Ribonuclease U2
Catalyses the two-stage endonucleolytic cleavage of nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in A-P or G-P with 2',3'-cyclic phosphate intermediates. The enzyme contains an isoaspartate residue.
Reference Protein and Structure
- Sequence
-
P00654
(4.6.1.20)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Ustilago sphaerogena (Smut fungus)
- PDB
-
1rtu
- USTILAGO SPHAEROGENA RIBONUCLEASE U2
(1.8 Å)
- Catalytic CATH Domains
-
3.10.450.30
(see all for 1rtu)
- Cofactors
- Calcium(2+) (2)
Enzyme Reaction (EC:4.6.1.20)
+
→
+
+
Alternative enzyme names: Pleospora RNase, Trichoderma koningi RNase III, RNase U(2), RNase U(3), Purine specific endoribonuclease, Purine-specific RNase, Purine-specific ribonuclease, Ribonuclease (purine), Ribonuclease U(3), Ribonuclease U2,
Enzyme Mechanism
Introduction
The reaction occurs in a two-step process with cleavage of the RNA chain by transesterification of a 5'-phosphoester bond to form a 2',3'-cyclic phosphate terminus in the first step, followed by hydrolysis of the cyclic phosphate to form a 3'-phosphate in a second, independent step.
Catalytic Residues Roles
| UniProt | PDB* (1rtu) | ||
| Arg85 | Arg85A | Helps stabilise the reactive intermediates and transition states formed during the course of the reaction. | electrostatic stabiliser |
| Glu62, His101, His41 | Glu62A, His101A, His41A | Acts as a general acid/base. | proton shuttle (general acid/base) |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
References
- Noguchi S et al. (1995), Biochemistry, 34, 15583-15591. Crystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8 A resolution. PMID:7492561.
- Noguchi S (2010), Acta Crystallogr D Biol Crystallogr, 66, 843-849. Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate. DOI:10.1107/S0907444910019621. PMID:20606265.
- Noguchi S (2010), Protein Pept Lett, 17, 1559-1561. Conformational variation revealed by the crystal structure of RNase U2A complexed with Ca ion and 2'-adenylic acid at 1.03 Å resolution. PMID:20858208.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Arg85A | electrostatic stabiliser |
| His41A | proton shuttle (general acid/base) |
| Glu62A | proton shuttle (general acid/base) |
| His101A | proton shuttle (general acid/base) |