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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1abr
Original Entry
Title:
Complex (glycosidase/carbohydrate)
Compound:
Abrin-a complexed with two sugar chains
Mutant:
No
UniProt/Swiss-Prot:
P11140-ABRA_ABRPR
EC Class:
3.2.2.22
Other CSA Entries:
Overview of all sites for 1abr
Homologues of 1abr
Entries for UniProt/Swiss-Prot: P11140
Entries for EC: 3.2.2.22
Other Databases:
PDB entry: 1abr
PDBsum entry: 1abr
UniProt/Swiss-Prot: P11140
IntEnz entry: 3.2.2.22
Literature Report:
Introduction:
Abrin-A from the seeds of Abrus precatorius is a type II ribosome-inactivating protein. It catalyses the endohydrolysis of the N-glycosidic bond at one specific adenosine A4324 on the 28S rRNA. This inhibition of protein biosynthesis is anti-carcinogenic. Abrin-A is composed of two chains which are linked by a disulphide bond.
Mechanism:
1. The C1'-N9 bond between adenine and ribose is broken, facilitated by the protonation of N3 by Arg 167.
2. The resulting oxycarbonium ion is stabilised by the negatively charged Glu 164 residue.
3. The loss of a proton from Arg 167 increases its basicity, causing it to deprotonate a water molecule, activating it for nucleophilic attack on the C1' atom of the oxycarbonium ion.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 164 0Sidechain
ElectrostaticSubstrate
Glu 164 stabilises the oxycarbonium ion intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 7608980 Current protein Structural similarity to homologue of known mechanism
PubMed ID 1433290 Current protein Structural similarity to homologue of known mechanism
PubMed ID 7608980 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 7608980 Current protein Mutagenesis of residue
PubMed ID 1433290 Current protein Mutagenesis of residue
PubMed ID 1433290 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 167 0Sidechain
Acid/baseWater
Acid/baseSubstrate
Arg 167 acts as a general acid by protonating the N3 atom of the substrate. It then acts as a general base by deprotonating a water molecule, activating it for nucleophilic attack.
Evidence from paper Evidence concerns Evidence type
PubMed ID 7608980 Current protein Mutagenesis of residue
PubMed ID 1433290 Current protein Mutagenesis of residue
PubMed ID 7608980 Current protein Structural similarity to homologue of known mechanism
PubMed ID 1433290 Current protein Structural similarity to homologue of known mechanism
Notes:
It is thought that, if mutation of Glu 164 occurs, Glu 195 can take its place by rotation of its side chain, without major changes in the structure of the backbone occuring.
References:
1
Crystal structure of abrin-a at 2.14 A.
T. H. Tahirov and T. H. Lu and Y. C. Liaw and Y. L. Chen and J. Y. Lin
J Mol Biol 250, (3) 354-67, (1995).
7608980
2
X-ray analysis of substrate analogs in the ricin A-chain active site.
A. F. Monzingo and J. D. Robertus
J Mol Biol 227, (4) 1136-45, (1992).
1433290
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