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Literature summary extracted from

  • Mori, T.; Ogawa, T.; Yoshimura, T.; Hemmi, H.
    Substrate specificity of undecaprenyl diphosphate synthase from the hyperthermophilic archaeon Aeropyrum pernix (2013), Biochem. Biophys. Res. Commun., 436, 230-234.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.5.1.29 gene ape_1385, recombinant expression in Escherichia coli strain BL21 (DE3) Aeropyrum pernix
2.5.1.B35 expressed in Escherichia coli Aeropyrum pernix
2.5.1.89 gene ape_1385, recombinant expression in Escherichia coli strain BL21 (DE3) Aeropyrum pernix

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.5.1.29 EDTA complete inhibition Aeropyrum pernix
2.5.1.B35 EDTA 5 mM, complete inhibition Aeropyrum pernix
2.5.1.89 EDTA complete inhibition Aeropyrum pernix

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.5.1.29 Ca2+ about 10% of the activity with Mg2+ Aeropyrum pernix
2.5.1.29 Cu2+ about 5% of the activity with Mg2+ Aeropyrum pernix
2.5.1.29 Mg2+ required Aeropyrum pernix
2.5.1.29 Mn2+ about 20% of the activity with Mg2+ Aeropyrum pernix
2.5.1.B35 Ca2+ a divalent metal ion is necessary for the activity. Ca2+, Mn2+ and Cu2+ all confer significantly lower activity than Mg2+ does Aeropyrum pernix
2.5.1.B35 Cu2+ a divalent metal ion is necessary for the activity. Ca2+, Mn2+ and Cu2+ all confer significantly lower activity than Mg2+ does Aeropyrum pernix
2.5.1.B35 Mg2+ a divalent metal ion is necessary for the activity. The addition of 5 mM Mg2+ gives the highest activity within the conditions tested. A 10fold higher concentration of Mg2+ continues to show activity that is comparable to 5 mM Mg2+ Aeropyrum pernix
2.5.1.B35 Mn2+ a divalent metal ion is necessary for the activity. Ca2+, Mn2+ and Cu2+ all confer significantly lower activity than Mg2+ does Aeropyrum pernix
2.5.1.89 Ca2+ about 10% of the activity with Mg2+ Aeropyrum pernix
2.5.1.89 Cu2+ about 5% of the activity with Mg2+ Aeropyrum pernix
2.5.1.89 Mg2+ required Aeropyrum pernix
2.5.1.89 Mn2+ about 20% of the activity with Mg2+ Aeropyrum pernix

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.5.1.29 additional information Aeropyrum pernix the undecaprenyl diphosphate synthase from Aeropyrum pernix that has anomalous substrate specificity, due to the fact that only dimethylallyl diphosphate and geranylfarnesyl diphosphate, both of which are unusual substrates for known cis-prenyltransferases, are likely available as an allylic primer substrate for the archaeal enzyme ?
-
 ?
2.5.1.29 additional information Aeropyrum pernix DSM 11879 the undecaprenyl diphosphate synthase from Aeropyrum pernix that has anomalous substrate specificity, due to the fact that only dimethylallyl diphosphate and geranylfarnesyl diphosphate, both of which are unusual substrates for known cis-prenyltransferases, are likely available as an allylic primer substrate for the archaeal enzyme ?
-
 ?
2.5.1.B35 geranylfarnesyl diphosphate + 6 isopentenyl diphosphate Aeropyrum pernix the enzyme is involved in the biosynthetic pathway for isoprenoid compounds 6 diphosphate + tetratrans,hexacis-undecaprenyl diphosphate
-
 ?
2.5.1.89 all-trans-geranylfarnesyl diphosphate + 6 isopentenyl diphosphate Aeropyrum pernix
-
 6 diphosphate + hexatrans,tetracis-undecaprenyl diphosphate
-
 ?
2.5.1.89 all-trans-geranylfarnesyl diphosphate + 6 isopentenyl diphosphate Aeropyrum pernix DSM 11879
-
 6 diphosphate + hexatrans,tetracis-undecaprenyl diphosphate
-
 ?
2.5.1.89 additional information Aeropyrum pernix the undecaprenyl diphosphate synthase from Aeropyrum pernix that has anomalous substrate specificity, due to the fact that only dimethylallyl diphosphate and geranylfarnesyl diphosphate, both of which are unusual substrates for known cis-prenyltransferases, are likely available as an allylic primer substrate for the archaeal enzyme ?
-
 ?
2.5.1.89 additional information Aeropyrum pernix DSM 11879 the undecaprenyl diphosphate synthase from Aeropyrum pernix that has anomalous substrate specificity, due to the fact that only dimethylallyl diphosphate and geranylfarnesyl diphosphate, both of which are unusual substrates for known cis-prenyltransferases, are likely available as an allylic primer substrate for the archaeal enzyme ?
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.5.1.29 Aeropyrum pernix Q9YC66 gene ape_1385
-
2.5.1.29 Aeropyrum pernix DSM 11879 Q9YC66 gene ape_1385
-
2.5.1.B35 Aeropyrum pernix Q9YC66
-
-
2.5.1.89 Aeropyrum pernix Q9YC66 gene ape_1385
-
2.5.1.89 Aeropyrum pernix DSM 11879 Q9YC66 gene ape_1385
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.5.1.B35
-
 Aeropyrum pernix

