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 15377
PubChem		22247451 962 22247451 962

1rtuA	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	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.

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