DB code: S00377

RLCP classification 3.944.290000.2 : Transfer
CATH domain 3.40.50.1810 : Rossmann fold Catalytic domain
E.C. 2.4.2.6
CSA 1f8x
M-CSA 1f8x
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
Q9R5V5 Nucleoside deoxyribosyltransferase
N-deoxyribosyltransferase
EC 2.4.2.6
PF05014 (Nuc_deoxyrib_tr)
[Graphical View]

KEGG enzyme name
nucleoside 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]

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q9R5V5 NTD_LACLE 2-deoxy-D-ribosyl-base(1) + base(2) = 2-deoxy- D-ribosyl-base(2) + base(1). Homohexamer.

KEGG Pathways
Map code Pathways E.C.
MAP00240 Pyrimidine metabolism

Compound table
Substrates Products Intermediates
KEGG-id C03216 C00701 C00559 C00330 C00881 C00214 C00147 C00242 C00380 C00178 C03216 C00701 C00559 C00330 C00881 C00214 C00147 C00242 C00380 C00178
E.C.
Compound 2-Deoxy-D-ribosyl-base1 Base2 Deoxyadenosine Deoxyguanosine Deoxycytidine Deoxythymidine Adenine Guanine Cytosine Thymine 2-Deoxy-D-ribosyl-base2 Base1 Deoxyadenosine Deoxyguanosine Deoxycytidine Deoxythymidine Adenine Guanine Cytosine Thymine
Type nucleoside aromatic ring (with nitrogen atoms) amine group,nucleoside amide group,amine group,nucleoside amine group,nucleoside amide group,nucleoside amine 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) nucleoside aromatic ring (with nitrogen atoms) amine group,nucleoside amide group,amine group,nucleoside amine group,nucleoside amide group,nucleoside amine 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)
ChEBI 17256
 17256
 		17172
 17172
 		15698
 15698
 		17748
 17748
 		16708
 16708
 		16235
 16235
 		16040
 16040
 		17821
 17821
 		17256
 17256
 		17172
 17172
 		15698
 15698
 		17748
 17748
 		16708
 16708
 		16235
 16235
 		16040
 16040
 		17821
 17821
PubChem 13730
 13730
 		187790
 187790
 		13711
 13711
 		5789
 5789
 		190
 190
 		764
 764
 		597
 597
 		1135
 1135
 		13730
 13730
 		187790
 187790
 		13711
 13711
 		5789
 5789
 		190
 190
 		764
 764
 		597
 597
 		1135
 1135
1f8xA Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f8xB Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f8yA Unbound Unbound Unbound Unbound Unbound Analogue:5MD Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f8yB Unbound Unbound Unbound Unbound Unbound Analogue:5MD Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1f8xA ASP 72;GLU 98
1f8xB ASP 272;GLU 298
1f8yA ASP 72;GLU 98
1f8yB ASP 272;GLU 298

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Scheme IV
[3]
p.4986
[4]
p.102-104

References
[1]
Resource
Comments
Medline ID
PubMed ID 7797550
Journal J Biol Chem
Year 1995
Volume 270
Pages 15551-6
Authors Porter DJ, Merrill BM, Short SA
Title Identification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 7797551
Journal J Biol Chem
Year 1995
Volume 270
Pages 15557-62
Authors Porter DJ, Short SA
Title Nucleoside 2-deoxyribosyltransferase. Pre-steady-state kinetic analysis of native enzyme and mutant enzyme with an alanyl residue replacing Glu-98.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8617773
Journal J Biol Chem
Year 1996
Volume 271
Pages 4978-87
Authors Short SA, Armstrong SR, Ealick SE, Porter DJ
Title Active site amino acids that participate in the catalytic mechanism of nucleoside 2'-deoxyribosyltransferase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8805514
Journal Structure
Year 1996
Volume 4
Pages 97-107
Authors Armstrong SR, Cook WJ, Short SA, Ealick SE
Title Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.
Related PDB 1f8x 1f8y
Related UniProtKB

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.

Created Updated
2002-07-11 2009-02-26