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.5.1.29 additional information the undecaprenyl diphosphate synthase from Aeropyrum pernix that has anomalous substrate specificity, due to the fact that only dimethylallyl diphosphate and geranylfarnesyl diphosphate, both of which are unusual substrates for known cis-prenyltransferases, are likely available as an allylic primer substrate for the archaeal enzyme Aeropyrum pernix ?
-
 ?
2.5.1.29 additional information the enzyme is a cis-prenyltransferas, determination of substrate specificity, product chain-length, and cofactor requirement, overview. The most preferred allylic substrates are farnesyl diphosphate and geranylfarnesyl diphosphate, the main product is UPP, regardless of the substrate. When the ratio of IPP to geranylfarnesyl diphosphate is decreased to 1, the UPP synthase predominately yields shorter C30-45 products. When the ratio is increased to 100, the main product is C60 dodecaprenyl diphosphate. The chain-length of the product of UPP synthase, which determines the structure of the glycosyl carrier lipid, is variable depending on the substrate ratio in the cells of Aeropyrum pernix. A 10fold increase in the substrate ratio results in a significant rise in the production of all-trans-hexaprenyl diphosphate. No activity with dimethylallyl diphosphate. The enzyme also shows the activity of hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific], EC 2.5.1.82, and of tritrans,polycis-undecaprenyl-diphosphate synthase [geranylgeranyl-diphosphate specific], EC 2.5.1.89 Aeropyrum pernix ?
-
 ?
2.5.1.29 additional information the undecaprenyl diphosphate synthase from Aeropyrum pernix that has anomalous substrate specificity, due to the fact that only dimethylallyl diphosphate and geranylfarnesyl diphosphate, both of which are unusual substrates for known cis-prenyltransferases, are likely available as an allylic primer substrate for the archaeal enzyme Aeropyrum pernix DSM 11879 ?
-
 ?
2.5.1.29 additional information the enzyme is a cis-prenyltransferas, determination of substrate specificity, product chain-length, and cofactor requirement, overview. The most preferred allylic substrates are farnesyl diphosphate and geranylfarnesyl diphosphate, the main product is UPP, regardless of the substrate. When the ratio of IPP to geranylfarnesyl diphosphate is decreased to 1, the UPP synthase predominately yields shorter C30-45 products. When the ratio is increased to 100, the main product is C60 dodecaprenyl diphosphate. The chain-length of the product of UPP synthase, which determines the structure of the glycosyl carrier lipid, is variable depending on the substrate ratio in the cells of Aeropyrum pernix. A 10fold increase in the substrate ratio results in a significant rise in the production of all-trans-hexaprenyl diphosphate. No activity with dimethylallyl diphosphate. The enzyme also shows the activity of hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific], EC 2.5.1.82, and of tritrans,polycis-undecaprenyl-diphosphate synthase [geranylgeranyl-diphosphate specific], EC 2.5.1.89 Aeropyrum pernix DSM 11879 ?
-
 ?
2.5.1.B35 (2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate about 95% of the activity with geranylfarnesyl diphosphate. The main product is undecaprenyl diphosphate, regardless of the substrate. If the ratio of IPP to the allylic substrate becomes lower, the product will be shorter, probably because of the shortage of isopentenyl diphosphate or because of the frequent dissociation of an intermediate from the active site by competitive binding of the hydrophobic allylic substrate Aeropyrum pernix 8 diphosphate + ditrans,octacis-undecaprenyl diphosphate the stereochemistry of the product is not experimentally determined ?
2.5.1.B35 geranyl diphosphate + 9 isopentenyl diphosphate about 65% of the activity with geranylfarnesyl diphosphate. The main product is undecaprenyl diphosphate, regardless of the substrate. If the ratio of IPP to the allylic substrate becomes lower, the product will be shorter, probably because of the shortage of isopentenyl diphosphate or because of the frequent dissociation of an intermediate from the active site by competitive binding of the hydrophobic allylic substrate Aeropyrum pernix 9 diphosphate + monotrans,nonacis-undecaprenyl diphosphate the stereochemistry of the product is not experimentally determined ?
2.5.1.B35 geranylfarnesyl diphosphate + 6 isopentenyl diphosphate the enzyme is involved in the biosynthetic pathway for isoprenoid compounds Aeropyrum pernix 6 diphosphate + tetratrans,hexacis-undecaprenyl diphosphate
-
 ?
2.5.1.B35 geranylfarnesyl diphosphate + 6 isopentenyl diphosphate geranylfarnesyl diphosphate is the most preferred allylic substrate. The main product is undecaprenyl diphosphate, regardless of the substrate. If the ratio of isopentenyl diphosphate to the allylic substrate becomes lower, the product will be shorter, probably because of the shortage of isopentenyl diphosphate or because of the frequent dissociation of an intermediate from the active site by competitive binding of the hydrophobic allylic substrate Aeropyrum pernix 6 diphosphate + tetratrans,hexacis-undecaprenyl diphosphate the stereochemistry of the product is not experimentally determined ?
