DB code: D00847

CATH domain 3.40.420.10 : Ricin (A subunit); domain 1 Catalytic domain
4.10.470.10 : Ricin (A Subunit), domain 2 Catalytic domain
E.C. 3.2.2.22
CSA
M-CSA
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Contains Pfam
P28522 Ribosome-inactivating protein
EC 3.2.2.22
rRNA N-glycosidase
Ribosome-inactivating protein alpha chain
Ribosome-inactivating protein beta chain
PF00161 (RIP)
[Graphical View]
P25891 Ribosome-inactivating protein 3
B-32 protein
rRNA N-glycosidase
EC 3.2.2.22
None PF00161 (RIP)
[Graphical View]

KEGG enzyme name
rRNA N-glycosylase
Ribosomal ribonucleate N-glycosidase
Nigrin b
RNA N-glycosidase
rRNA N-glycosidase;
Ricin
Momorcochin-S
Mirabilis antiviral protein
Momorcochin-S
Gelonin
Saporins

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P25891 RIP3_MAIZE Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA. Monomer. Cytoplasm.
P28522 RIPX_MAIZE Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA. Synthesized 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.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00240 C00001 L00063 C00147
E.C.
Compound rRNA H2O Deadenylated rRNA Adenine
Type nucleic acids H2O nucleic acids amine group,aromatic ring (with nitrogen atoms)
ChEBI 15377
16708
PubChem 22247451
962
190
2k6hA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqiB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqiC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ADE
2pqjB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ADE
2pqjC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ADE
2pqgA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqgB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2k6hA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqiB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqiC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqjB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqjC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqgA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pqgB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2k6hA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 167
2pqiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 207
2pqiB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 207
2pqiC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 207
2pqjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 207
2pqjB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 207
2pqjC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 207
2pqgA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 207
2pqgB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 207
2k6hA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 170
2pqiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 210
2pqiB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 210
2pqiC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 210
2pqjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 210
2pqjB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 210
2pqjC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 210
2pqgA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 210
2pqgB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 210

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Figure 6

References
[1]
Resource
Comments NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 13-49; 155-161 AND 187-215.
Medline ID
PubMed ID 1744135
Journal J Biol Chem
Year 1991
Volume 266
Pages 23422-7
Authors Walsh TA, Morgan AE, Hey TD
Title Characterization 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.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 10727935
Journal Eur J Biochem
Year 2000
Volume 267
Pages 1966-74
Authors Krawetz JE, Boston RS
Title Substrate specificity of a maize ribosome-inactivating protein differs across diverse taxa.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID
Journal CRC Crit Rev Plant Sci
Year 2001
Volume 20
Pages 395-465
Authors Van Damme EJM, Hao Q, Chen Y, Barre A, Vandenbussche F, Desmyter S, Rouge P, Peumans WJ
Title Ribosome-inactivating proteins: A family of plant proteins that do more than inactivate ribosomes.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 17855394
Journal Nucleic Acids Res
Year 2007
Volume 35
Pages 6259-67
Authors Mak AN, Wong YT, An YJ, Cha SS, Sze KH, Au SW, Wong KB, Shaw PC
Title Structure-function study of maize ribosome-inactivating protein: implications for the internal inactivation region and the sole glutamate in the active site.
Related PDB 2pqi 2pqj 2pqg
Related UniProtKB P28522 P25891
[5]
Resource
Comments
Medline ID
PubMed ID 19900464
Journal J Mol Biol
Year 2010
Volume 395
Pages 897-907
Authors Yang Y, Mak AN, Shaw PC, Sze KH
Title Solution structure of an active mutant of maize ribosome-inactivating protein (MOD) and its interaction with the ribosomal stalk protein P2.
Related PDB 2k6h
Related UniProtKB P28522

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.

Created Updated
2010-12-15 2011-11-01