DB code: M00140

CATH domain 3.40.420.10 : Ricin (A subunit); domain 1 Catalytic domain
4.10.470.10 : Ricin (A Subunit), domain 2 Catalytic domain
2.40.50.70 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
2.40.50.70 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
2.40.50.70 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
2.40.50.70 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
2.40.50.70 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
E.C. 3.2.2.22
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.420.10 : Ricin (A subunit); domain 1 D00847
4.10.470.10 : Ricin (A Subunit), domain 2 D00847

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P10149 Shiga-like toxin 1 subunit A
SLT-1 A subunit
SLT-1a
SLT-Ia
EC 3.2.2.22
Verotoxin 1 subunit A
Verocytotoxin 1 subunit A
rRNA N-glycosidase 1
PF00161 (RIP)
[Graphical View]
P69178 Shiga-like toxin 1 subunit B
SLT-1 B subunit
SLT-1b
SLT-Ib
Verocytotoxin 1 subunit B
Verotoxin 1 subunit B
PF02258 (SLT_beta)
[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
P10149 STXA_BPH30 Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA. Shiga-like toxin contains a single subunit A and five copies of subunit B. Secreted.
P69178 STXB_BPH30 Shiga-like toxin contains a single subunit A and five copies of subunit B. Secreted.

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
1dm0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0L01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0L02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0E Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0F Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0G Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0H Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0I Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0J Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1dm0K Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P10149

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dm0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 167
1dm0L01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 167
1dm0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 170
1dm0L02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 170
1dm0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dm0C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dm0D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dm0E Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dm0F Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dm0G Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dm0H Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dm0I Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dm0J Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dm0K Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis

References
[1]
Resource
Comments
Medline ID
PubMed ID 1717316
Journal FEBS Lett
Year 1991
Volume 290
Pages 65-8
Authors Hartley MR, Legname G, Osborn R, Chen Z, Lord JM
Title Single-chain ribosome inactivating proteins from plants depurinate Escherichia coli 23S ribosomal RNA.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1619659
Journal J Mol Biol
Year 1992
Volume 226
Pages 281-3
Authors Miyano M, Appelt K, Arita M, Habuka N, Kataoka J, Ago H, Tsuge H, Noma M, Ashford V, Xuong N
Title Crystallization and preliminary X-ray crystallographic analysis of Mirabilis antiviral protein.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-ray Diffraction
Medline ID
PubMed ID 8345529
Journal J Mol Biol
Year 1993
Volume 232
Pages 704-6
Authors Kozlov YV, Chernaia MM, Fraser ME, James MN
Title Purification and crystallization of Shiga toxin from Shigella dysenteriae.
Related PDB 1dm0
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8218413
Journal Biochim Biophys Acta
Year 1993
Volume 1216
Pages 31-42
Authors Ferreras JM, Barbieri L, Girbes T, Battelli MG, Rojo MA, Arias FJ, Rocher MA, Soriano F, Mendez E, Stirpe F
Title Distribution and properties of major ribosome-inactivating proteins (28 S rRNA N-glycosidases) of the plant Saponaria officinalis L. (Caryophyllaceae).
Related PDB
Related UniProtKB
[5]
Resource
Comments X-ray Diffraction
Medline ID
PubMed ID 7656009
Journal Nat Struct Biol
Year 1994
Volume 1
Pages 59-64
Authors Fraser ME, Chernaia MM, Kozlov YV, James MN
Title Crystal structure of the holotoxin from Shigella dysenteriae at 2.5 A resolution.
Related PDB 1dm0
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8912688
Journal Biochem J
Year 1996
Volume 319
Pages 507-13
Authors Barbieri L, Valbonesi P, Gorini P, Pession A, Stirpe F
Title Polynucleotide: adenosine glycosidase activity of saporin-L1: effect on DNA, RNA and poly(A).
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9398319
Journal Biochemistry
Year 1997
Volume 36
Pages 15865-72
Authors Menikh A, Saleh MT, Gariepy J, Boggs JM
Title Orientation in lipid bilayers of a synthetic peptide representing the C-terminus of the A1 domain of shiga toxin. A polarized ATR-FTIR study.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9367352
Journal FASEB J
Year 1997
Volume 11
Pages 1169-76
Authors Fabbrini MS, Carpani D, Bello-Rivero I, Soria MR
Title The amino-terminal fragment of human urokinase directs a recombinant chimeric toxin to target cells: internalization is toxin mediated.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9761860
Journal Acta Crystallogr D Biol Crystallogr
Year 1998
Volume 54
Pages 636-8
Authors Savino C, Federici L, Brancaccio A, Ippoliti R, Lendaro E, Tsernoglou D
Title Crystallization and preliminary X-ray study of saporin, a ribosome-inactivating protein from Saponaria officinalis.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9989237
Journal Biochim Biophys Acta
Year 1999
Volume 1429
Pages 506-11
Authors Kumar M, Dattagupta S, Kannan KK, Hosur MV
Title Purification, crystallisation and preliminary X-ray diffraction study of ribosome inactivating protein: saporin.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 10745075
Journal FEBS Lett
Year 2000
Volume 470
Pages 239-43
Authors Savino C, Federici L, Ippoliti R, Lendaro E, Tsernoglou D
Title The crystal structure of saporin SO6 from Saponaria officinalis and its interaction with the ribosome.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to ribosome-inactivating protein (RIP) family (see [5]).

Created Updated
2004-03-19 2011-11-01