2.5.1.B35 geranylgeranyl diphosphate + 7 isopentenyl diphosphate about 45% of the activity with geranylfarnesyl diphosphate. The main product is undecaprenyl diphosphate, regardless of the substrate. If the ratio of IPP to the allylic substrate becomes lower, the product will be shorter, probably because of the shortage of isopentenyl diphosphate or because of the frequent dissociation of an intermediate from the active site by competitive binding of the hydrophobic allylic substrate. When the ratio of isopentenyl diphosphate to geranylfarnesyl diphosphate is decreased to 1, the UPP synthase predominately yields shorter C30–45 products Aeropyrum pernix 7 diphosphate + tritrans,heptacis-undecaprenyl diphosphate the stereochemistry of the product is not experimentally determined ?
2.5.1.B35 additional information dimethylallyl diphosphate does not react with the enzyme. If the ratio of IPP to the allylic substrate becomes lower, the product will be shorter, probably because of the shortage of isopentenyl diphosphate or because of the frequent dissociation of an intermediate from the active site by competitive binding of the hydrophobic allylic substrate Aeropyrum pernix ?
-
 ?
2.5.1.89 all-trans-geranylfarnesyl diphosphate + 6 isopentenyl diphosphate
-
 Aeropyrum pernix 6 diphosphate + hexatrans,tetracis-undecaprenyl diphosphate
-
 ?
2.5.1.89 all-trans-geranylfarnesyl diphosphate + 6 isopentenyl diphosphate
-
 Aeropyrum pernix 6 diphosphate + hexatrans,tetracis-undecaprenyl diphosphate i.e. (Z,Z,Z,Z,Z,Z,E,E,E,E)-UPP [(2Z,6Z,10Z,14Z,18Z,22Z,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyl-2,6,10,14,18,22,26,30,34,38,42-tetratetracontaundecaen-1-yl diphosphate] ?
2.5.1.89 all-trans-geranylfarnesyl diphosphate + 6 isopentenyl diphosphate
-
 Aeropyrum pernix DSM 11879 6 diphosphate + hexatrans,tetracis-undecaprenyl diphosphate
-
 ?
2.5.1.89 additional information the undecaprenyl diphosphate synthase from Aeropyrum pernix that has anomalous substrate specificity, due to the fact that only dimethylallyl diphosphate and geranylfarnesyl diphosphate, both of which are unusual substrates for known cis-prenyltransferases, are likely available as an allylic primer substrate for the archaeal enzyme Aeropyrum pernix ?
-
 ?
2.5.1.89 additional information the enzyme is a cis-prenyltransferas, determination of substrate specificity, product chain-length, and cofactor requirement, overview. The most preferred allylic substrates are farnesyl diphosphate and geranylfarnesyl diphosphate, the main product is UPP, regardless of the substrate. When the ratio of IPP to geranylfarnesyl diphosphate is decreased to 1, the UPP synthase predominately yields shorter C30-45 products. When the ratio is increased to 100, the main product is C60 dodecaprenyl diphosphate. The chain-length of the product of UPP synthase, which determines the structure of the glycosyl carrier lipid, is variable depending on the substrate ratio in the cells of Aeropyrum pernix. A 10fold increase in the substrate ratio results in a significant rise in the production of all-trans-hexaprenyl diphosphate. No activity with dimethylallyl diphosphate. The enzyme also shows the activity of hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific], EC 2.5.1.82, and of geranylgeranyl diphosphate synthase, EC 2.5.1.29 Aeropyrum pernix ?
-
 ?
2.5.1.89 additional information the undecaprenyl diphosphate synthase from Aeropyrum pernix that has anomalous substrate specificity, due to the fact that only dimethylallyl diphosphate and geranylfarnesyl diphosphate, both of which are unusual substrates for known cis-prenyltransferases, are likely available as an allylic primer substrate for the archaeal enzyme Aeropyrum pernix DSM 11879 ?
-
 ?
2.5.1.89 additional information the enzyme is a cis-prenyltransferas, determination of substrate specificity, product chain-length, and cofactor requirement, overview. The most preferred allylic substrates are farnesyl diphosphate and geranylfarnesyl diphosphate, the main product is UPP, regardless of the substrate. When the ratio of IPP to geranylfarnesyl diphosphate is decreased to 1, the UPP synthase predominately yields shorter C30-45 products. When the ratio is increased to 100, the main product is C60 dodecaprenyl diphosphate. The chain-length of the product of UPP synthase, which determines the structure of the glycosyl carrier lipid, is variable depending on the substrate ratio in the cells of Aeropyrum pernix. A 10fold increase in the substrate ratio results in a significant rise in the production of all-trans-hexaprenyl diphosphate. No activity with dimethylallyl diphosphate. The enzyme also shows the activity of hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific], EC 2.5.1.82, and of geranylgeranyl diphosphate synthase, EC 2.5.1.29 Aeropyrum pernix DSM 11879 ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.5.1.B35 ape_1385 locus name Aeropyrum pernix
2.5.1.B35 undecaprenyl diphosphate synthase ambiguous Aeropyrum pernix
2.5.1.B35 UPP synthase
-
 Aeropyrum pernix
2.5.1.89 undecaprenyl diphosphate synthase
-
 Aeropyrum pernix

