.; Kao, C.C.; Hudak, K.A.
Pokeweed antiviral protein inhibits brome mosaic virus replication in plant cells
J. Biol. Chem.
280
20069-20075
2005
Phytolacca americana
Manually annotated by BRENDA team
Wang, M.; Hudak, K.A.
A novel interaction of pokeweed antiviral protein with translation initiation factors 4G and iso4G: a potential indirect mechanism to access viral RNAs
Nucleic Acids Res.
34
1174-1181
2006
Phytolacca americana
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
Roday, S.; Saen-oon, S.; Schramm, V.L.
Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin A-chain
Biochemistry
46
6169-6182
2007
Phytolacca americana, Ricinus communis (P02879)
Manually annotated by BRENDA team
Baykal, U.; Tumer, N.E.
The C-terminus of pokeweed antiviral protein has distinct roles in transport to the cytosol, ribosome depurination and cytotoxicity
Plant J.
49
995-1007
2007
Phytolacca americana
Manually annotated by BRENDA team
Mansouri, S.; Nourollahzadeh, E.; Hudak, K.A.
Pokeweed antiviral protein depurinates the sarcin/ricin loop of the rRNA prior to binding of aminoacyl-tRNA to the ribosomal A-site
RNA
12
1683-1692
2006
Phytolacca americana
Manually annotated by BRENDA team
Baldwin, A.E.; Khan, M.A.; Tumer, N.E.; Goss, D.J.; Friedland, D.E.
Characterization of pokeweed antiviral protein binding to mRNA cap analogs: competition with nucleotides and enhancement by translation initiation factor iso4G
Biochim. Biophys. Acta
1789
109-116
2009
Phytolacca americana
Manually annotated by BRENDA team
Bertholdo-Vargas, L.R.; Martins, J.N.; Bordin, D.; Salvador, M.; Schafer, A.E.; Barros, N.M.; Barbieri, L.; Stirpe, F.; Carlini, C.R.
Type 1 ribosome-inactivating proteins - entomotoxic, oxidative and genotoxic action on Anticarsia gemmatalis (Huebner) and Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae)
J. Insect Physiol.
55
51-58
2009
Suregada multiflora, Momordica charantia, Phytolacca americana, Saponaria officinalis, Silene chalcedonica
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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