Information on EC 2.5.1.81 - geranylfarnesyl diphosphate synthase

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The expected taxonomic range for this enzyme is: Archaea

EC NUMBER
COMMENTARY
2.5.1.81
-
RECOMMENDED NAME
GeneOntology No.
geranylfarnesyl diphosphate synthase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
geranylgeranyl diphosphate + isopentenyl diphosphate = (2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
show the reaction diagram
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
geranylgeranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 1 isopentenyl unit)
The enzyme from Methanosarcina mazei is involved in biosynthesis of the polyprenyl side-chain of methanophenazine, an electron carrier utilized for methanogenesis. It prefers geranylgeranyl diphosphate and farnesyl diphosphate as allylic substrate [1]. The enzyme from Aeropyrum pernix prefers farnesyl diphosphate as allylic substrate. The enzyme is involved in the biosynthesis of C25-C25 membrane lipids [2].
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
C25 FGPP synthase
Q9UWR6
-
FGPP synthase
Q9UWR6
-
FGPP synthase
-
-
Fgs
Q9UWR6
gene name
MM_0789
Q8PYS1
gene name
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + 2 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 2 diphosphate
show the reaction diagram
-, Q9UWR6
Aeropyrum pernix does not possess geranylgeranyl diphosphate synthase and has only C25-C25 ether lipids, but no C20-containing ether lipids. Aeropyrum pernix farnesylgeranyl diphosphate synthase is important in the biosynthesis of the hydrocarbon moiety of membrane lipids
-
-
?
(2E,6E)-farnesyl diphosphate + 2 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 2 diphosphate
show the reaction diagram
-, Q9UWR6
farnesyl diphosphate is the allylic substrate with the highest activity
-
-
?
(2E,6E)-farnesyl diphosphate + 2 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 2 diphosphate
show the reaction diagram
-
farnesyl diphosphate shows 93% of the activity with geranylgeranyl diphosphate. Stereochemistry of farnesylgeranyl diphosphate synthesized by FGPP synthase is unclear, but may be an all-E isomer because the same isomer is produced when dimethylallyl diphosphate, geranyl diphosphate, and (all-E)-farnesyl diphosphate, as well as (all-E)-geranylgeranyl diphosphate, are used as substrates. The stereochemistry of the C25 moiety of C20,C25-diether lipids is identical with that of the C20 moiety
-
-
?
dimethylallyl diphosphate + 4 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 4 diphosphate
show the reaction diagram
-, Q9UWR6
dimethylallyl diphosphate shows 28% of the activity with farnesyl diphosphate
large amounts of intermediates are formed: geranyl diphosphate, farnesyl diphosphate, geranylgeranyl diphosphate
-
?
dimethylallyl diphosphate + 4 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 4 diphosphate
show the reaction diagram
-
dimethylallyl diphosphate shows 51% of the activity with farnesyl diphosphate. Stereochemistry of farnesylgeranyl diphosphate synthesized by FGPP synthase is unclear, but may be an all-E isomer because the same isomer is produced when dimethylallyl diphosphate, geranyl diphosphate, and (all-E)-farnesyl diphosphate, as well as (all-E)-geranylgeranyl diphosphate, are used as substrates. The stereochemistry of the C25 moiety of C20,C25-diether lipids is identical with that of the C20 moiety
large amounts of intermediates are formed: geranyl diphosphate, farnesyl diphosphate, geranylgeranyl diphosphate
-
?
farnesyl diphosphate + 2 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 2 diphosphate
show the reaction diagram
-, Q8PYS1
biosynthesis of the polyprenyl side-chain of methanophenazine, an electron carrier utilized for methanogenesis
-
-
?
farnesyl diphosphate + 2 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 2 diphosphate
show the reaction diagram
-, Q8PYS1
the enzyme prefers geranylgeranyl diphosphate and farnesyl diphosphate as allylic substrate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate is the main product, a considerable amount of geranylgeranyl diphosphate as an intermediate is also observed
-
?
geranyl diphosphate + 3 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 3 diphosphate
show the reaction diagram
-, Q8PYS1
slight activity
-
-
?
geranyl diphosphate + 3 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 3 diphosphate
show the reaction diagram
-, Q9UWR6
geranyl diphosphate shows 72% of the activity with farnesyl diphosphate
-
-
?
geranyl diphosphate + 3 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 3 diphosphate
show the reaction diagram
-
geranyl diphosphate shows 81% of the activity with farnesyl diphosphate. Stereochemistry of farnesylgeranyl diphosphate synthesized by FGPP synthase is unclear, but may be an all-E isomer because the same isomer is produced when dimethylallyl diphosphate, geranyl diphosphate, and (all-E)-farnesyl diphosphate, as well as (all-E)-geranylgeranyl diphosphate, are used as substrates. The stereochemistry of the C25 moiety of C20,C25-diether lipids is identical with that of the C20 moiety
-
-
?
