DB code: S00467

RLCP classification 1.15.60000.82 : Hydrolysis
CATH domain 3.90.730.10 : Ribonuclease Rh; Chain A Catalytic domain
E.C. 3.1.27.1
CSA 1bol
M-CSA 1bol
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam RefSeq
P08056 Ribonuclease Rh
RNase Rh
EC 3.1.27.1
PF00445 (Ribonuclease_T2)
[Graphical View]
P23540 Ribonuclease MC
RNase MC
EC 3.1.27.1
PF00445 (Ribonuclease_T2)
[Graphical View]
P80022 Extracellular ribonuclease LE
RNase LE
EC 3.1.27.1
PF00445 (Ribonuclease_T2)
[Graphical View]
NP_001234195.1 (Protein)
NM_001247266.1 (DNA/RNA sequence)
Q9SSV1
RNase NGR3 (Ribonuclease NGR3)
PF00445 (Ribonuclease_T2)
[Graphical View]

KEGG enzyme name
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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P08056 RNRH_RHINI Two-stage endonucleolytic cleavage to nucleoside 3''-phosphates and 3''-phosphooligonucleotides with 2'',3''-cyclic phosphate intermediates.
P23540 RNMC_MOMCH Two-stage endonucleolytic cleavage to nucleoside 3''-phosphates and 3''-phosphooligonucleotides with 2'',3''-cyclic phosphate intermediates.
P80022 RNLE_SOLLC Two-stage endonucleolytic cleavage to nucleoside 3''-phosphates and 3''-phosphooligonucleotides with 2'',3''-cyclic phosphate intermediates. Secreted, extracellular space. Secreted, cell wall.
Q9SSV1 Q9SSV1_NICGU

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00046 C00001 C00172 C03419 C01199
E.C.
Compound RNA H2O 3'-Phosphooligonucleotide Nucleoside 3'-phosphate 5'-Hydroxyoligonucleotide 2',3'-cyclic phosphate mononucleotide
Type nucleic acids H2O nucleic acids nucleotide nucleic acids
ChEBI 15377
PubChem 22247451
962
1bolA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1bk7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1j1fA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:5GP Unbound Unbound Unbound Unbound
1j1gA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:5GP_295 Unbound Unbound Unbound Unbound
1ucaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1uccA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ucdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:U5P Unbound Unbound Unbound Unbound
1ucgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ucgB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1v9hA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:U5P Unbound Unbound Unbound Unbound
1dixA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1vczA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:5GP_295-5GP_296 Unbound Unbound Unbound Unbound
1vd1A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1vd3A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:U2P

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
1bolA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 46;HIS 104;GLU 105;LYS 108;HIS 109
1bk7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 34;HIS 83;GLU 84;LYS 87;HIS 88
1j1fA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 34;HIS 83;GLU 84;LYS 87;HIS 88
1j1gA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 34;HIS 83;GLU 84;LYS 87;HIS 88
1ucaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 34;HIS 83;GLU 84;LYS 87;HIS 88
1uccA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 34;HIS 83;GLU 84;LYS 87;HIS 88
1ucdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 34;HIS 83;GLU 84;LYS 87;HIS 88
1ucgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 34;HIS 83;GLU 84;LYS 87;HIS 88
1ucgB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 34;HIS 83;GLU 84;LYS 87;HIS 88
1v9hA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 34;HIS 83;GLU 84;LYS 87;HIS 88
1dixA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 39;HIS 92;GLU 93;LYS 96;HIS 97
1vczA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 39;HIS 92;GLU 93;LYS 96;HIS 97
1vd1A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 39;HIS 92;GLU 93;LYS 96;HIS 97
1vd3A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 39;HIS 92;GLU 93;LYS 96;HIS 97

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.317
[4]
p.122, Fig.3, Fig.7 2
[6]
p.863-866
[8]

References
[1]
Resource
Comments X-ray crystallography (2.5 Angstroms)
Medline ID 92339548
PubMed ID 1633875
Journal FEBS Lett
Year 1992
Volume 306
Pages 189-92
Authors Kurihara H, Mitsui Y, Ohgi K, Irie M, Mizuno H, Nakamura KT
Title Crystal and molecular structure of RNase Rh, a new class of microbial ribonuclease from Rhizopus niveus.
Related PDB
Related UniProtKB P08056
[2]
Resource
Comments
Medline ID
PubMed ID 8218254
Journal Biochemistry
Year 1993
Volume 32
Pages 11825-37
Authors Nonaka T, Nakamura KT, Uesugi S, Ikehara M, Irie M, Mitsui Y
Title Crystal structure of ribonuclease Ms (as a ribonuclease T1 homologue) complexed with a guanylyl-3',5'-cytidine analogue.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-ray crystallography (2.0 Angstroms)
Medline ID
PubMed ID 8551522
Journal J Mol Biol
Year 1996
Volume 255
Pages 310-20
Authors Kurihara H, Nonaka T, Mitsui Y, Ohgi K, Irie M, Nakamura KT
Title The crystal structure of ribonuclease Rh from Rhizopus niveus at 2.0 A resolution.
Related PDB 1bol
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID
Journal In "Ribonucleases: Structures and Functions"
Year 1997
Volume (Academic Press, New York)
Pages 101-130
Authors Irie M. (D'Alessio G, Riordan J.)
Title RNase T1/RNase T2 family RNases.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-ray crystallography (1.75 Angstroms)
Medline ID
PubMed ID 10446375
Journal Biochim Biophys Acta
Year 1999
Volume 1433
Pages 253-60
Authors Nakagawa A, Tanaka I, Sakai R, Nakashima T, Funatsu G, Kimura M
Title Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution.
Related PDB 1bk7
Related UniProtKB
[6]
Resource
Comments X-ray crystallography (1.65 Angstroms)
Medline ID
PubMed ID 10801354
Journal J Mol Biol
Year 2000
Volume 298
Pages 859-73
Authors Tanaka N, Arai J, Inokuchi N, Koyama T, Ohgi K, Irie M, Nakamura KT
Title Crystal structure of a plant ribonuclease, RNase LE.
Related PDB 1dix
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 10964705
Journal Biochem Biophys Res Commun
Year 2000
Volume 275
Pages 572-6
Authors Suzuki A, Yao M, Tanaka I, Numata T, Kikukawa S, Yamasaki N, Kimura M
Title Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity.
Related PDB 1uca 1ucc
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11577107
Journal J Biol Chem
Year 2001
Volume 276
Pages 45261-9
Authors Matsuura T, Sakai H, Unno M, Ida K, Sato M, Sakiyama F, Norioka S
Title Crystal structure at 1.5-A resolution of Pyrus pyrifolia pistil ribonuclease responsible for gametophytic self-incompatibility.
Related PDB 1iqq
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 12731868
Journal Biochemistry
Year 2003
Volume 42
Pages 5270-8
Authors Numata T, Suzuki A, Kakuta Y, Kimura K, Yao M, Tanaka I, Yoshida Y, Ueda T, Kimura M
Title Crystal structures of the ribonuclease MC1 mutants N71T and N71S in complex with 5'-GMP: structural basis for alterations in substrate specificity.
Related PDB 1j1f 1j1g 1ucg
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 15322360
Journal Biosci Biotechnol Biochem
Year 2004
Volume 68
Pages 1748-57
Authors Kimura K, Numata T, Kakuta Y, Kimura M
Title Amino acids conserved at the C-terminal half of the ribonuclease T2 family contribute to protein stability of the enzymes.
Related PDB 1v9h
Related UniProtKB

Comments
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.
Accoriding to the literature [3], reaction mechanism is described as follows:
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.

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