S00377
type: Enzyme
rlcp: p2
cath: Rossmann fold
ec: https://purl.uniprot.org/enzyme/2.4.2.6
csa: 1f8x
uniprot: Q9R5V5
kegg enzyme: nucleoside deoxyribosyltransferase
kegg enzyme: purine(pyrimidine) nucleoside:purine(pyrimidine) deoxyribosyltransferase
kegg enzyme: deoxyribose transferase
kegg enzyme: nucleoside trans-N-deoxyribosylase
kegg enzyme: trans-deoxyribosylase
kegg enzyme: trans-N-deoxyribosylase
kegg enzyme: trans-N-glycosidase
kegg enzyme: nucleoside deoxyribosyltransferase I (purine nucleoside:purinedeoxyribosyltransferase: strictly specific for transfer betweenpurine bases)
kegg enzyme: nucleoside deoxyribosyltransferase II [purine(pyrimidine)nucleoside:purine(pyrimidine) deoxyribosyltransferase]
kegg pathway: Pyrimidine metabolism
kegg substrate: 2-Deoxy-D-ribosyl-base1
kegg substrate: Base2
kegg substrate: Deoxyadenosine
kegg substrate: Deoxyguanosine
kegg substrate: Deoxycytidine
kegg substrate: Deoxythymidine
kegg substrate: Adenine
kegg substrate: Guanine
kegg substrate: Cytosine
kegg substrate: Thymine
kegg product: 2-Deoxy-D-ribosyl-base1
kegg product: Base2
kegg product: Deoxyadenosine
kegg product: Deoxyguanosine
kegg product: Deoxycytidine
kegg product: Deoxythymidine
kegg product: Adenine
kegg product: Guanine
kegg product: Cytosine
kegg product: Thymine
pdb: 1f8xA
pdb: 1f8xB
pdb: 1f8yA
pdb: 1f8yB
pdb bound state: Unbound
  compound: 2-Deoxy-D-ribosyl-base1
  pdb: 1f8xA
pdb bound state: Unbound
  compound: 2-Deoxy-D-ribosyl-base1
  pdb: 1f8xB
pdb bound state: Unbound
  compound: 2-Deoxy-D-ribosyl-base1
  pdb: 1f8yA
pdb bound state: Unbound
  compound: 2-Deoxy-D-ribosyl-base1
  pdb: 1f8yB
pdb bound state: Unbound
  compound: Base2
  pdb: 1f8xA
pdb bound state: Unbound
  compound: Base2
  pdb: 1f8xB
pdb bound state: Unbound
  compound: Base2
  pdb: 1f8yA
pdb bound state: Unbound
  compound: Base2
  pdb: 1f8yB
pdb bound state: Unbound
  compound: Deoxyadenosine
  pdb: 1f8xA
pdb bound state: Unbound
  compound: Deoxyadenosine
  pdb: 1f8xB
pdb bound state: Unbound
  compound: Deoxyadenosine
  pdb: 1f8yA
pdb bound state: Unbound
  compound: Deoxyadenosine
  pdb: 1f8yB
pdb bound state: Unbound
  compound: Deoxyguanosine
  pdb: 1f8xA
pdb bound state: Unbound
  compound: Deoxyguanosine
  pdb: 1f8xB
pdb bound state: Unbound
  compound: Deoxyguanosine
  pdb: 1f8yA
pdb bound state: Unbound
  compound: Deoxyguanosine
  pdb: 1f8yB
pdb bound state: Unbound
  compound: Deoxycytidine
  pdb: 1f8xA
pdb bound state: Unbound
  compound: Deoxycytidine
  pdb: 1f8xB
pdb bound state: Unbound
  compound: Deoxycytidine
  pdb: 1f8yA
pdb bound state: Unbound
  compound: Deoxycytidine
  pdb: 1f8yB
pdb bound state: Unbound
  compound: Deoxythymidine
  pdb: 1f8xA
pdb bound state: Unbound
  compound: Deoxythymidine
  pdb: 1f8xB
pdb bound state: Analogue
  compound: Deoxythymidine
  pdb: 1f8yA
  ligand het code: 5MD
pdb bound state: Analogue
  compound: Deoxythymidine
  pdb: 1f8yB
  ligand het code: 5MD
pdb bound state: Unbound
  compound: Adenine
  pdb: 1f8xA
pdb bound state: Unbound
  compound: Adenine
  pdb: 1f8xB
pdb bound state: Unbound
  compound: Adenine
  pdb: 1f8yA
pdb bound state: Unbound
  compound: Adenine
  pdb: 1f8yB
pdb bound state: Unbound
  compound: Guanine
  pdb: 1f8xA
pdb bound state: Unbound
  compound: Guanine
  pdb: 1f8xB
pdb bound state: Unbound
  compound: Guanine
  pdb: 1f8yA
pdb bound state: Unbound
  compound: Guanine
  pdb: 1f8yB
pdb bound state: Unbound
  compound: Cytosine
  pdb: 1f8xA
pdb bound state: Unbound
  compound: Cytosine
  pdb: 1f8xB
pdb bound state: Unbound
  compound: Cytosine
  pdb: 1f8yA
references: Identification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98.
references: Nucleoside 2-deoxyribosyltransferase. Pre-steady-state kinetic analysis of native enzyme and mutant enzyme with an alanyl residue replacing Glu-98.
references: Active site amino acids that participate in the catalytic mechanism of nucleoside 2'-deoxyribosyltransferase.
references: Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.
comment: 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.

