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Information on EC 2.5.1.83 - hexaprenyl diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] and Organism(s) Micrococcus luteus and UniProt Accession O66127

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IUBMB Comments
The enzyme prefers farnesyl diphosphate to geranylgeranyl diphosphate as an allylic substrate and does not show activity for geranyl diphosphate and dimethylallyl diphosphate .
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This record set is specific for:
Micrococcus luteus
UNIPROT: O66127 not found.
The expected taxonomic range for this enzyme is: Micrococcus luteus
The taxonomic range for the selected organisms is: Micrococcus luteus
Synonyms
hexaprenyl pyrophosphate synthetase, hexaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific], HexPP synthase, HexPPs, HexPS, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexaprenyl pyrophosphate synthetase
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hexaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2E,6E)-farnesyl diphosphate + 3 isopentenyl diphosphate = 3 diphosphate + all-trans-hexaprenyl diphosphate
show the reaction diagram
mechanism: farnesyl diphosphate binds to the components of the enzyme (A and B) to form an aggregate, A-B-(farnesyl diphosphate)-Mg2+, which probably represents an intermediary state of enzyme catalysis
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SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 3 isopentenyl units)
The enzyme prefers farnesyl diphosphate to geranylgeranyl diphosphate as an allylic substrate and does not show activity for geranyl diphosphate and dimethylallyl diphosphate [1].
CAS REGISTRY NUMBER
COMMENTARY hide
83745-07-7
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + 1 but-3-enyl diphosphate
diphosphate + (E)-norgeranylgeranyl diphosphate
show the reaction diagram
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-
-
?
(2E,6E)-farnesyl diphosphate + 3 isopentenyl diphosphate
3 diphosphate + all-trans-hexaprenyl diphosphate
show the reaction diagram
(2E,6E)-farnesyl diphosphate + 3-ethylbut-3-enyl diphosphate
diphosphate + (all-E)-3-ethyl-7,11,15-trimethylhexadeca-2,6,10,14-tetraenyl diphosphate + (all-E)-3,7-diethyl-11,15,19-trimethyleicosa-2,6,10,14,18-pentaenyl diphosphate
show the reaction diagram
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-
-
-
?
(2E,6E)-farnesyl diphosphate + 3-ethylbut-3-enyl diphosphate
diphosphate + (all-E)-3-ethyl-7,11,15-trimethylhexadeca-2,6,10,14-tetraenyl diphosphate + (all-E)-3,7-diethyl-11,15,19-trimethylicosa-2,6,10,14,18-pentaenyl diphosphate
show the reaction diagram
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-
-
?
(2E,6E)-farnesyl diphosphate + 3-propylbut-3-enyl diphosphate
?
show the reaction diagram
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-
-
-
?
(2E,6E)-farnesyl diphosphate + but-3-enyl diphosphate
diphosphate + (E)-norgeranylgeranyl diphosphate
show the reaction diagram
-
-
-
-
?
geranyl diphosphate + 4 isopentenyl diphosphate
4 diphosphate + all-trans-hexaprenyl diphosphate
show the reaction diagram
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geranyl diphosphate is a poor substrate
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-
?
geranylgeranyl diphosphate + 2 isopentenyl diphosphate
2 diphosphate + all-trans-hexaprenyl diphosphate
show the reaction diagram
additional information
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + 3 isopentenyl diphosphate
3 diphosphate + all-trans-hexaprenyl diphosphate
show the reaction diagram
O66127 and O66129
the enzyme prefers farnesyl diphosphate to geranylgeranyl diphosphate (activity is 3fold higher) as an allylic substrate and does not show activity for geranyl diphosphate and dimethylallyl diphosphate
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-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,2-Cyclohexanedione
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results in a rapid loss of the component B activity. Component A is resistant, retaining the initial activity almost completely. Farnesyl diphosphate, isopentenyl diphosphate, farnesyl monophosphate and inorganic diphosphate protect the synthase against the inactivation by N-ethylmaleimide, farnesyl diphosphate being the most effective. The presence of Mg2+ is essential for the protection by isopentenyl diphosphate and inorganic diphosphate. For protection of the synthase activity against the inactivation by 2,3-butanedione, the presence of farnesyl diphosphate, isopentenyl diphosphate and Mg2+ is more effective than that of the individual substrates and Mg2+. Inorganic diphosphate provides substantial protection. In the absence of component A, the component B activity is not protected by any substrates or its analogue
2,3-Butanedione
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results in a rapid loss of the component B activity. Component A is resistant, retaining the initial activity almost completely. Farnesyl diphosphate, isopentenyl diphosphate, farnesyl monophosphate and inorganic diphosphate protect the synthase against the inactivation by N-ethylmaleimide, farnesyl diphosphate being the most effective. The presence of Mg2+ is essential for the protection by isopentenyl diphosphate and inorganic diphosphate. For protection of the synthase activity against the inactivation by 2,3-butanedione, the presence of farnesyl diphosphate, isopentenyl diphosphate and Mg2+ is more effective than that of the individual substrates and Mg2+. Inorganic diphosphate provides substantial protection. In the absence of component A, the component B activity is not protected by any substrates or its analogue
7,11-dimethyl-2,6,10-dodecatrien-1-yl diphosphate
analogue of farnesyl diphosphate. Two aspartate-rich motifs and the other characteristic motifs in subunit HexB are located around the diphosphate part of 7,11-dimethyl-2,6,10-dodecatrien-1-yl diphosphate
iodoacetamide
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results in a rapid loss of the component B activity. Component A is resistant, retaining the initial activity almost completely. Farnesyl diphosphate, isopentenyl diphosphate, farnesyl monophosphate and inorganic diphosphate protect the synthase against the inactivation by N-ethylmaleimide, farnesyl diphosphate being the most effective. The presence of Mg2+ is essential for the protection by isopentenyl diphosphate and inorganic diphosphate. For protection of the synthase activity against the inactivation by 2,3-butanedione, the presence of farnesyl diphosphate, isopentenyl diphosphate and Mg2+ is more effective than that of the individual substrates and Mg2+. Inorganic diphosphate provides substantial protection. In the absence of component A, the component B activity is not protected by any substrates or its analogue
