EzCatDB: D00847
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DB codeD00847
CATH domainDomain 13.40.420.10 : Ricin (A subunit); domain 1Catalytic domain
Domain 24.10.470.10 : Ricin (A Subunit), domain 2Catalytic domain
E.C.3.2.2.22

CATH domainRelated DB codes (homologues)
3.40.420.10 : Ricin (A subunit); domain 1M00140
4.10.470.10 : Ricin (A Subunit), domain 2M00140

Enzyme Name
UniProtKBKEGG

P28522P25891
Protein nameRibosome-inactivating proteinRibosome-inactivating protein 3rRNA N-glycosylase
Ribosomal ribonucleate N-glycosidase
Nigrin b
RNA N-glycosidase
rRNA N-glycosidase;
Ricin
Momorcochin-S
Mirabilis antiviral protein
Momorcochin-S
Gelonin
Saporins
SynonymsEC 3.2.2.22
rRNA N-glycosidase
B-32 protein
rRNA N-glycosidase
EC 3.2.2.22
ContainsRibosome-inactivating protein alpha chain
Ribosome-inactivating protein beta chain
None
PfamPF00161 (RIP)
[Graphical view]
PF00161 (RIP)
[Graphical view]


UniProtKB:Accession NumberP28522P25891
Entry nameRIPX_MAIZERIP3_MAIZE
ActivityEndohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
SubunitSynthesized and stored in the kernel as a 34 kDa inactive precursor. During germination, this neutral precursor is converted into a basic, active form by limited proteolysis, which removes 25 AA of net charge -6 from the center of the polypeptide chain. Additional processing also occurs at the N- and C-termini of the polypeptide. A two-chain active RIP (comprised of 16.5 and 8.5 kDa fragments that remain tightly associated) is produced from this processing event.Monomer.
Subcellular location
Cytoplasm.
Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00240C00001L00063C00147
CompoundrRNAH2ODeadenylated rRNAAdenine
Typenucleic acidsH2Onucleic acidsamine group,aromatic ring (with nitrogen atoms)
ChEBI
15377

16708
PubChem
962
22247451

190
            
2k6hA01Unbound UnboundUnbound
2pqiA01Unbound UnboundUnbound
2pqiB01Unbound UnboundUnbound
2pqiC01Unbound UnboundUnbound
2pqjA01Unbound UnboundBound:ADE
2pqjB01Unbound UnboundBound:ADE
2pqjC01Unbound UnboundBound:ADE
2pqgA01Unbound UnboundUnbound
2pqgB01Unbound UnboundUnbound
2k6hA02Unbound UnboundUnbound
2pqiA02Unbound UnboundUnbound
2pqiB02Unbound UnboundUnbound
2pqiC02Unbound UnboundUnbound
2pqjA02Unbound UnboundUnbound
2pqjB02Unbound UnboundUnbound
2pqjC02Unbound UnboundUnbound
2pqgA02Unbound UnboundUnbound
2pqgB02Unbound UnboundUnbound

Active-site residues
resource
literature [4]
pdbCatalytic residues
         
2k6hA01GLU 167
2pqiA01GLU 207
2pqiB01GLU 207
2pqiC01GLU 207
2pqjA01GLU 207
2pqjB01GLU 207
2pqjC01GLU 207
2pqgA01GLU 207
2pqgB01GLU 207
2k6hA02ARG 170
2pqiA02ARG 210
2pqiB02ARG 210
2pqiC02ARG 210
2pqjA02ARG 210
2pqjB02ARG 210
2pqjC02ARG 210
2pqgA02ARG 210
2pqgB02ARG 210

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Figure 6

references
[1]
CommentsNUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 13-49; 155-161 AND 187-215.
PubMed ID1744135
JournalJ Biol Chem
Year1991
Volume266
Pages23422-7
AuthorsWalsh TA, Morgan AE, Hey TD
TitleCharacterization and molecular cloning of a proenzyme form of a ribosome-inactivating protein from maize. Novel mechanism of proenzyme activation by proteolytic removal of a 2.8-kilodalton internal peptide segment.
[2]
PubMed ID10727935
JournalEur J Biochem
Year2000
Volume267
Pages1966-74
AuthorsKrawetz JE, Boston RS
TitleSubstrate specificity of a maize ribosome-inactivating protein differs across diverse taxa.
[3]
JournalCRC Crit Rev Plant Sci
Year2001
Volume20
Pages395-465
AuthorsVan Damme EJM, Hao Q, Chen Y, Barre A, Vandenbussche F, Desmyter S, Rouge P, Peumans WJ
TitleRibosome-inactivating proteins: A family of plant proteins that do more than inactivate ribosomes.
[4]
PubMed ID17855394
JournalNucleic Acids Res
Year2007
Volume35
Pages6259-67
AuthorsMak AN, Wong YT, An YJ, Cha SS, Sze KH, Au SW, Wong KB, Shaw PC
TitleStructure-function study of maize ribosome-inactivating protein: implications for the internal inactivation region and the sole glutamate in the active site.
Related PDB2pqi,2pqj,2pqg
Related UniProtKBP28522,P25891
[5]
PubMed ID19900464
JournalJ Mol Biol
Year2010
Volume395
Pages897-907
AuthorsYang Y, Mak AN, Shaw PC, Sze KH
TitleSolution structure of an active mutant of maize ribosome-inactivating protein (MOD) and its interaction with the ribosomal stalk protein P2.
Related PDB2k6h
Related UniProtKBP28522

comments
This enzyme belongs to either Type-III or atypical Type-I ribosome-inactivating protein (RIP) family (see [5]). Type-I RIPs are single polypeptide proteins consisting of an active chain, whereas Type-II RIPs are heterodimeric proteins, which are linked through a disulfide bond (see [5]). Here, this enzyme is synthesized as a single polypeptide chain, which undergoes activation by proteolytic removal of N-terminal region, 25-residues from the central domain, and C-terminal region.

createdupdated
2010-12-152011-11-01


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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