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Literature summary for 2.4.2.6 extracted from

  • Ghiorghi, Y.K.; Zeller, K.I.; Dang, C.V.; Kaminski, P.A.
    The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5-monophosphate N-glycosidase (2007), J. Biol. Chem., 282, 8150-8156.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
gene Rc1, expression of soluble unmodified enzyme and His-tagged enzymes in Escherichia coli strain Bli5 (BL21 (DE3) pDIA17) Rattus norvegicus

Protein Variants

Protein Variants Comment Organism
E105A site-directed mutagenesis, the mutant shows about 200fold reduced activity and a 170fold increased Km compared to the wild-type enzyme Rattus norvegicus

Inhibitors

Inhibitors Comment Organism Structure
6-methylthio-GMP competitive versus dGMP Rattus norvegicus
GMP competitive versus dGMP Rattus norvegicus
Zn2+
-
Rattus norvegicus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information kinetics and substrate specifiicty Rattus norvegicus
0.048
-
dGMP pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus
0.25
-
dAMP pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus
0.45
-
dIMP pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus
4
-
dCMP pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus
5
-
dGMP pH 7.5, 37°C, recombinant mutant E105A Rattus norvegicus
15
-
dUMP pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus
50
-
dTMP above, pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus

Metals/Ions

Metals/Ions Comment Organism Structure
additional information no effect by Ca2+, Mg2+, Na+, and K+ Rattus norvegicus

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
17649
-
1 * 17649, unmodified recombinant enzyme, mass spectrometry, 1 * 19812, His-tagged recombinant enzyme, mass spectrometry, 1 * 20440, His-tagged recombinant enzyme, SDS-PAGE Rattus norvegicus
17649
-
2 * 17649, unmodified recombinant enzyme, mass spectrometry, 2 * 17649, unmodified recombinant enzyme, mass spectrometry, 2 * 20440, His-tagged recombinant enzyme, SDS-PAGE Rattus norvegicus
19812
-
1 * 17649, unmodified recombinant enzyme, mass spectrometry, 1 * 19812, His-tagged recombinant enzyme, mass spectrometry, 1 * 20440, His-tagged recombinant enzyme, SDS-PAGE Rattus norvegicus
20440
-
monomeric enzyme, equilibrium sedimentation ultracentrifugation Rattus norvegicus
40520
-
monomeric enzyme, equilibrium sedimentation ultracentrifugation Rattus norvegicus

Organism

Organism UniProt Comment Textmining
Rattus norvegicus
-
gene Rc1
-

Purification (Commentary)

Purification (Comment) Organism
recombinant unmodified enzyme from Escherichia coli strain Bli5 (BL21 (DE3) pDIA17) by anion exchange chromatography and gel filtration, recombinant His-tagged enzyme by nickel affinity chromatography, over 95% purity Rattus norvegicus

Reaction

Reaction Comment Organism Reaction ID
2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1 Glu105, Asp-99 and Asn-172 are catalytic active site residues Rattus norvegicus

Source Tissue

Source Tissue Comment Organism Textmining
fibroblast
-
Rattus norvegicus
-

Storage Stability

Storage Stability Organism
-20°C, purified recombinant enzyme, 1 mg/ml, at least 1 year without loss of activity Rattus norvegicus

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
dAMP + base
-
Rattus norvegicus dNMP + adenine
-
r
dCMP + base
-
Rattus norvegicus dNMP + cytidine
-
r
dGMP + base dGMP is the best substrate Rattus norvegicus dNMP + guanine
-
r
dIMP + base
-
Rattus norvegicus dNMP + hypoxanthine
-
r
dTMP + base
-
Rattus norvegicus dNMP + thymine
-
r
dUMP + base
-
Rattus norvegicus dNMP + uracil
-
r
additional information RCL cleaves the N-glycosidic bond of deoxynucleoside 5'-monophosphates to yield two reaction products, deoxyribose 5-phosphate and purine or pyrimidine base Rattus norvegicus ?
-
?

Subunits

Subunits Comment Organism
dimer 2 * 17649, unmodified recombinant enzyme, mass spectrometry, 2 * 17649, unmodified recombinant enzyme, mass spectrometry, 2 * 20440, His-tagged recombinant enzyme, SDS-PAGE Rattus norvegicus
monomer 1 * 17649, unmodified recombinant enzyme, mass spectrometry, 1 * 19812, His-tagged recombinant enzyme, mass spectrometry, 1 * 20440, His-tagged recombinant enzyme, SDS-PAGE Rattus norvegicus
More at 0.003 mM the His-RCL is mostly monomeric, at 0.03 mM, His-RCL is mostly dimeric, at 0.01 mM His-RCL is at equilibrium between monomeric and dimeric states, overview Rattus norvegicus

Synonyms

Synonyms Comment Organism
deoxynucleoside 5-monophosphate N-glycosidase
-
Rattus norvegicus
RCL
-
Rattus norvegicus

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
assay at Rattus norvegicus

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0066
-
dAMP pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus
0.0066
-
dIMP pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus
0.0178
-
dGMP pH 7.5, 37°C, recombinant mutant E105A Rattus norvegicus
0.0231
-
dCMP pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus
0.0297
-
dGMP pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus
0.158
-
dUMP pH 7.5, 37°C, recombinant wild-type enzyme Rattus norvegicus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
6
-
-
Rattus norvegicus

pH Range

pH Minimum pH Maximum Comment Organism
5 8 50% of maximal activity at pH 7.0 with substrate dCMP, 20% with dGMP, 10% of maximal activity at pH 8.0 with both substrates Rattus norvegicus

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.01
-
6-methylthio-GMP pH 7.5, 37°C, recombinant wild-type enzyme, versus dGMP Rattus norvegicus
0.02
-
GMP pH 7.5, 37°C, recombinant wild-type enzyme, versus dGMP Rattus norvegicus