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Information on EC 3.1.3.89 - 5'-deoxynucleotidase and Organism(s) Escherichia coli and UniProt Accession P76491

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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.3 Phosphoric-monoester hydrolases
                3.1.3.89 5'-deoxynucleotidase
IUBMB Comments
The enzyme, characterized from the bacterium Escherichia coli, shows strict specificity towards deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. A divalent metal cation is required for activity, with cobalt providing the highest activity.
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This record set is specific for:
Escherichia coli
UNIPROT: P76491
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The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
Synonyms
5'-deoxynucleotidase, ygl101w, deoxyribonucleoside 5'-monophosphatase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PATHWAY SOURCE
PATHWAYS
SYSTEMATIC NAME
IUBMB Comments
2'-deoxyribonucleoside 5'-monophosphate phosphohydrolase
The enzyme, characterized from the bacterium Escherichia coli, shows strict specificity towards deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. A divalent metal cation is required for activity, with cobalt providing the highest activity.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5'-dAMP + H2O
deoxyadenosine + phosphate
show the reaction diagram
-
-
-
?
4-nitrophenyl phosphate + H2O
4-nitrophenol + phosphate
show the reaction diagram
-
-
-
-
?
5'-dAMP + H2O
deoxyadenosine + phosphate
show the reaction diagram
-
-
-
-
?
5'-dCMP + H2O
deoxycytidine + phosphate
show the reaction diagram
-
-
-
-
?
5'-dGMP + H2O
deoxyguanosine + phosphate
show the reaction diagram
-
-
-
-
?
5'-dIMP + H2O
deoxyinosine + phosphate
show the reaction diagram
-
-
-
-
?
5'-dTMP + H2O
thymidine + phosphate
show the reaction diagram
-
-
-
-
?
5'-dUMP + H2O
deoxyuridine + phosphate
show the reaction diagram
-
-
-
-
?
additional information
?
-
-
enzyme is strictly specific to deoxyribonucleoside 5'-monophosphates and does not hydrolyze ribonucleotides or deoxyribonucleoside 3'-monophosphates. It has similar levels of activity against all tested deoxyribonucleoside 5'-monophosphates
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
presence of divalent cation absolutely required. Maximum activity with Co2+, followed in decreasing order by Mn2+, Cu2+. Apparent Kd value for Co2+ 0.8 mM
Cu2+
-
presence of divalent cation absolutely required. Maximum activity with Co2+, followed in decreasing order by Mn2+, Cu2+
Mn2+
-
presence of divalent cation absolutely required. Maximum activity with Co2+, followed in decreasing order by Mn2+, Cu2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ADP
-
0.2 mM, 21% residual activity
ATP
-
0.2 mM, 18% residual activity
CTP
-
0.2 mM, 29% residual activity
dATP
-
0.2 mM, 15% residual activity
dCTP
-
0.2 mM, 19% residual activity
dGTP
-
0.2 mM, 13% residual activity
dTTP
-
0.2 mM, 15% residual activity
GTP
-
0.2 mM, 28% residual activity
ITP
-
0.2 mM, 29% residual activity
TTP
-
0.2 mM, 14% residual activity
UTP
-
0.2 mM, 26% residual activity
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.016 - 0.042
5'-dAMP
2.09
4-nitrophenyl phosphate
-
presence of Co2+, pH 8.0, 37°C
0.012
5'-dAMP
-
presence of Co2+, pH 8.0, 37°C
0.036
5'-dCMP
-
presence of Co2+, pH 8.0, 37°C
0.047
5'-dGMP
-
presence of Co2+, pH 8.0, 37°C
0.017
5'-dIMP
-
presence of Co2+, pH 8.0, 37°C
0.008
5'-dTMP
-
presence of Co2+, pH 8.0, 37°C
0.02
5'-dUMP
-
presence of Co2+, pH 8.0, 37°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.06 - 0.14
5'-dAMP
0.56
4-nitrophenyl phosphate
-
presence of Co2+, pH 8.0, 37°C
0.3
5'-dAMP
-
presence of Co2+, pH 8.0, 37°C
0.23
5'-dCMP
-
presence of Co2+, pH 8.0, 37°C
0.2
5'-dGMP
-
presence of Co2+, pH 8.0, 37°C
0.24
5'-dIMP
-
presence of Co2+, pH 8.0, 37°C
0.16
5'-dTMP
-
presence of Co2+, pH 8.0, 37°C
0.23
5'-dUMP
-
presence of Co2+, pH 8.0, 37°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.72 - 8.41
5'-dAMP
0.27
4-nitrophenyl phosphate
-
presence of Co2+, pH 8.0, 37°C
25.6
5'-dAMP
-
presence of Co2+, pH 8.0, 37°C
6.42
5'-dCMP
-
presence of Co2+, pH 8.0, 37°C
4.22
5'-dGMP
-
presence of Co2+, pH 8.0, 37°C
14.1
5'-dIMP
-
presence of Co2+, pH 8.0, 37°C
21.3
5'-dTMP
-
presence of Co2+, pH 8.0, 37°C
11.6
5'-dUMP
-
presence of Co2+, pH 8.0, 37°C
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
100000
-
and 71300, gel filtration
24000
71300
-
and above 100000, gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
-
and trimer, 4 * 24000, SDS-PAGE
trimer
-
and tetramer, 3 * 24000, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
free state and two complexes with natural substrates, to 2.1 A resolution. The free-state structure contains a large cavity accommodating the metal-coordinating HD motif of residues H33, H68, D69, and D137 and other conserved residues, i.e. R18, E72, and D77. These residues are important for activity. Residue R18 stabilizes the phosphate on the Co2+, and residue D77 forms a strong hydrogen bond critical for binding the ribose. The indole side chain of W19 is located close to the 2'-carbon atom of the deoxyribose moiety and is proposed to act as the selectivity switch for deoxyribonucleotide. The nucleotide bases of both dAMP and TMP make no specific hydrogen bonds with the protein, explaining the lack of nucleotide base selectivity. The E72A substrate complex structures also suggest a plausible single-step nucleophilic substitution mechanism
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D137A
complete loss of activity
D69A
almost complete loss of activity
D77A
complete loss of activity
E122A
almost complete loss of activity
E72A
catalytically inactive. Structures complexed with Co2+ and either TMP or dAMP disclose the unusual binding mode of deoxyribonucleotides in the active site
H33A
about 20% of wild-type activity
H68A
almost complete loss of activity
R18A
almost complete loss of activity
V30A
about 80% of wild-type activity
V37A
about 85% of wild-type activity
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Proudfoot, M.; Kuznetsova, E.; Brown, G.; Rao, N.N.; Kitagawa, M.; Mori, H.; Savchenko, A.; Yakunin, A.F.
General Enzymatic Screens Identify Three New Nucleotidases in Escherichia coli. Biochemical Characterization of SurE, YfbR, and Yjjg
J. Biol. Chem.
279
54687-54694
2004
Escherichia coli
Manually annotated by BRENDA team
Zimmerman, M.D.; Proudfoot, M.; Yakunin, A.; Minor, W.
Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5-deoxyribonucleotidase YfbR from Escherichia coli
J. Mol. Biol.
378
215-226
2008
Escherichia coli (P76491)
Manually annotated by BRENDA team