geranylgeranyl diphosphate + isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
show the reaction diagram
Q8PYS1
-
among mutants, in which the bulky residues that constitute the bottom of the product-accommodating cavity is replaced with alanine, those having mutations on an alpha-helix existing at the subunit interface yield longer products
-
?
geranylgeranyl diphosphate + isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
show the reaction diagram
-, Q8PYS1
biosynthesis of the polyprenyl side-chain of methanophenazine, an electron carrier utilized for methanogenesis
-
-
?
geranylgeranyl diphosphate + isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
show the reaction diagram
-
the enzyme may synthesize a precursor for the C25 moiety of C20,C25 diether lipids, geranylgeranyl diphosphate is the allylic substrate with the highest activity. Stereochemistry of farnesylgeranyl diphosphate synthesized by FGPP synthase is unclear, but may be an all-E isomer because the same isomer is produced when dimethylallyl diphosphate, geranyl diphosphate, and (all-E)-farnesyl diphosphate, as well as (all-E)-geranylgeranyl diphosphate, are used as substrates. The stereochemistry of the C25 moiety of C20,C25-diether lipids is identical with that of the C20 moiety
-
-
?
geranylgeranyl diphosphate + isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
show the reaction diagram
-, Q9UWR6
geranylgeranyl diphosphate shows 65% of the activity with farnesyl diphosphate
-
-
?
geranylgeranyl diphosphate + isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
show the reaction diagram
-, Q8PYS1
the enzyme prefers geranylgeranyl diphosphate and farnesyl diphosphate as allylic substrate
-
-
?
additional information
?
-
-, Q8PYS1
dimethylally diphosphate is not accepted as substrate
-
-
-
additional information
?
-
Q8PYS1
the residues in chain length determination region III are the predominant factor in the determination of the product specificity
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate + 2 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 2 diphosphate
show the reaction diagram
-, Q9UWR6
Aeropyrum pernix does not possess geranylgeranyl diphosphate synthase and has only C25-C25 ether lipids, but no C20-containing ether lipids. Aeropyrum pernix farnesylgeranyl diphosphate synthase is important in the biosynthesis of the hydrocarbon moiety of membrane lipids
-
-
?
farnesyl diphosphate + 2 isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + 2 diphosphate
show the reaction diagram
-, Q8PYS1
biosynthesis of the polyprenyl side-chain of methanophenazine, an electron carrier utilized for methanogenesis
-
-
?
geranylgeranyl diphosphate + isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
show the reaction diagram
-, Q8PYS1
biosynthesis of the polyprenyl side-chain of methanophenazine, an electron carrier utilized for methanogenesis
-
-
?
geranylgeranyl diphosphate + isopentenyl diphosphate
(2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
show the reaction diagram
-
the enzyme may synthesize a precursor for the C25 moiety of C20,C25 diether lipids
-
-
?
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Mg2+
Q8PYS1
maximal activity around 5.0 mM, no activity with other divalent cations such as Ca2+, Mn2+, and Zn2+
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
-
-
assay at
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
PDB
SCOP
CATH
ORGANISM
Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
48900
-
Q8PYS1
gel filtration
76000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
Q8PYS1
x * 33000, SDS-PAGE, calculated from sequence
dimer
Q8PYS1
2 * 33836, calculated
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
model structure of mutant I112A, calculated using the model of wild-type GFPS as a template. In wild-type enzyme, the I112 on each subunit is located next to the I112 on the other at the dimer interface, to separate the two reaction cavities. In the mutant enzyme, the substitution of I112 by alanine results in the formation of a large tunnel between dimer subunits, enabling prenyl diphosphates to elongate through the newly-created path from one cavity to the other, thus yielding extremely lengthened prenyl diphosphates
Q8PYS1
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Escherichia coli as a glutathione S-transferase fusion protein
-
expression of wild-type and mutant enzymes in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
D109A
Q8PYS1
mutation leads to the production of longer prenyl diphosphates from C30 to C35, but at small rates
I112A
Q8PYS1
chain length of the products of mutant I112A reaches up to C70 or longer, which is three times as long as that of the wild type. A large fraction of the longer products is C45-50, which is nearly twice as long as wild-type
II116A
Q8PYS1
mutation leads to the production of longer prenyl diphosphates from C30 to C35, but at small rates
M137A
Q8PYS1
slight increase in chain length of products
M72A
Q8PYS1
slight increase in chain length of products
additional information
-
directed evolution is used to create mutant FGPP synthases that confirm the importance of amino acids upstream of the FARM of prenyl diphosphate synthases and demonstrate the significance of mutations upstream of an additional conserved region (141GQ142). Product chain-length distribution can be also controlled by a structural change provoked by a cooperative interaction of amino acids