EzCatDB: S00377

DB codeS00377
RLCP classification3.944.290000.2
CATH domainDomain 13.40.50.1810Catalytic domain
E.C.2.4.2.6
CSA1f8x


Enzyme Name
Swiss-protKEGG

Q9R5V5
Protein nameNucleoside deoxyribosyltransferasenucleoside deoxyribosyltransferase
purine(pyrimidine) nucleoside:purine(pyrimidine) deoxyribosyltransferase
deoxyribose transferase
nucleoside trans-N-deoxyribosylase
trans-deoxyribosylase
trans-N-deoxyribosylase
trans-N-glycosidase
nucleoside deoxyribosyltransferase I (purine nucleoside:purinedeoxyribosyltransferase: strictly specific for transfer betweenpurine bases)
nucleoside deoxyribosyltransferase II [purine(pyrimidine)nucleoside:purine(pyrimidine) deoxyribosyltransferase]
SynonymsN-deoxyribosyltransferase
EC 2.4.2.6

KEGG pathways
MAP codePathways
MAP00240Pyrimidine metabolism

Swiss-prot:Accession NumberQ9R5V5
Entry nameNTD_LACLE
Activity2-deoxy-D-ribosyl-base(1) + base(2) = 2-deoxy- D-ribosyl-base(2) + base(1).
SubunitHomohexamer.
Subcellular location
Cofactor


SubstratesProducts
KEGG-idC03216C00701C00559C00330C00881C00214C00147C00242C00380C00178C03216C00701C00559C00330C00881C00214C00147C00242C00380C00178
Compound2-Deoxy-D-ribosyl-base1Base2DeoxyadenosineDeoxyguanosineDeoxycytidineDeoxythymidineAdenineGuanineCytosineThymine2-Deoxy-D-ribosyl-base2Base1DeoxyadenosineDeoxyguanosineDeoxycytidineDeoxythymidineAdenineGuanineCytosineThymine
Typenucleosidearomatic ring (with nitrogen atoms)amine group,nucleosideamide group,amine group,nucleosideamine group,nucleosideamide group,nucleosideamine group,aromatic ring (with nitrogen atoms)amide group,amine group,aromatic ring (with nitrogen atoms)amide group,amine group,aromatic ring (with nitrogen atoms)amide group,aromatic ring (with nitrogen atoms)nucleosidearomatic ring (with nitrogen atoms)amine group,nucleosideamide group,amine group,nucleosideamine group,nucleosideamide group,nucleosideamine group,aromatic ring (with nitrogen atoms)amide group,amine group,aromatic ring (with nitrogen atoms)amide group,amine group,aromatic ring (with nitrogen atoms)amine group,aromatic ring (with nitrogen atoms)
1f8xAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1f8xBUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1f8yAUnboundUnboundUnboundUnboundUnboundAnalogue:5MDUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1f8yBUnboundUnboundUnboundUnboundUnboundAnalogue:5MDUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
pdbCatalytic residues
1f8xAASP  72;GLU  98
1f8xBASP 272;GLU 298
1f8yAASP  72;GLU  98
1f8yBASP 272;GLU 298

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Scheme IV
[3]p.4986
[4]p.102-104

references
[1]
PubMed ID7797550
JournalJ Biol Chem
Year1995
Volume270
Pages15551-6
AuthorsPorter DJ, Merrill BM, Short SA
TitleIdentification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98.
[2]
PubMed ID7797551
JournalJ Biol Chem
Year1995
Volume270
Pages15557-62
AuthorsPorter DJ, Short SA
TitleNucleoside 2-deoxyribosyltransferase. Pre-steady-state kinetic analysis of native enzyme and mutant enzyme with an alanyl residue replacing Glu-98.
[3]
PubMed ID8617773
JournalJ Biol Chem
Year1996
Volume271
Pages4978-87
AuthorsShort SA, Armstrong SR, Ealick SE, Porter DJ
TitleActive site amino acids that participate in the catalytic mechanism of nucleoside 2'-deoxyribosyltransferase.
[4]
PubMed ID8805514
JournalStructure
Year1996
Volume4
Pages97-107
AuthorsArmstrong SR, Cook WJ, Short SA, Ealick SE
TitleCrystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.
Related PDB1f8x,1f8y

comments
This enzyme catalyzes the cleavage of the exchange of nucleobase from a 2'-deoxyribosylnucleoside with free purine or pyrimidine.
According to the literature [4], Asp72, whose sidechain carboxylate could be protonated, may stabilize the oxocarbonium transition state of deoxyribosyl moiety.
Glu98 acts as a nucleophile that will make attack on the C1' atom of the transferred deoxyribosyl group, to form a covalent enzyme-substrate complex. In the course of catalysis, Asp72 may act as a general acid, which protonates the leaving nucleobase group. In the next step, this enzyme might place the free base in the proper position to accept the deoxyribose.

createdupdated
2002-07-112009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
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 2010)
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)

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