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Literature summary extracted from

  • Zakataeva, N.P.; Romanenkov, D.V.; Yusupova, Y.R.; Skripnikova, V.S.; Asahara, T.; Gronskiy, S.V.
    Identification, heterologous expression, and functional characterization of Bacillus subtilis YutF, a HAD superfamily 5'-nucleotidase with broad substrate specificity (2016), PLoS ONE, 11, e0167580 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.1.3.5 expressed in Escherichia coli BL21(DE3) cells Bacillus subtilis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.1.3.5 1.27
-
 5-phosphoribosyl-1-diphosphate at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 1.53
-
 5'-XMP at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 1.64
-
 4-nitrophenyl phosphate at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 6.65
-
 5'-GMP at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 24
-
 D-ribose 5-phosphate at pH 8.9 and 25°C Bacillus subtilis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.1.3.5 Mg2+ absolute requirement for Mg2+, 5 mM is the optimal concentration Bacillus subtilis

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
3.1.3.5 65000
-
 gel filtration Bacillus subtilis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.1.3.5 a 5'-ribonucleotide + H2O Bacillus subtilis
-
 a ribonucleoside + phosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.1.3.5 Bacillus subtilis O32125
-
-
3.1.3.5 Bacillus subtilis 168 O32125
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.1.3.5 HisTrap column chromatography and Sephadex G-25 gel filtration Bacillus subtilis

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
3.1.3.5 0.0245
-
 at pH 8.9 and 25°C Bacillus subtilis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.1.3.5 4-nitrophenyl phosphate + H2O best substrate, very high activity Bacillus subtilis 4-nitrophenol + phosphate
-
 ?
3.1.3.5 5'-ADP + H2O very low activity Bacillus subtilis AMP + phosphate
-
 ?
3.1.3.5 5'-AMP + H2O low activity Bacillus subtilis adenosine + phosphate
-
 ?
3.1.3.5 5'-AMP + H2O low activity Bacillus subtilis 168 adenosine + phosphate
-
 ?
3.1.3.5 5'-ATP + H2O very low activity Bacillus subtilis ADP + phosphate
-
 ?
3.1.3.5 5'-CTP + H2O low activity Bacillus subtilis CDP + phosphate
-
 ?
3.1.3.5 5'-dAMP + H2O low activity Bacillus subtilis deoxyadenosine + phosphate
-
 ?
3.1.3.5 5'-dAMP + H2O low activity Bacillus subtilis 168 deoxyadenosine + phosphate
-
 ?
3.1.3.5 5'-dGMP + H2O low activity Bacillus subtilis deoxyguanosine + phosphate
-
 ?
3.1.3.5 5'-dIMP + H2O low activity Bacillus subtilis deoxyinosine + phosphate
-
 ?
3.1.3.5 5'-GDP + H2O very low activity Bacillus subtilis GMP + phosphate
-
 ?
3.1.3.5 5'-GMP + H2O low activity Bacillus subtilis guanosine + phosphate
-
 ?
3.1.3.5 5'-GTP + H2O very low activity Bacillus subtilis GDP + phosphate
-
 ?
3.1.3.5 5'-IDP + H2O very low activity Bacillus subtilis IMP + phosphate
-
 ?
3.1.3.5 5'-IMP + H2O low activity Bacillus subtilis inosine + phosphate
-
 ?
3.1.3.5 5'-UMP + H2O low activity Bacillus subtilis uridine + phosphate
-
 ?
3.1.3.5 5'-UMP + H2O low activity Bacillus subtilis 168 uridine + phosphate
-
 ?
3.1.3.5 5'-XMP + H2O third best substrate Bacillus subtilis xanthosine + phosphate
-
 ?
3.1.3.5 5-phosphoribosyl-1-diphosphate + H2O
-
 Bacillus subtilis ?
-
 ?
3.1.3.5 a 5'-ribonucleotide + H2O
-
 Bacillus subtilis a ribonucleoside + phosphate
-
 ?
3.1.3.5 D-glucose 6-phosphate + H2O very low activity Bacillus subtilis D-glucose + phosphate
-
 ?
3.1.3.5 D-ribose 5-phosphate + H2O second best substrate Bacillus subtilis D-ribose + phosphate
-
 ?
3.1.3.5 D-ribose 5-phosphate + H2O second best substrate Bacillus subtilis 168 D-ribose + phosphate
-
 ?
3.1.3.5 ITP + H2O very low activity Bacillus subtilis IDP + phosphate
-
 ?
3.1.3.5 additional information no activity with 3'-CMP, 3'-AMP, and UDP-D-glucose Bacillus subtilis ?
-
 ?
3.1.3.5 additional information no activity with 3'-CMP, 3'-AMP, and UDP-D-glucose Bacillus subtilis 168 ?
-
 ?
3.1.3.5 UTP + H2O very low activity Bacillus subtilis UDP + phosphate
-
 ?

Subunits

EC Number Subunits Comment Organism
3.1.3.5 homodimer 2 * 29200, His6-tagged enzyme, calculated from amino acid sequence Bacillus subtilis
3.1.3.5 homodimer 2 * 30000, His6-tagged enzyme, SDS-PAGE Bacillus subtilis

Synonyms

EC Number Synonyms Comment Organism
3.1.3.5 YutF
-
 Bacillus subtilis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.1.3.5 0.06
-
 5'-GMP at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 0.17
-
 5-phosphoribosyl-1-diphosphate at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 0.31
-
 5'-XMP at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 1.84
-
 D-ribose 5-phosphate at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 61
-
 4-nitrophenyl phosphate at pH 8.9 and 25°C Bacillus subtilis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.1.3.5 6 6.5 in 100 mM MES buffer with 5'-IMP as a substrate Bacillus subtilis
3.1.3.5 8.7 9 in 100 mM Tris-HCl with 4-nitrophenyl phosphate as substrate Bacillus subtilis

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.1.3.5 0.009
-
 5'-GMP at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 0.077
-
 D-ribose 5-phosphate at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 0.13
-
 5-phosphoribosyl-1-diphosphate at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 0.21
-
 5'-XMP at pH 8.9 and 25°C Bacillus subtilis
3.1.3.5 37
-
 4-nitrophenyl phosphate at pH 8.9 and 25°C Bacillus subtilis