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.
MAP00230 Purine metabolism
MAP00760 Nicotinate and nicotinamide 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
 29108
 		18255
 18255
 		15377
 15377
 		47013
 47013
 		17258
 35586
 35588
 35589
 17258
 35586
 35588
 35589
PubChem 271
 271
 		68368
 68368
 		22247451
 962
 22247451
 962
 		5779
 5779
 		1044
 1044
3fz0A00 Bound:_CA Unbound Analogue:BTB Unbound
3fz0B00 Bound:_CA Unbound Analogue:BTB Unbound
3fz0C00 Bound:_CA Unbound Analogue:BTB Unbound
3fz0D00 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 ASP 11 ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)
3fz0B00 ASP 11 ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)
3fz0C00 ASP 11 ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)
3fz0D00 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