DB code: S00751

RLCP classification 1.40.14550.574 : Hydrolysis
CATH domain 3.90.245.10 : Inosine-uridine Nucleoside N-ribohydrolase; Chain A Catalytic domain
E.C. 3.2.2.8
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.90.245.10 : Inosine-uridine Nucleoside N-ribohydrolase; Chain A S00910 S00461

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P33022 Pyrimidine-specific ribonucleoside hydrolase RihB
EC 3.2.2.8
Cytidine/uridine-specific hydrolase
NP_416667.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490401.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01156 (IU_nuc_hydro)
[Graphical View]

KEGG enzyme name
Ribosylpyrimidine nucleosidase
N-ribosylpyrimidine nucleosidase
Pyrimidine nucleosidase
N-ribosylpyrimidine ribohydrolase
Pyrimidine nucleoside hydrolase
RihB
YeiK
Nucleoside ribohydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P33022 RIHB_ECOLI Homotetramer. Binds 1 calcium ion per monomer.

KEGG Pathways
Map code Pathways E.C.
MAP00240 Pyrimidine metabolism
MAP00230 Purine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00076 C03169 C00001 C00121 C00396
E.C.
Compound Calcium pyrimidine nucleoside H2O D-ribose pyrimidine base
Type divalent metal (Ca2+, Mg2+) nucleoside H2O carbohydrate amide group,carboxyl group,sulfide group
ChEBI 29108
15377
47013
16898
PubChem 271
439920
22247451
962
5779
9260
1q8fA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound
1q8fB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound
1q8fC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound
1q8fD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound
3b9xA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Analogue:NOS Unbound Unbound
3b9xB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Analogue:NOS Unbound Unbound
3b9xC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Analogue:NOS Unbound Unbound
3b9xD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Analogue:NOS Unbound Unbound
3mkmA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound
3mkmB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound
3mkmC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound
3mkmD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Unbound Unbound
3mknA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Analogue:DNB Unbound Unbound
3mknB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Analogue:DNB Unbound Unbound
3mknC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Analogue:DNB Unbound Unbound
3mknD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Analogue:DNB Unbound Unbound

Reference for Active-site residues
resource references E.C.
Literature [4], [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1q8fA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
1q8fB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
1q8fC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
1q8fD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
3b9xA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
3b9xB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
3b9xC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
3b9xD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
3mkmA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
3mkmB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
3mkmC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
3mkmD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
3mknA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
3mknB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11; ;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding) invisible 79-85
3mknC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11; ;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding) invisible 79-83
3mknD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11;HIS 82;HIS 239 ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.744-746
[5]
FIGURE 4

References
[1]
Resource
Comments
Medline ID
PubMed ID 8634237
Journal Biochemistry
Year 1996
Volume 35
Pages 5963-70
Authors Gopaul DN, Meyer SL, Degano M, Sacchettini JC, Schramm VL
Title Inosine-uridine nucleoside hydrolase from Crithidia fasciculata. Genetic characterization, crystallization, and identification of histidine 241 as a catalytic site residue.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8634238
Journal Biochemistry
Year 1996
Volume 35
Pages 5971-81
Authors Degano M, Gopaul DN, Scapin G, Schramm VL, Sacchettini JC
Title Three-dimensional structure of the inosine-uridine nucleoside N-ribohydrolase from Crithidia fasciculata.
Related PDB 1mas 2mas
Related UniProtKB Q27546
[3]
Resource
Comments
Medline ID
PubMed ID 12465969
Journal J Am Chem Soc
Year 2002
Volume 124
Pages 14591-600
Authors Mazumder D, Bruice TC
Title Exploring nucleoside hydrolase catalysis in silico: molecular dynamics study of enzyme-bound substrate and transition state.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH CALCIUM IONS, MUTAGENESIS OF HIS-82 AND HIS-239, SUBUNIT.
Medline ID
PubMed ID 15130467
Journal Structure
Year 2004
Volume 12
Pages 739-49
Authors Giabbai B, Degano M
Title Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy.
Related PDB 1q8f
Related UniProtKB P33022
[5]
Resource
Comments
Medline ID
PubMed ID 18361502
Journal Biochemistry
Year 2008
Volume 47
Pages 4418-26
Authors Iovane E, Giabbai B, Muzzolini L, Matafora V, Fornili A, Minici C, Giannese F, Degano M
Title Structural basis for substrate specificity in group I nucleoside hydrolases.
Related PDB 3b9x
Related UniProtKB P33022
[6]
Resource
Comments
Medline ID
PubMed ID 21082835
Journal J Am Chem Soc
Year 2010
Volume 132
Pages 17570?7
Authors Fornili A, Giabbai B, Garau G, Degano M
Title Energy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures.
Related PDB 3mkm 3mkn
Related UniProtKB

Comments
This enzyme is homologous to purine nucleosidase (EC 3.2.2.-; S00461 in EzCatDB).
According to the literature [4] and [5], this enzyme catalyzes the following reaction:
(1) The distortion of the ribosyl group of nucleoside leads to an oxonium ion, which produces a partial positive charge at the ribosyl group.
(2) The negative charge must develop at the leaving group, the nitrogenous base. The negative charge must be stabilized or protonated by His239. Thus, His239 may act as a general acid, leading to cleavage of the N-glycosidic bond. This step suggests SN1-like reaction.
(3) Asp11, which is bound to the calcium ion, acts as a general base to deprotonate a water molecule, which is also bound to the calcium ion, for the activation of the water.
(4) The activated water makes a nucleophilic attack on the C1 atom of the ribosyl group, completing the reaction.

Created Updated
2010-10-07 2011-09-22