EzCatDB: S00467

DB codeS00467
RLCP classification1.15.60000.82
CATH domainDomain 13.90.730.10Catalytic domain
E.C.3.1.27.1
CSA1bol


Enzyme Name
Swiss-protKEGG

P08056P23540P80022Q9SSV1
Protein nameRibonuclease RhRibonuclease MCExtracellular ribonuclease LE
ribonuclease T2
ribonuclease II
base-non-specific ribonuclease
nonbase-specific RNase
RNase (non-base specific)
non-base specific ribonuclease
nonspecific RNase
RNase Ms
RNase M
RNase II
Escherichia coli ribonuclease II
ribonucleate nucleotido-2'-transferase (cyclizing)
acid ribonuclease
RNAase CL
Escherichia coli ribonuclease I' ribonuclease PP2
ribonuclease N2
ribonuclease M
acid RNase
ribonnuclease (non-base specific)
ribonuclease (non-base specific)
RNase T2
ribonuclease PP3
ribonucleate 3'-oligonucleotide hydrolase
RNase II
ribonuclease U4
SynonymsRNase Rh
EC 3.1.27.1
RNase MC
EC 3.1.27.1
RNase LE
EC 3.1.27.1
RNase NGR3 (Ribonuclease NGR3)


Swiss-prot:Accession NumberP08056P23540P80022Q9SSV1
Entry nameRNRH_RHINIRNMC_MOMCHRNLE_SOLLCQ9SSV1_NICGU
ActivityTwo-stage endonucleolytic cleavage to nucleoside 3''-phosphates and 3''-phosphooligonucleotides with 2'',3''-cyclic phosphate intermediates.Two-stage endonucleolytic cleavage to nucleoside 3''-phosphates and 3''-phosphooligonucleotides with 2'',3''-cyclic phosphate intermediates.Two-stage endonucleolytic cleavage to nucleoside 3''-phosphates and 3''-phosphooligonucleotides with 2'',3''-cyclic phosphate intermediates.
Subunit



Subcellular location

Secreted, extracellular space. Secreted, cell wall.
Cofactor





SubstratesProductsintermediates
KEGG-idC00046C00001C00172C03419C01199
CompoundRNAH2O3'-PhosphooligonucleotideNucleoside 3'-phosphate5'-Hydroxyoligonucleotide2',3'-cyclic phosphate mononucleotide
Typenucleic acidsH2Onucleic acidsnucleotidenucleic acids
1bolAUnbound
UnboundUnboundUnboundUnbound
1bk7AUnbound
UnboundUnboundUnboundUnbound
1j1fAAnalogue:5GP
UnboundUnboundUnboundUnbound
1j1gAAnalogue:5GP 295
UnboundUnboundUnboundUnbound
1ucaAUnbound
UnboundUnboundUnboundUnbound
1uccAUnbound
UnboundUnboundUnboundUnbound
1ucdAAnalogue:U5P
UnboundUnboundUnboundUnbound
1ucgAUnbound
UnboundUnboundUnboundUnbound
1ucgBUnbound
UnboundUnboundUnboundUnbound
1v9hAAnalogue:U5P
UnboundUnboundUnboundUnbound
1dixAUnbound
UnboundUnboundUnboundUnbound
1vczAAnalogue:5GP 295-5GP 296
UnboundUnboundUnboundUnbound
1vd1AUnbound
UnboundUnboundUnboundUnbound
1vd3AUnbound
UnboundUnboundUnboundAnalogue:U2P

Active-site residues
pdbCatalytic residues
1bolAHIS  46;HIS 104;GLU 105;LYS 108;HIS 109
1bk7AHIS  34;HIS  83;GLU  84;LYS  87;HIS  88
1j1fAHIS  34;HIS  83;GLU  84;LYS  87;HIS  88
1j1gAHIS  34;HIS  83;GLU  84;LYS  87;HIS  88
1ucaAHIS  34;HIS  83;GLU  84;LYS  87;HIS  88
1uccAHIS  34;HIS  83;GLU  84;LYS  87;HIS  88
1ucdAHIS  34;HIS  83;GLU  84;LYS  87;HIS  88
1ucgAHIS  34;HIS  83;GLU  84;LYS  87;HIS  88
1ucgBHIS  34;HIS  83;GLU  84;LYS  87;HIS  88
1v9hAHIS  34;HIS  83;GLU  84;LYS  87;HIS  88
1dixAHIS  39;HIS  92;GLU  93;LYS  96;HIS  97
1vczAHIS  39;HIS  92;GLU  93;LYS  96;HIS  97
1vd1AHIS  39;HIS  92;GLU  93;LYS  96;HIS  97
1vd3AHIS  39;HIS  92;GLU  93;LYS  96;HIS  97

