EzCatDB: S00174

DB codeS00174
RLCP classification1.15.60000.85
CATH domainDomain 13.10.450.30Catalytic domain
E.C.3.1.27.4
CSA1rtu

CATH domainRelated DB codes (homologues)
3.10.450.30S00175

Enzyme Name
Swiss-protKEGG

P00654
Protein nameRibonuclease U2ribonuclease U2
purine specific endoribonuclease
ribonuclease U3
RNase U3
RNase U2
purine-specific ribonuclease
purine-specific RNase
Pleospora RNase
Trichoderma koningi RNase III
ribonuclease (purine)
SynonymsRNase U2
EC 3.1.27.4


Swiss-prot:Accession NumberP00654
Entry nameRNU2_USTSP
ActivityTwo-stage endonucleolytic cleavage to nucleoside 3''-phosphates and 3''-phosphooligonucleotides ending in A-P or G-P with 2'',3''-cyclic phosphate intermediates.
Subunit
Subcellular location
Cofactor


SubstratesProducts
KEGG-idC00046C00001C03419C00172C01199
CompoundRNAH2ONucleoside 3'-phosphate3'-Phosphooligonucleotide5'-Hydroxyoligonucleotide
Typenucleic acidsH2Onucleotidenucleic acids,phosphate group/phosphate ionnucleic acids
1rtuAAnalogue:SO4
UnboundUnboundUnbound

Active-site residues
pdbCatalytic residues
1rtuATYR 39;HIS 41;GLU 62;ARG 85;HIS 101

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[7]p.286

references
[1]
PubMed ID408330
JournalJ Biochem (Tokyo)
Year1977
Volume81
Pages1237-46
AuthorsUchida T, Funayama-Machida C
TitleSystematic synthesis of dinucleotides and trinucleotides with RNases U2, N1, and a non-specific RNase from B. subtilis.
[2]
PubMed ID6202507
JournalEMBO J
Year1982
Volume1
Pages1259-65
AuthorsBranlant C, Krol A, Ebel JP, Lazar E, Haendler B, Jacob M
TitleU2 RNA shares a structural domain with U1, U4, and U5 RNAs.
[3]
PubMed ID6737414
JournalJ Med Chem
Year1984
Volume27
Pages726-33
AuthorsTorrence PF, Imai J, Lesiak K, Jamoulle JC, Sawai H
TitleOligonucleotide 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.
[4]
PubMed ID2124675
JournalNucleic Acids Res
Year1990
Volume18
Pages7041-7
AuthorsHall KB, Sampson JR
TitleStructural investigation of the in vitro transcript of the yeast tRNA(phe) precursor by NMR and nuclease mapping.
[5]
PubMed ID7798182
JournalJ Biochem (Tokyo)
Year1994
Volume116
Pages26-33
AuthorsNomura H, Inokuchi N, Kobayashi H, Koyama T, Iwama M, Ohgi K, Irie M
TitlePurification and primary structure of a new guanylic acid specific ribonuclease from Pleurotus ostreatus.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), AND REVISIONS.
Medline ID96082150
PubMed ID7492561
JournalBiochemistry
Year1995
Volume34
Pages15583-91
AuthorsNoguchi S, Satow Y, Uchida T, Sasaki C, Matsuzaki T
TitleCrystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8 A resolution.
Related PDB1rtu
Related Swiss-protP00654
[7]
PubMed ID9586111
JournalNucleic Acids Symp Ser
Year1997
Volume
Pages285-6
AuthorsNoda N, Noguchi S, Satow Y
TitleCrystal structures of nucleic acid complexes of ribonuclease U2.
[8]
PubMed ID11733014
JournalEur J Biochem
Year2001
Volume268
Pages6190-6
AuthorsMasip M, Lacadena J, Mancheno JM, Onaderra M, Martinez-Ruiz A, Martinez del Pozo A, Gavilanes JG
TitleArginine 121 is a crucial residue for the specific cytotoxic activity of the ribotoxin alpha-sarcin.
[9]
PubMed ID11582789
JournalMethods Enzymol
Year2001
Volume341
Pages335-51
AuthorsMartinez-Ruiz A, Garcia-Ortega L, Kao R, Lacadena J, Onaderra M, Mancheno JM, Davies J, Martinez del Pozo A, Gavilanes JG
TitleRNase U2 and alpha-sarcin: a study of relationships.
[10]
PubMed ID11897788
JournalJ Biol Chem
Year2002
Volume277
Pages18632-9
AuthorsGarcia-Ortega L, Masip M, Mancheno JM, Onaderra M, Lizarbe MA, Garcia-Mayoral MF, Bruix M, Martinez del Pozo A, Gavilanes JG
TitleDeletion of the NH2-terminal beta-hairpin of the ribotoxin alpha-sarcin produces a nontoxic but active ribonuclease.

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.

createdupdated
2002-07-012010-02-04
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 2010)
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)

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