DB code: S00174

RLCP classification 1.15.60000.85 : Hydrolysis
CATH domain 3.10.450.30 : Nuclear Transport Factor 2; Chain Catalytic domain
E.C. 3.1.27.4
CSA 1rtu
M-CSA 1rtu
MACiE

CATH domain Related DB codes (homologues)
3.10.450.30 : Nuclear Transport Factor 2; Chain S00175

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P00654 Ribonuclease U2
RNase U2
EC 3.1.27.4
PF00545 (Ribonuclease)
[Graphical View]

KEGG enzyme name
ribonuclease U2
purine specific endoribonuclease
ribonuclease U3
RNase U3
RNase U2
purine-specific ribonuclease
purine-specific RNase
Pleospora RNase
Trichoderma koningi RNase III
ribonuclease (purine)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00654 RNU2_USTSP Two-stage endonucleolytic cleavage to nucleoside 3''-phosphates and 3''-phosphooligonucleotides ending in A-P or G-P with 2'',3''-cyclic phosphate intermediates.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00046 C00001 C03419 C00172 C01199
E.C.
Compound RNA H2O Nucleoside 3'-phosphate 3'-Phosphooligonucleotide 5'-Hydroxyoligonucleotide
Type nucleic acids H2O nucleotide nucleic acids,phosphate group/phosphate ion nucleic acids
ChEBI 15377
PubChem 22247451
962
1rtuA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:SO4 Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1rtuA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 39;HIS 41;GLU 62;ARG 85;HIS 101

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[7]
p.286

References
[1]
Resource
Comments
Medline ID
PubMed ID 408330
Journal J Biochem (Tokyo)
Year 1977
Volume 81
Pages 1237-46
Authors Uchida T, Funayama-Machida C
Title Systematic synthesis of dinucleotides and trinucleotides with RNases U2, N1, and a non-specific RNase from B. subtilis.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6202507
Journal EMBO J
Year 1982
Volume 1
Pages 1259-65
Authors Branlant C, Krol A, Ebel JP, Lazar E, Haendler B, Jacob M
Title U2 RNA shares a structural domain with U1, U4, and U5 RNAs.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 6737414
Journal J Med Chem
Year 1984
Volume 27
Pages 726-33
Authors Torrence PF, Imai J, Lesiak K, Jamoulle JC, Sawai H
Title Oligonucleotide structural parameters that influence binding of 5'-O-triphosphoadenylyl-(2'----5')-adenylyl-(2'----5')-adenosine to the 5'-O-triphosphoadenylyl-(2'----5')-adenylyl-(2'----5')-adenosine dependent endoribonuclease: chain length, phosphorylation state, and heterocyclic base.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 2124675
Journal Nucleic Acids Res
Year 1990
Volume 18
Pages 7041-7
Authors Hall KB, Sampson JR
Title Structural investigation of the in vitro transcript of the yeast tRNA(phe) precursor by NMR and nuclease mapping.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7798182
Journal J Biochem (Tokyo)
Year 1994
Volume 116
Pages 26-33
Authors Nomura H, Inokuchi N, Kobayashi H, Koyama T, Iwama M, Ohgi K, Irie M
Title Purification and primary structure of a new guanylic acid specific ribonuclease from Pleurotus ostreatus.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), AND REVISIONS.
Medline ID 96082150
PubMed ID 7492561
Journal Biochemistry
Year 1995
Volume 34
Pages 15583-91
Authors Noguchi S, Satow Y, Uchida T, Sasaki C, Matsuzaki T
Title Crystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8 A resolution.
Related PDB 1rtu
Related UniProtKB P00654
[7]
Resource
Comments
Medline ID
PubMed ID 9586111
Journal Nucleic Acids Symp Ser
Year 1997
Volume
Pages 285-6
Authors Noda N, Noguchi S, Satow Y
Title Crystal structures of nucleic acid complexes of ribonuclease U2.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11733014
Journal Eur J Biochem
Year 2001
Volume 268
Pages 6190-6
Authors Masip M, Lacadena J, Mancheno JM, Onaderra M, Martinez-Ruiz A, Martinez del Pozo A, Gavilanes JG
Title Arginine 121 is a crucial residue for the specific cytotoxic activity of the ribotoxin alpha-sarcin.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 11582789
Journal Methods Enzymol
Year 2001
Volume 341
Pages 335-51
Authors Martinez-Ruiz A, Garcia-Ortega L, Kao R, Lacadena J, Onaderra M, Mancheno JM, Davies J, Martinez del Pozo A, Gavilanes JG
Title RNase U2 and alpha-sarcin: a study of relationships.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 11897788
Journal J Biol Chem
Year 2002
Volume 277
Pages 18632-9
Authors Garcia-Ortega L, Masip M, Mancheno JM, Onaderra M, Lizarbe MA, Garcia-Mayoral MF, Bruix M, Martinez del Pozo A, Gavilanes JG
Title Deletion of the NH2-terminal beta-hairpin of the ribotoxin alpha-sarcin produces a nontoxic but active ribonuclease.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to RNase T1 family.
It is suggested that either His41 or Glu62 acts as a general base and His101 acts as a general acid in the first step of RNA hydrolysis [6], [7].
(1) According to the literature [7], His41 is the first candidate for the general base that abstracts a hydrogen atom from the O2', in the first step of hydrolysis. Another candidate for the general base is Glu62. As counterpart of Glu62, Glu96 of a homologous enzyme, alpha-sarcin (S00175 in EzCatDB) acts as a general base to activate the O2' atom of RNA, Glu62 is a more likely base.
(2) After the attack on the phosphate P atom by the activated O2' atom, the bond between the phosphate P and O5' atoms is cleaved, resulting the formation of a 2',3'-cyclic nucleotide and a 5'-hydroxy product.
(3) A protonation is prerequisite to the formation of the 5'-hydroxy product. The possible candidate for the hydrogen donor to the O5' atom of the second nucleotide is the NE2 atom of His101.
(4) Arg85 may stabilizes the negative charge on the phosphoryl group.
(5) 2',3'-cyclic intermediate is formed.
(6) Glu62 and His101 act as a general acid and base, respectively. Glu62 activates a water molecule, which attacks on the cyclic intermediate, whereas His101 protonates the leaving 2'-oxygen.

Created Updated
2002-07-01 2010-02-04