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.317
[4]p.122, Fig.3, Fig.72
[6]p.863-866
[8]


references
[1]
CommentsX-ray crystallography (2.5 Angstroms)
Medline ID92339548
PubMed ID1633875
JournalFEBS Lett
Year1992
Volume306
Pages189-92
AuthorsKurihara H, Mitsui Y, Ohgi K, Irie M, Mizuno H, Nakamura KT
TitleCrystal and molecular structure of RNase Rh, a new class of microbial ribonuclease from Rhizopus niveus.
Related Swiss-protP08056
[2]
PubMed ID8218254
JournalBiochemistry
Year1993
Volume32
Pages11825-37
AuthorsNonaka T, Nakamura KT, Uesugi S, Ikehara M, Irie M, Mitsui Y
TitleCrystal structure of ribonuclease Ms (as a ribonuclease T1 homologue) complexed with a guanylyl-3',5'-cytidine analogue.
[3]
CommentsX-ray crystallography (2.0 Angstroms)
PubMed ID8551522
JournalJ Mol Biol
Year1996
Volume255
Pages310-20
AuthorsKurihara H, Nonaka T, Mitsui Y, Ohgi K, Irie M, Nakamura KT
TitleThe crystal structure of ribonuclease Rh from Rhizopus niveus at 2.0 A resolution.
Related PDB1bol
[4]
JournalIn "Ribonucleases: Structures and Functions"
Year1997
Volume(Academic Press, New York)
Pages101-130
AuthorsIrie M. (D'Alessio G, Riordan J.)
TitleRNase T1/RNase T2 family RNases.
[5]
CommentsX-ray crystallography (1.75 Angstroms)
PubMed ID10446375
JournalBiochim Biophys Acta
Year1999
Volume1433
Pages253-60
AuthorsNakagawa A, Tanaka I, Sakai R, Nakashima T, Funatsu G, Kimura M
TitleCrystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution.
Related PDB1bk7
[6]
CommentsX-ray crystallography (1.65 Angstroms)
PubMed ID10801354
JournalJ Mol Biol
Year2000
Volume298
Pages859-73
AuthorsTanaka N, Arai J, Inokuchi N, Koyama T, Ohgi K, Irie M, Nakamura KT
TitleCrystal structure of a plant ribonuclease, RNase LE.
Related PDB1dix
[7]
PubMed ID10964705
JournalBiochem Biophys Res Commun
Year2000
Volume275
Pages572-6
AuthorsSuzuki A, Yao M, Tanaka I, Numata T, Kikukawa S, Yamasaki N, Kimura M
TitleCrystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity.
Related PDB1uca,1ucc
[8]
PubMed ID11577107
JournalJ Biol Chem
Year2001
Volume276
Pages45261-9
AuthorsMatsuura T, Sakai H, Unno M, Ida K, Sato M, Sakiyama F, Norioka S
TitleCrystal structure at 1.5-A resolution of Pyrus pyrifolia pistil ribonuclease responsible for gametophytic self-incompatibility.
Related PDB1iqq
[9]
PubMed ID12731868
JournalBiochemistry
Year2003
Volume42
Pages5270-8
AuthorsNumata T, Suzuki A, Kakuta Y, Kimura K, Yao M, Tanaka I, Yoshida Y, Ueda T, Kimura M
TitleCrystal structures of the ribonuclease MC1 mutants N71T and N71S in complex with 5'-GMP: structural basis for alterations in substrate specificity.
Related PDB1j1f,1j1g,1ucg
[10]
PubMed ID15322360
JournalBiosci Biotechnol Biochem
Year2004
Volume68
Pages1748-57
AuthorsKimura K, Numata T, Kakuta Y, Kimura M
TitleAmino acids conserved at the C-terminal half of the ribonuclease T2 family contribute to protein stability of the enzymes.
Related PDB1v9h

comments
Accoriding to the literature [3], reaction mechanism is described as follows:
His109 (1bol) accepts the proton form the 2'-OH group of the substrate in the first reaction step, whereas His46 is supposed to act as a general acid in the first step.
Glu105 (1bol) seems to play a more important role than just adjusting the pKa value of the neighboring histidine residues [3]. The paper [6] suggests the corresponding glutamic acid is catalytically crucial and probably polarize the P=O bond or stabilize a pentacovalent intermediate together with the catalytic histidine residues. Since the pentacovalent intermediate should carry excess negative charge, it is reasonable to say that the non-ionized glutamic acid residue is appropriate for enhancing the catalysis.
Moreover, according to the literature [4], [6] & [8], His104, Lys108 and protonated form of Glu105 stabilizes the pentacovalent intermediate in the transition state.
Taken together, the catalytic reaction proceeds as follows:
(1) His109 acts as a general base to activate 2'-OH of RNA substrate.
(2) The activated 2'-hydroxyl oxygen makes a nucleophilic attack on the phosphoryl atom of the phosphodiester group, leading to pentacovalent transition state. The transition state must be stabilized by His104, Glu105 and Lys108.
(3) The reaction leads to formation of 2',3'-cyclic nucleotide, and leaving 5'-OH group of the next nucleotide. Here, His46 acts as a general acid to protonate the leaving 5'-hydroxyl oxygen.
(4) Probably His46 now acts as a general base to activate a water, which will complete the hydrolysis, along with the stabilizers (His104, Glu105 and Lys108). Meanwhile, His109 acts as a general acid to protonate the leaving 2'-oxygen atom.

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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