DB code: S00910

CATH domain 3.90.245.10 : Inosine-uridine Nucleoside N-ribohydrolase; Chain A Catalytic domain
E.C. 3.2.2.1
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.90.245.10 : Inosine-uridine Nucleoside N-ribohydrolase; Chain A S00751 S00461

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q57X73
Nucleoside hydrolase, putative
EC 3.2.2.1
XP_846080.1 (Protein)
XM_840987.1 (DNA/RNA sequence)
PF01156 (IU_nuc_hydro)
[Graphical View]

KEGG enzyme name
purine nucleosidase
nucleosidase
purine beta-ribosidase
purine nucleoside hydrolase
purine ribonucleosidase
ribonucleoside hydrolase
nucleoside hydrolase
N-ribosyl purine ribohydrolase
nucleosidase g
N-D-ribosylpurine ribohydrolase
inosine-adenosine-guanosine preferring nucleoside hydrolase
purine-specific nucleoside N-ribohydrolase
IAG-nucleoside hydrolase
IAG-NH

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q57X73 Q57X73_9TRYP

KEGG Pathways
Map code Pathways E.C.
MAP00760 Nicotinate and nicotinamide metabolism
MAP00230 Purine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00076 C15586 C00001 C00121 C15587
E.C.
Compound Calcium N-D-Ribosylpurine H2O D-ribose Purine
Type divalent metal (Ca2+, Mg2+) nucleoside H2O carbohydrate aromatic ring (with nitrogen atoms)
ChEBI 29108
18255
15377
47013
17258
35586
35588
35589
PubChem 271
68368
22247451
962
5779
1044
3fz0A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Analogue:BTB Unbound
3fz0B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Analogue:BTB Unbound
3fz0C00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Analogue:BTB Unbound
3fz0D00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CA Unbound Analogue:BTB 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
3fz0A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11 ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)
3fz0B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11 ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)
3fz0C00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11 ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)
3fz0D00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 11 ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.744-746
[5]
Fig.4
[7]

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
[7]
Resource
Comments
Medline ID
PubMed ID 20825170
Journal Biochemistry
Year 2010
Volume 49
Pages 8999-9010
Authors Vandemeulebroucke A, Minici C, Bruno I, Muzzolini L, Tornaghi P, Parkin DW, Versees W, Steyaert J, Degano M
Title Structure and mechanism of the 6-oxopurine nucleosidase from Trypanosoma brucei brucei.
Related PDB 3fz0
Related UniProtKB

Comments
This enzyme is homologous to purine nucleosidase (EC 3.2.2.-; S00461 in EzCatDB) and ribosylpyrimidine nucleosidase (EC 3.2.2.8; S00751 in EzCatDB). Altough this enzyme share some active-site residues with those homologous enzymes, it lacks catalytic histidine residues, which could act as a general acid to protonate the leaving group, purine (inosine or guanosine) (see [7]).
Therefore, the reaction mechanism will have to be elucidated.

Created Updated
2010-10-07 2011-09-27