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.5.1.29 60
-
-
 Aeropyrum pernix
2.5.1.B35 60
-
 assay at Aeropyrum pernix
2.5.1.89 60
-
-
 Aeropyrum pernix

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
2.5.1.29 60
-
 purified recombinant enzyme, 1 h, completely stable up to, substrate (2E,6E)-farnesyl diphosphate Aeropyrum pernix
2.5.1.29 90
-
 purified recombinant enzyme, 1 h, 90% activity remains, substrate (2E,6E)-farnesyl diphosphate Aeropyrum pernix
2.5.1.29 100
-
 purified recombinant enzyme, 1 h, inactivation, (2E,6E)-farnesyl diphosphate Aeropyrum pernix
2.5.1.B35 90
-
 1 h, the enzyme retains more than 80% of its activity Aeropyrum pernix
2.5.1.B35 100
-
 1 h, complete inactivation Aeropyrum pernix

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.5.1.29 7
-
 assay at Aeropyrum pernix
2.5.1.B35 7
-
 assay at Aeropyrum pernix
2.5.1.89 7
-
 assay at Aeropyrum pernix

General Information

EC Number General Information Comment Organism
2.5.1.B35 physiological function the enzyme is involved in the biosynthetic pathway for isoprenoid compounds Aeropyrum pernix