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Information on EC 3.2.2.22 - rRNA N-glycosylase and Organism(s) Zea mays and UniProt Accession P25891
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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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- 3.2.2.22
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checkpoint
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immunotherapy
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death-ligand
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recist
The taxonomic range for the selected organisms is: Zea mays
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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Mirabilis antiviral protein
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-
-
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momorcochin-S
-
-
-
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nigrin b
-
-
-
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ribosomal ribonucleate N-glycosidase
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-
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ricin
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-
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RNA N-glycosidase
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-
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rRNA N-glycosidase
saporins
-
-
-
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rRNA N-glycosidase
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-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
large rRNA + H2O
?
inhibition of translation and protein synthesis, cytotoxic
-
-
?
large rRNA + H2O
large rRNA fragments, partially deadenylated
substrate are intact rabbit ribosomes, best substrate, or ribosomes from Aspergillus flavus, low activity, or Zea mays, the latter are poor substrates, depurination of specific sites in rRNA, formation of RNA fragments
fragment size overview, product determination using aniline coupling
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?
rRNA + H2O
?
inhibition of translation and protein synthesis, cytotoxic
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-
?
rRNA + H2O
?
inhibition of translation and protein synthesis, cytotoxic
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-
?
additional information
?
-
the isozyme RIP1 has defense-related function in maize plants
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-
?
additional information
?
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the isozyme RIP1 has defense-related function in maize plants
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-
?
additional information
?
-
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the isozyme RIP1 has defense-related function in maize plants
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-
?
additional information
?
-
the isozyme RIP1 has defense-related function in maize plants
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-
?
additional information
?
-
-
isozyme RIP1 shows relatively low cytotoxic activity and ressembles type I RIPs concerning its substrate specificity
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-
?
additional information
?
-
isozyme RIP1 shows relatively low cytotoxic activity and ressembles type I RIPs concerning its substrate specificity
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-
?
additional information
?
-
-
the isozyme RIP2 has defense-related function in maize plants
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-
?
additional information
?
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the isozyme RIP2 has defense-related function in maize plants
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-
?
additional information
?
-
-
isozyme RIP2 shows relatively low cytotoxic activity and ressembles type I RIPs concerning its substrate specificity
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-
?
additional information
?
-
isozyme RIP2 shows relatively low cytotoxic activity and ressembles type I RIPs concerning its substrate specificity
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?
additional information
?
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ribosome-inactivating proteins, RIPs, are N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of ribosomal RNA
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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
large rRNA + H2O
?
inhibition of translation and protein synthesis, cytotoxic
-
-
?
rRNA + H2O
?
inhibition of translation and protein synthesis, cytotoxic
-
-
?
rRNA + H2O
?
inhibition of translation and protein synthesis, cytotoxic
-
-
?
additional information
?
-
the isozyme RIP1 has defense-related function in maize plants
-
-
?
additional information
?
-
-
the isozyme RIP1 has defense-related function in maize plants
-
-
?
additional information
?
-
-
the isozyme RIP1 has defense-related function in maize plants
-
-
?
additional information
?
-
the isozyme RIP1 has defense-related function in maize plants
-
-
?
additional information
?
-
-
the isozyme RIP2 has defense-related function in maize plants
-
-
?
additional information
?
-
the isozyme RIP2 has defense-related function in maize plants
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
expression of gene RIP3:2 is up-regulated by drought
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
additional information
additional information
the isozyme accumulates as inactive precursor protein
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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). RIP3_MAIZE
300
0
33257
Swiss-Prot
other Location (Reliability: 2)
PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
type III RIP isozyme RIP1 forms dimers and ressembles type II RIPs concerning its subunit structure
dimer
type III RIP isozyme RIP2 forms dimers and ressembles type II RIPs concerning its subunit structure
additional information
additional information
-
MOD structure determination and comparison using the crystal structure of DELTAN5-MOD, PDB ID 2PQI, and by determination of the NMR solution structure of MOD, PDB ID 2k6H, detailed overview. MOD has shorter beta6 and alphaB segments, probably for accommodating easier substrate binding, and an alpha-helix instead of an antiparallel beta-sheet in the C-terminal domain, which is involved in binding ribosomal protein P2 in some RIPs, compared to type I and II RIPs. The P2 binding site on MOD is located at the N-terminal domain near the internal inactivation region
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
proteolytic modification
proteolytic modification
proteolytic modification
isozyme RIP1 is synthesized as inactive precursor protein B-32 or proRIP, which is activated by proteolytic cleavage into two polypeptide chains forming the dimeric enzyme, the enzyme can be activated by papain
proteolytic modification
isozyme RIP1 is synthesized as inactive precursor protein B-32 or proRIP, which is activated by proteolytic cleavage into two polypeptide chains forming the dimeric enzyme, the enzyme can be activated by papain
proteolytic modification
isozyme RIP2 is synthesized as inactive precursor protein proRIP2, which is activated by proteolytic cleavage into two polypeptide chains forming the dimeric enzyme, the enzyme can be activated by papain
proteolytic modification
-
enzyme is synthesized as an inactive precursor with a 25-amino acid internal inactivation region, which is removed in the active form
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization of precursor protein and active form, at 2.4 and 2.5 A resolution, respectively. In the precursor, the inactivation region is found on the protein surface and consists of a flexible loop followed by a long alpha-helix. Presence of this region diminishes both the interaction with ribosome and cytotoxicity, but not cellular uptake. The active site of the enzyme is too small to accomodate two glutamate residues
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
construction of an active deletion mutant MOD1 of recombinant proRIP1 with reduced activity compared to recombinant RIP1 after activation of both by papain
additional information
-
construction of an active deletion mutant MOD1 of recombinant proRIP1 with reduced activity compared to recombinant RIP1 after activation of both by papain
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene RIP3:2, genomic DNA library screening, DNA and amino acid sequence determination and analyis, RNA mapping and expression profiling, expression is not under control of the Opaque-2 promoter, expression of gene RIP3:2 encoding isozyme RIP2 in Escherichia coli strain BL21(DE3) as N-terminally His-tagged protein
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Krawetz, J.E.; Boston, R.S.
Substrate specificity of a maize ribosome-inactivating protein differs across diverse taxa
Eur. J. Biochem.
267
1966-1974
2000
Zea mays (P25891), Zea mays
Bass, H.W.; Krawetz, J.E.; GR, O.B.; Zinselmeier, C.; Habben, J.E.; Boston, R.S.
Maize ribosome-inactivating proteins (RIPs) with distinct expression patterns have similar requirements for proenzyme activation
J. Exp. Bot.
55
2219-2233
2004
Zea mays, Zea mays (P25891)
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
Mak, A.N.; Wong, Y.T.; An, Y.J.; Cha, S.S.; Sze, K.H.; Au, S.W.; Wong, K.B.; Shaw, P.C.
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
6259-6267
2007
Zea mays
Yang, Y.; Mak, A.N.; Shaw, P.C.; Sze, K.H.
Solution structure of an active mutant of maize ribosome-inactivating protein (MOD) and its interaction with the ribosomal stalk protein P2
J. Mol. Biol.
395
897-907
2010
Zea mays
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