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Literature summary for 3.1.3.7 extracted from

  • Cummings, J.A.; Vetting, M.; Ghodge, S.V.; Xu, C.; Hillerich, B.; Seidel, R.D.; Almo, S.C.; Raushel, F.M.
    Prospecting for unannotated enzymes: discovery of a 3',5'-nucleotide bisphosphate phosphatase within the amidohydrolase superfamily (2014), Biochemistry, 53, 591-600.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
-
Chromobacterium violaceum

Crystallization (Commentary)

Crystallization (Comment) Organism
to 1.9 resolution, with AMP and orthophosphate bound in the active site. The enzyme has a trinuclear metal center in the active site with three Mn2+ ions. It belongs to the Cluster of Orthologous Groups cog0613 from the polymerase and histidinol phosphatase family of enzymes Chromobacterium violaceum

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0015
-
adenosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
0.0016
-
5'-phosphoadenylyl-(3'->5')-adenosine pH 7.5, 3°C Chromobacterium violaceum
0.0052
-
2'-deoxyguanosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
0.0054
-
N6-methyl-5'-phosphoadenylyl-(3'->5')-adenosine pH 7.5, 3°C Chromobacterium violaceum
0.0088
-
uridine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
0.0093
-
thymidine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
0.0102
-
2'-deoxyadenosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
0.0173
-
guanosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
0.022
-
2'-deoxythymidine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
0.026
-
2'-deoxycytidine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
0.029
-
2'-deoxyuridine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum

Metals/Ions

Metals/Ions Comment Organism Structure
Mn2+ enzyme has a trinuclear metal center in the active site with three Mn2+ ions Chromobacterium violaceum

Organism

Organism UniProt Comment Textmining
Chromobacterium violaceum Q7NXD4
-
-
Chromobacterium violaceum DSM 30191 Q7NXD4
-
-

Purification (Commentary)

Purification (Comment) Organism
-
Chromobacterium violaceum

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2'-deoxyadenosine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum 2'-deoxyadenosine 5'-phosphate + phosphate
-
?
2'-deoxyadenosine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum DSM 30191 2'-deoxyadenosine 5'-phosphate + phosphate
-
?
2'-deoxycytidine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum 2'-deoxycytidine 5'-phosphate + phosphate
-
?
2'-deoxycytidine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum DSM 30191 2'-deoxycytidine 5'-phosphate + phosphate
-
?
2'-deoxyguanosine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum 2'-deoxyguanosine 5'-phosphate + phosphate
-
?
2'-deoxythymidine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum 2'-deoxythymidine 5'-phosphate + phosphate
-
?
2'-deoxyuridine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum 2'-deoxyuridine 5'-phosphate + phosphate
-
?
5'-phosphoadenylyl-(3'->5')-adenosine + H2O
-
Chromobacterium violaceum ? + phosphate
-
?
adenosine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum adenosine 5'-phosphate + phosphate
-
?
adenosine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum DSM 30191 adenosine 5'-phosphate + phosphate
-
?
cytidine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum cytidine 5'-phosphate + phosphate
-
?
guanosine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum guanosine 5'-phosphate + phosphate
-
?
guanosine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum DSM 30191 guanosine 5'-phosphate + phosphate
-
?
additional information enzyme is promiscuous and is able to hydrolyze several 3',5'-bisphosphonucleotides such as pGp, pCp, pUp, and pIp, and 2'-deoxynucleotides with comparable catalytic efficiency. In addition, it is capable of hydrolyzing short oligonucleotides such as (pdA)5, albeit at rates much lower than that of adenosine 3',5'-bisphosphate Chromobacterium violaceum ?
-
?
additional information enzyme is promiscuous and is able to hydrolyze several 3',5'-bisphosphonucleotides such as pGp, pCp, pUp, and pIp, and 2'-deoxynucleotides with comparable catalytic efficiency. In addition, it is capable of hydrolyzing short oligonucleotides such as (pdA)5, albeit at rates much lower than that of adenosine 3',5'-bisphosphate Chromobacterium violaceum DSM 30191 ?
-
?
N6-methyl-5'-phosphoadenylyl-(3'->5')-adenosine + H2O
-
Chromobacterium violaceum ? + phosphate
-
?
thymidine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum thymidine 5'-phosphate + phosphate
-
?
uridine 3',5'-bisphosphate + H2O
-
Chromobacterium violaceum uridine 5'-phosphate + phosphate
-
?

Synonyms

Synonyms Comment Organism
Cv1693
-
Chromobacterium violaceum

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.05
-
5'-phosphoadenylyl-(3'->5')-adenosine pH 7.5, 3°C Chromobacterium violaceum
3.3
-
thymidine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
4.2
-
2'-deoxyguanosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
4.3
-
2'-deoxythymidine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
5.2
-
2'-deoxyuridine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
5.4
-
uridine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
7.1
-
2'-deoxyadenosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
9.4
-
2'-deoxycytidine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
11.6
-
N6-methyl-5'-phosphoadenylyl-(3'->5')-adenosine pH 7.5, 3°C Chromobacterium violaceum
12.3
-
guanosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
22
-
adenosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
32
-
5'-phosphoadenylyl-(3'->5')-adenosine pH 7.5, 3°C Chromobacterium violaceum
180
-
2'-deoxyuridine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
190
-
2'-deoxythymidine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
360
-
thymidine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
360
-
2'-deoxycytidine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
610
-
uridine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
700
-
2'-deoxyadenosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
710
-
guanosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
790
-
2'-deoxyguanosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
1400
-
adenosine 3',5'-bisphosphate pH 7.5, 3°C Chromobacterium violaceum
2100
-
N6-methyl-5'-phosphoadenylyl-(3'->5')-adenosine pH 7.5, 3°C Chromobacterium violaceum