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Information on EC 3.1.3.34 - deoxynucleotide 3'-phosphatase
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3.1.3.34 deoxynucleotide 3'-phosphataseIUBMB Comments
Also catalyses the selective removal of 3'-phosphate groups from DNA and oligodeoxyribonucleotides. Induced in Escherichia coli by T-even phages.
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The enzyme appears in viruses and cellular organisms
Reaction Schemes
a 2'-deoxyribonucleoside 3'-phosphate
+
=
+
Synonyms
3'-deoxynucleotidase, cdN, mdN, nucleotidase, 3'-deoxyribo, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3'-deoxynucleotidase
-
-
-
-
cdN
nucleotidase, 3'-deoxyribo
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a 2'-deoxyribonucleoside 3'-phosphate + H2O = a 2'-deoxyribonucleoside + phosphate
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
deoxyribonucleotide 3'-phosphohydrolase
Also catalyses the selective removal of 3'-phosphate groups from DNA and oligodeoxyribonucleotides. Induced in Escherichia coli by T-even phages.
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CAS REGISTRY NUMBER
COMMENTARY
37288-18-9
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(E)-5-(2-bromovinyl)-2'-deoxyuridine 5'-phosphate + H2O
(E)-5-(2-bromovinyl)-2'-deoxyuridine + phosphate
-
-
-
-
?
3'-azido-2',3'-dideoxythymidine 5'-phosphate + H2O
3'-azido-2',3'-dideoxythymidine + phosphate
-
-
-
-
?
additional information
?
-
-
cdN has higher activity for purine nucleotides than does mdN, active site residues Leu45 and Tyr65 in cdN form a more favorable binding surface for purine nucleotides than the corresponding Trp75 and Trp76 in mdN
-
-
?
deoxynucleoside 3'-phosphate + H2O
deoxynucleoside + phosphate
-
-
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
deoxynucleoside 3'-phosphate + H2O
deoxynucleoside + phosphate
-
-
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). KIPN_BPT4
301
0
34620
Swiss-Prot
other Location (Reliability: 3)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
by hanging drop vapor diffusion method, cdN in complex with 2'deoxyuridine 5'-phosphate to 1.2 A resolution, space group P1, mutant of mdN in complex with the nucleotide analogues 3'-azido-2',3'-dideoxythymidine 5'-phosphate to 1.8 A resolution, space group P43212, and in complex with (E)-5-(2-bromovinyl)-2'deoxyuridine 5'-phosphate to 1.95 A resolution, space group P432132
-
by hanging drop vapor diffusion method, D12N mutant in complex with 3'-dUMP to 1.9 A resolution, space group P62, and in complex with 3'-dGMP to 2.0 A resolution, space group P62
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, pH 8.0, 2 mM dithiothreitol, at least 1 week without loss of activity
-
liquid N2, as precipitate in 80% ammonium sulfate, 2 mM dithiothreitol, no inactivation after 1 year
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
drug development
-
introduction of substituents in the 3'-position may result in nucleoside analogues with increased resistance to dephosphorylation, design of drugs that are less prone to inactivation by the deoxyribonucleotidases
drug development
introduction of substituents in the 3'-position may result in nucleoside analogues with increased resistance to dephosphorylation, design of drugs that are less prone to inactivation by the deoxyribonucleotidases
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Becker, A.; Hurwitz, J.
The enzymatic cleavage of phosphate termini from polynucleotides
J. Biol. Chem.
242
936-950
1967
Escherichia coli
brenda
Richardson, C.C.
Enzymes in DNA metabolism
Annu. Rev. Biochem.
38
795-840
1969
Escherichia coli
brenda
Magnusson, G.
Deoxyribonucleotide phosphatase from rat liver and cultured mouse fibroblasts
Eur. J. Biochem.
20
225-230
1971
Mus musculus, Rattus norvegicus
brenda
Wallden, K.; Rinaldo-Matthis, A.; Ruzzenente, B.; Rampazzo, C.; Bianchi, V.; Nordlund, P.
Crystal structures of human and murine deoxyribonucleotidases: Insights into recognition of substrates and nucleotide analogues
Biochemistry
46
13809-13818
2007
Homo sapiens, Mus musculus (Q9JM14)
brenda
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