N-ethylmaleimide
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results in a rapid loss of the component B activity. Component A is resistant, retaining the initial activity almost completely. Farnesyl diphosphate, isopentenyl diphosphate, farnesyl monophosphate and inorganic diphosphate protect the synthase against the inactivation by N-ethylmaleimide, farnesyl diphosphate being the most effective. The presence of Mg2+ is essential for the protection by isopentenyl diphosphate and inorganic diphosphate. For protection of the synthase activity against the inactivation by 2,3-butanedione, the presence of farnesyl diphosphate, isopentenyl diphosphate and Mg2+ is more effective than that of the individual substrates and Mg2+. Inorganic diphosphate provides substantial protection. In the absence of component A, the component B activity is not protected by any substrates or its analogue
p-chloromercuribenzoate
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results in a rapid loss of the component B activity. Component A is resistant, retaining the initial activity almost completely. Farnesyl diphosphate, isopentenyl diphosphate, farnesyl monophosphate and inorganic diphosphate protect the synthase against the inactivation by N-ethylmaleimide, farnesyl diphosphate being the most effective. The presence of Mg2+ is essential for the protection by isopentenyl diphosphate and inorganic diphosphate. For protection of the synthase activity against the inactivation by 2,3-butanedione, the presence of farnesyl diphosphate, isopentenyl diphosphate and Mg2+ is more effective than that of the individual substrates and Mg2+. Inorganic diphosphate provides substantial protection. In the absence of component A, the component B activity is not protected by any substrates or its analogue
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0067 - 0.0105
(2E,6E)-farnesyl diphosphate
0.0124 - 0.385
geranylgeranyl diphosphate
0.0137 - 0.0216
isopentenyl diphosphate
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
Sequence
HEXA_MICLU
143
0
16942
Swiss-Prot
HEXB_MICLU
325
0
37083
Swiss-Prot
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20000
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x * 20000 (component A), + x * 60000 (component B), during the course of purification the enzyme is resolved into two components (A and B), each of which has no catalytic activity but restore the hexaprenyl diphosphate synthase activity when combined with each other, gel filtration
50000
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a stable complex of the two essential components of hexaprenyl diphosphate synthase, which represents the catalytically active state of this enzyme, gel filtration
60000
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x * 20000 (component A), + x * 60000 (component B), during the course of purification the enzyme is resolved into two components (A and B), each of which has no catalytic activity but restore the hexaprenyl diphosphate synthase activity when combined with each other, gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
crystal structure both in the substrate-free form and in complex with 7,11-dimethyl-2,6,10-dodecatrien-1-yl diphosphate ammonium salt, an analog of farnesyl diphosphate, to 2.5 A and 2.7 A resolution, respectively. The structure of subunit HexB is composed of mostly antiparallel alpha-helices joined by connecting loops. Two aspartate-rich motifs and the other characteristic motifs in HexB are located around the diphosphate part of 7,11-dimethyl-2,6,10-dodecatrien-1-yl diphosphate. Despite the very low amino acid sequence identity and the distinct polypeptide chain lengths between subunits HexA and HexB, the structure of HexA is quite similar to that of HexB. The aliphatic tail of 7,11-dimethyl-2,6,10-dodecatrien-1-yl diphosphate is accommodated in a large hydrophobic cleft starting from HexB and penetrating to the inside of HexA suggesting that HexB catalyzes the condensation reactions and that HexA is directly involved in the product chain length control in cooperation with HexB
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A79F
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mutant enzyme subunit-A(wild-type)/subunit-B(A79L) shows 10fold increased Vmax-values and 11fold decreased Km-values for geranyl diphosphate, which becomes the most preferred substrate of the allylic primers. 5fold increase in KM-value for geranylgeranyl diphosphate. Mutation results in shortening the chain length of the major product. The major products are farnesylgeranyl diphosphate and geranylgeranyl diphosphate
A79L
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mutant enzyme subunit-A(wild-type)/subunit-B(A79L) shows 7fold increased Vmax-values and 6fold decreased Km-values for geranyl diphosphate, which becomes the most preferred substrate of the allylic primers. 3.9fold increase in KM-value for geranylgeranyl diphosphate. Mutation results in shortening the chain length of the major product. The major product is farnesylgeranyl diphosphate
V76G
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mutant enzyme subunit-A(wild-type)/subunit-B(V76G) gives octaprenyl diphosphate as the final products with farnesyl diphosphate as an allylic primer
additional information
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several amino acid residues in the larger subunits Bacillus subtilis heptaprenyl diphosphate synthase are selected for substitutions by site-directed mutagenesis and examined by combination with the corresponding wild type or mutated smaller subunits
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
component A is more stable against heat treatment than component B. The former retains 75% of its original activity for restoration after a 5 min treatment at 50°C while the latter loses 75% of its activity
PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
during the course of purification the enzyme is resolved into two components (A and B), each of which has no catalytic activity but restore the hexaprenyl pyrophosphate synthetase activity when combined with each other
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purification of component A, purification of component B
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Fujii, H.; Koyama, T.; Ogura, K.
