EzCatDB: M00140
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeM00140
CATH domainDomain 13.40.420.10 : Ricin (A subunit); domain 1Catalytic domain
Domain 24.10.470.10 : Ricin (A Subunit), domain 2Catalytic domain
Domain 32.40.50.70 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 42.40.50.70 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 52.40.50.70 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 62.40.50.70 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 72.40.50.70 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
E.C.3.2.2.22

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

Enzyme Name
UniProtKBKEGG

P10149P69178
Protein nameShiga-like toxin 1 subunit AShiga-like toxin 1 subunit BrRNA N-glycosylase
ribosomal ribonucleate N-glycosidase
nigrin b
RNA N-glycosidase
rRNA N-glycosidase
ricin
momorcochin-S
Mirabilis antiviral protein
momorcochin-S
gelonin
saporins
SynonymsSLT-1 A subunit
SLT-1a
SLT-Ia
EC 3.2.2.22
Verotoxin 1 subunit A
Verocytotoxin 1 subunit A
rRNA N-glycosidase 1
SLT-1 B subunit
SLT-1b
SLT-Ib
Verocytotoxin 1 subunit B
Verotoxin 1 subunit B
PfamPF00161 (RIP)
[Graphical view]
PF02258 (SLT_beta)
[Graphical view]


UniProtKB:Accession NumberP10149P69178
Entry nameSTXA_BPH30STXB_BPH30
ActivityEndohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
SubunitShiga-like toxin contains a single subunit A and five copies of subunit B.Shiga-like toxin contains a single subunit A and five copies of subunit B.
Subcellular locationSecreted.Secreted.
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
            
1dm0A01Unbound UnboundUnbound
1dm0L01Unbound UnboundUnbound
1dm0A02Unbound UnboundUnbound
1dm0L02Unbound UnboundUnbound
1dm0BUnbound UnboundUnbound
1dm0CUnbound UnboundUnbound
1dm0DUnbound UnboundUnbound
1dm0EUnbound UnboundUnbound
1dm0FUnbound UnboundUnbound
1dm0GUnbound UnboundUnbound
1dm0HUnbound UnboundUnbound
1dm0IUnbound UnboundUnbound
1dm0JUnbound UnboundUnbound
1dm0KUnbound UnboundUnbound

Active-site residues
resource
Swiss-prot;P10149
pdbCatalytic residues
         
1dm0A01GLU 167
1dm0L01GLU 167
1dm0A02ARG 170
1dm0L02ARG 170
1dm0B 
1dm0C 
1dm0D 
1dm0E 
1dm0F 
1dm0G 
1dm0H 
1dm0I 
1dm0J 
1dm0K 


references
[1]
PubMed ID1717316
JournalFEBS Lett
Year1991
Volume290
Pages65-8
AuthorsHartley MR, Legname G, Osborn R, Chen Z, Lord JM
TitleSingle-chain ribosome inactivating proteins from plants depurinate Escherichia coli 23S ribosomal RNA.
[2]
PubMed ID1619659
JournalJ Mol Biol
Year1992
Volume226
Pages281-3
AuthorsMiyano M, Appelt K, Arita M, Habuka N, Kataoka J, Ago H, Tsuge H, Noma M, Ashford V, Xuong N
TitleCrystallization and preliminary X-ray crystallographic analysis of Mirabilis antiviral protein.
[3]
CommentsX-ray Diffraction
PubMed ID8345529
JournalJ Mol Biol
Year1993
Volume232
Pages704-6
AuthorsKozlov YV, Chernaia MM, Fraser ME, James MN
TitlePurification and crystallization of Shiga toxin from Shigella dysenteriae.
Related PDB1dm0
[4]
PubMed ID8218413
JournalBiochim Biophys Acta
Year1993
Volume1216
Pages31-42
AuthorsFerreras JM, Barbieri L, Girbes T, Battelli MG, Rojo MA, Arias FJ, Rocher MA, Soriano F, Mendez E, Stirpe F
TitleDistribution and properties of major ribosome-inactivating proteins (28 S rRNA N-glycosidases) of the plant Saponaria officinalis L. (Caryophyllaceae).
[5]
CommentsX-ray Diffraction
PubMed ID7656009
JournalNat Struct Biol
Year1994
Volume1
Pages59-64
AuthorsFraser ME, Chernaia MM, Kozlov YV, James MN
TitleCrystal structure of the holotoxin from Shigella dysenteriae at 2.5 A resolution.
Related PDB1dm0
[6]
PubMed ID8912688
JournalBiochem J
Year1996
Volume319
Pages507-13
AuthorsBarbieri L, Valbonesi P, Gorini P, Pession A, Stirpe F
TitlePolynucleotide: adenosine glycosidase activity of saporin-L1: effect on DNA, RNA and poly(A).
[7]
PubMed ID9398319
JournalBiochemistry
Year1997
Volume36
Pages15865-72
AuthorsMenikh A, Saleh MT, Gariepy J, Boggs JM
TitleOrientation in lipid bilayers of a synthetic peptide representing the C-terminus of the A1 domain of shiga toxin. A polarized ATR-FTIR study.
[8]
PubMed ID9367352
JournalFASEB J
Year1997
Volume11
Pages1169-76
AuthorsFabbrini MS, Carpani D, Bello-Rivero I, Soria MR
TitleThe amino-terminal fragment of human urokinase directs a recombinant chimeric toxin to target cells: internalization is toxin mediated.
[9]
PubMed ID9761860
JournalActa Crystallogr D Biol Crystallogr
Year1998
Volume54
Pages636-8
AuthorsSavino C, Federici L, Brancaccio A, Ippoliti R, Lendaro E, Tsernoglou D
TitleCrystallization and preliminary X-ray study of saporin, a ribosome-inactivating protein from Saponaria officinalis.
[10]
PubMed ID9989237
JournalBiochim Biophys Acta
Year1999
Volume1429
Pages506-11
AuthorsKumar M, Dattagupta S, Kannan KK, Hosur MV
TitlePurification, crystallisation and preliminary X-ray diffraction study of ribosome inactivating protein: saporin.
[11]
PubMed ID10745075
JournalFEBS Lett
Year2000
Volume470
Pages239-43
AuthorsSavino C, Federici L, Ippoliti R, Lendaro E, Tsernoglou D
TitleThe crystal structure of saporin SO6 from Saponaria officinalis and its interaction with the ribosome.

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

createdupdated
2004-03-192011-11-01


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
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 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.