EzCatDB: S00910
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DB codeS00910
CATH domainDomain 13.90.245.10 : Inosine-uridine Nucleoside N-ribohydrolase; Chain ACatalytic domain
E.C.3.2.2.1

CATH domainRelated DB codes (homologues)
3.90.245.10 : Inosine-uridine Nucleoside N-ribohydrolase; Chain AS00751,S00461

Enzyme Name
UniProtKBKEGG

Q57X73
Protein 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
SynonymsNucleoside hydrolase, putative
EC 3.2.2.1
RefSeqXP_846080.1 (Protein)
XM_840987.1 (DNA/RNA sequence)
PfamPF01156 (IU_nuc_hydro)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00760Nicotinate and nicotinamide metabolism

UniProtKB:Accession NumberQ57X73
Entry nameQ57X73_9TRYP
Activity
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00076C15586C00001C00121C15587
CompoundCalciumN-D-RibosylpurineH2OD-ribosePurine
Typedivalent metal (Ca2+, Mg2+)nucleosideH2Ocarbohydratearomatic ring (with nitrogen atoms)
ChEBI29108
18255
15377
47013
35589
35588
35586
17258
PubChem271
68368
962
22247451
5779
1044
             
3fz0A00Bound:_CAUnbound Analogue:BTBUnbound
3fz0B00Bound:_CAUnbound Analogue:BTBUnbound
3fz0C00Bound:_CAUnbound Analogue:BTBUnbound
3fz0D00Bound:_CAUnbound Analogue:BTBUnbound

Active-site residues
resource
Literature [4], [5]
pdbCatalytic residuesCofactor-binding residues
          
3fz0A00ASP 11
ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)
3fz0B00ASP 11
ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)
3fz0C00ASP 11
ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)
3fz0D00ASP 11
ASP 11;ASP 16;LEU 131;ASP 280(Calcium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.744-746
[5]Fig.4
[7]


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
[7]
PubMed ID20825170
JournalBiochemistry
Year2010
Volume49
Pages8999-9010
AuthorsVandemeulebroucke A, Minici C, Bruno I, Muzzolini L, Tornaghi P, Parkin DW, Versees W, Steyaert J, Degano M
TitleStructure and mechanism of the 6-oxopurine nucleosidase from Trypanosoma brucei brucei.
Related PDB3fz0

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.

createdupdated
2010-10-072011-09-27


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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