Hexaprenyl pyrophosphate synthetase from Micrococcus luteus B-P 26. Separation of two essential components
J. Biol. Chem.
257
14610-14612
1982
Micrococcus luteus (O66127 and O66129), Micrococcus luteus B-P 26, Micrococcus luteus B-P 26 (O66127 and O66129)
Manually annotated by BRENDA team
Yoshida, I.; Koyama, T.; Ogura, K.
Formation of a stable and catalytically active complex of the two essential components of hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26
Biochem. Biophys. Res. Commun.
160
448-452
1989
Micrococcus luteus (O66127 and O66129), Micrococcus luteus B-P 26 (O66127 and O66129)
Manually annotated by BRENDA team
Yoshida, I.; Koyama, T.; Ogura, K.
Protection of hexaprenyl-diphosphate synthase of Micrococcus luteus B-P 26 against inactivation by sulphydryl reagents and arginine-specific reagents
Biochim. Biophys. Acta
995
138-143
1989
Micrococcus luteus (O66127 and O66129), Micrococcus luteus B-P 26 (O66127 and O66129)
Manually annotated by BRENDA team
Shimizu, N.; Koyama, T.; Ogura, K.
Molecular cloning, expression, and characterization of the genes encoding the two essential protein components of Micrococcus luteus B-P 26 hexaprenyl diphosphate synthase
J. Bacteriol.
180
1578-1581
1998
Micrococcus luteus (O66127 and O66129), Micrococcus luteus B-P 26 (O66127 and O66129)
Manually annotated by BRENDA team
Nagaki, M.; Kimura, K.; Kimura, H.; Maki, Y.; Goto, E.; Nishino, T.; Koyama, T.
Artificial substrates of medium-chain elongating enzymes, hexaprenyl- and heptaprenyl diphosphate synthases
Bioorg. Med. Chem. Lett.
11
2157-2159
2001
Micrococcus luteus (O66127 and O66129), Micrococcus luteus B-P 26 (O66127 and O66129)
Manually annotated by BRENDA team
Nagaki, M.; Miki, Y.; Nakada, M.; Kawakami, J.; Kitahara, H.; Maki, Y.; Gotoh, Y.; Nishino, T.; Koyama, T.
Substrate specificities of several prenyl chain elongating enzymes with respect to 4-methyl-4-pentenyl diphosphate
Biosci. Biotechnol. Biochem.
68
2070-2075
2004
Micrococcus luteus (O66127 and O66129), Micrococcus luteus B-P 26 (O66127 and O66129)
Manually annotated by BRENDA team
Yoshida, I.; Koyama, T.; Ogura, K.
Dynamic Interaction between Components of Hexaprenyl Diphosphate Synthase from Micrococcus luteus BP-26
Biochemistry
26
6840-6845
1987
Micrococcus luteus (O66127 and O66129), Micrococcus luteus BP-26 (O66127 and O66129)
Manually annotated by BRENDA team
Zhang, Y.W.; Li, X.Y.; Koyama, T.
Chain length determination of prenyltransferases: both heteromeric subunits of medium-chain (E)-prenyl diphosphate synthase are involved in the product chain length determination
Biochemistry
39
12717-12722
2000
Micrococcus luteus (O66127 and O66129), Micrococcus luteus B-P 26 (O66127 and O66129)
Manually annotated by BRENDA team
Sasaki, D.; Fujihashi, M.; Okuyama, N.; Kobayashi, Y.; Noike, M.; Koyama, T.; Miki, K.
Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation
J. Biol. Chem.
286
3729-3740
2011
Micrococcus luteus (O66129 and O66127), Micrococcus luteus B-P 26 (O66129 and O66127)
Manually annotated by BRENDA team
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