EzCatDB: S00751
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DB codeS00751
RLCP classification1.40.14550.574 : Hydrolysis
CATH domainDomain 13.90.245.10 : Inosine-uridine Nucleoside N-ribohydrolase; Chain ACatalytic domain
E.C.3.2.2.8

CATH domainRelated DB codes (homologues)
3.90.245.10 : Inosine-uridine Nucleoside N-ribohydrolase; Chain AS00910,S00461

Enzyme Name
UniProtKBKEGG

P33022
Protein namePyrimidine-specific ribonucleoside hydrolase rihBRibosylpyrimidine nucleosidase
N-ribosylpyrimidine nucleosidase
Pyrimidine nucleosidase
N-ribosylpyrimidine ribohydrolase
Pyrimidine nucleoside hydrolase
RihB
YeiK
Nucleoside ribohydrolase
SynonymsEC 3.2.2.8
Cytidine/uridine-specific hydrolase
RefSeqNP_416667.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490401.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF01156 (IU_nuc_hydro)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00240Pyrimidine metabolism

UniProtKB:Accession NumberP33022
Entry nameRIHB_ECOLI
Activity
SubunitHomotetramer.
Subcellular location
CofactorBinds 1 calcium ion per monomer.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00076C03169C00001C00121C00396
CompoundCalciumpyrimidine nucleosideH2OD-ribosepyrimidine base
Typedivalent metal (Ca2+, Mg2+)nucleosideH2Ocarbohydrateamide group,carboxyl group,sulfide group
ChEBI29108

15377
47013
16898
PubChem271
439920
962
22247451
5779
9260
             
1q8fA00Bound:_CAUnbound UnboundUnbound
1q8fB00Bound:_CAUnbound UnboundUnbound
1q8fC00Bound:_CAUnbound UnboundUnbound
1q8fD00Bound:_CAUnbound UnboundUnbound
3b9xA00Bound:_CAAnalogue:NOS UnboundUnbound
3b9xB00Bound:_CAAnalogue:NOS UnboundUnbound
3b9xC00Bound:_CAAnalogue:NOS UnboundUnbound
3b9xD00Bound:_CAAnalogue:NOS UnboundUnbound
3mkmA00Bound:_CAUnbound UnboundUnbound
3mkmB00Bound:_CAUnbound UnboundUnbound
3mkmC00Bound:_CAUnbound UnboundUnbound
3mkmD00Bound:_CAUnbound UnboundUnbound
3mknA00Bound:_CAAnalogue:DNB UnboundUnbound
3mknB00Bound:_CAAnalogue:DNB UnboundUnbound
3mknC00Bound:_CAAnalogue:DNB UnboundUnbound
3mknD00Bound:_CAAnalogue:DNB UnboundUnbound

Active-site residues
resource
Literature [4], [5]
pdbCatalytic residuesCofactor-binding residuescomment
           
1q8fA00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
1q8fB00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
1q8fC00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
1q8fD00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
3b9xA00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
3b9xB00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
3b9xC00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
3b9xD00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
3mkmA00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
3mkmB00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
3mkmC00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
3mkmD00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
3mknA00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 
3mknB00ASP 11;      ;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
invisible 79-85
3mknC00ASP 11;      ;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
invisible 79-83
3mknD00ASP 11;HIS 82;HIS 239
ASP 11;ASP 16;VAL 124;ASP 240(Calcium binding)
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.744-746
[5]FIGURE 4

references
[1]
PubMed ID8634237
JournalBiochemistry
Year1996
Volume35
Pages5963-70
AuthorsGopaul DN, Meyer SL, Degano M, Sacchettini JC, Schramm VL
TitleInosine-uridine nucleoside hydrolase from Crithidia fasciculata. Genetic characterization, crystallization, and identification of histidine 241 as a catalytic site residue.
[2]
PubMed ID8634238
JournalBiochemistry
Year1996
Volume35
Pages5971-81
AuthorsDegano M, Gopaul DN, Scapin G, Schramm VL, Sacchettini JC
TitleThree-dimensional structure of the inosine-uridine nucleoside N-ribohydrolase from Crithidia fasciculata.
Related PDB1mas,2mas
Related UniProtKBQ27546
[3]
PubMed ID12465969
JournalJ Am Chem Soc
Year2002
Volume124
Pages14591-600
AuthorsMazumder D, Bruice TC
TitleExploring nucleoside hydrolase catalysis in silico: molecular dynamics study of enzyme-bound substrate and transition state.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH CALCIUM IONS, MUTAGENESIS OF HIS-82 AND HIS-239, SUBUNIT.
PubMed ID15130467
JournalStructure
Year2004
Volume12
Pages739-49
AuthorsGiabbai B, Degano M
TitleCrystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy.
Related PDB1q8f
Related UniProtKBP33022
[5]
PubMed ID18361502
JournalBiochemistry
Year2008
Volume47
Pages4418-26
AuthorsIovane E, Giabbai B, Muzzolini L, Matafora V, Fornili A, Minici C, Giannese F, Degano M
TitleStructural basis for substrate specificity in group I nucleoside hydrolases.
Related PDB3b9x
Related UniProtKBP33022
[6]
PubMed ID21082835
JournalJ Am Chem Soc
Year2010
Volume132
Pages17570?7
AuthorsFornili A, Giabbai B, Garau G, Degano M
TitleEnergy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures.
Related PDB3mkm,3mkn

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.

createdupdated
2010-10-072011-09-22


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