Rossmann fold
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.50.1810
catalytic domain: index.html

Pyrimidine metabolism
type: KeggPathway
references: KEGG:MAP00240

2-Deoxy-D-ribosyl-base1
type: KeggSubstrate
references: KEGG:C03216
compound type: nucleoside
type: KeggProduct
label: 2-Deoxy-D-ribosyl-base2

Base2
type: KeggSubstrate
references: KEGG:C00701
compound type: aromatic ring (with nitrogen atoms)
type: KeggProduct
label: Base1

Deoxyadenosine
type: KeggSubstrate
references: KEGG:C00559
compound type: amine group
compound type: nucleoside
references: CHEBI:17256
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct

Deoxyguanosine
type: KeggSubstrate
references: KEGG:C00330
compound type: amide group
compound type: amine group
compound type: nucleoside
references: CHEBI:17172
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct

Deoxycytidine
type: KeggSubstrate
references: KEGG:C00881
compound type: amine group
compound type: nucleoside
references: CHEBI:15698
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct

Deoxythymidine
type: KeggSubstrate
references: KEGG:C00214
compound type: amide group
compound type: nucleoside
references: CHEBI:17748
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct

Adenine
type: KeggSubstrate
references: KEGG:C00147
compound type: amine group
compound type: aromatic ring (with nitrogen atoms)
references: CHEBI:16708
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct

Guanine
type: KeggSubstrate
references: KEGG:C00242
compound type: amide group
compound type: amine group
compound type: aromatic ring (with nitrogen atoms)
references: CHEBI:16235
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct

Cytosine
type: KeggSubstrate
references: KEGG:C00380
compound type: amide group
compound type: amine group
compound type: aromatic ring (with nitrogen atoms)
references: CHEBI:16040
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct

Thymine
type: KeggSubstrate
references: KEGG:C00178
compound type: amide group
compound type: aromatic ring (with nitrogen atoms)
references: CHEBI:17821
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct
compound type: amine group

1f8xA
type: Pdb
references: 1f8x
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8x
catalytic residue: ASP 72;GLU 98

1f8xB
type: Pdb
references: 1f8x
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8x
catalytic residue: ASP 272;GLU 298

1f8yA
type: Pdb
references: 1f8y
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8y
catalytic residue: ASP 72;GLU 98

1f8yB
type: Pdb
references: 1f8y
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1f8y
catalytic residue: ASP 272;GLU 298

Identification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7797550
journal: J Biol Chem
volume: 270
pages: 15551-6
published year: 1995
authors:
  item: Porter DJ
  item: Merrill BM
  item: Short SA

Nucleoside 2-deoxyribosyltransferase. Pre-steady-state kinetic analysis of native enzyme and mutant enzyme with an alanyl residue replacing Glu-98.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7797551
journal: J Biol Chem
volume: 270
pages: 15557-62
published year: 1995
authors:
  item: Porter DJ
  item: Short SA

Active site amino acids that participate in the catalytic mechanism of nucleoside 2'-deoxyribosyltransferase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8617773
journal: J Biol Chem
volume: 271
pages: 4978-87
published year: 1996
authors:
  item: Short SA
  item: Armstrong SR
  item: Ealick SE
  item: Porter DJ

Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8805514
journal: Structure
volume: 4
pages: 97-107
published year: 1996
authors:
  item: Armstrong SR
  item: Cook WJ
  item: Short SA
  item: Ealick SE
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

ReferenceForCatalyticMechanism
reference index: 2
reference section: Scheme IV

ReferenceForCatalyticMechanism
reference index: 3
reference section: p.4986

ReferenceForCatalyticMechanism
reference index: 4
reference section: p.102-104