DB code: S00024

RLCP classification 5.304.3380000.2135 : Elimination
CATH domain 1.10.600.10 : Farnesyl Diphosphate Synthase Catalytic domain
E.C. 2.5.1.1 2.5.1.10
CSA 1fps
M-CSA 1fps
MACiE M0253

CATH domain Related DB codes (homologues)
1.10.600.10 : Farnesyl Diphosphate Synthase S00026 S00027

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Includes Pfam RefSeq
P08836 Farnesyl pyrophosphate synthetase
FPP synthetase
FPS
Farnesyl diphosphate synthetase
Dimethylallyltranstransferase
EC 2.5.1.1
Geranyltranstransferase
EC 2.5.1.10
PF00348 (polyprenyl_synt)
[Graphical View]
P14324 Farnesyl pyrophosphate synthetase
FPP synthetase
FPS
Farnesyl diphosphate synthetase
Dimethylallyltranstransferase
EC 2.5.1.1
Geranyltranstransferase
EC 2.5.1.10
PF00348 (polyprenyl_synt)
[Graphical View] 		NP_001129293.1 (Protein)
NM_001135821.1 (DNA/RNA sequence)
NP_001129294.1 (Protein)
NM_001135822.1 (DNA/RNA sequence)
NP_001229753.1 (Protein)
NM_001242824.1 (DNA/RNA sequence)
NP_001229754.1 (Protein)
NM_001242825.1 (DNA/RNA sequence)
NP_001995.1 (Protein)
NM_002004.3 (DNA/RNA sequence)

KEGG enzyme name
dimethylallyltranstransferase
(EC 2.5.1.1 )
geranyl-diphosphate synthase
(EC 2.5.1.1 )
prenyltransferase
(EC 2.5.1.1 )
dimethylallyltransferase
(EC 2.5.1.1 )
DMAPP:IPP-dimethylallyltransferase
(EC 2.5.1.1 )
(2E,6E)-farnesyl diphosphate synthetase
(EC 2.5.1.1 )
diprenyltransferase
(EC 2.5.1.1 )
geranyl pyrophosphate synthase
(EC 2.5.1.1 )
geranyl pyrophosphate synthetase
(EC 2.5.1.1 )
trans-farnesyl pyrophosphate synthetase
(EC 2.5.1.1 )
geranyltranstransferase
(EC 2.5.1.10 )
farnesyl-diphosphate synthase
(EC 2.5.1.10 )
geranyl transferase I
(EC 2.5.1.10 )
prenyltransferase
(EC 2.5.1.10 )
farnesyl pyrophosphate synthetase
(EC 2.5.1.10 )
farnesylpyrophosphate synthetase
(EC 2.5.1.10 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P08836 FPPS_CHICK Dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate. Geranyl diphosphate + isopentenyl diphosphate = diphosphate + trans,trans-farnesyl diphosphate. Homodimer. Cytoplasm.
P14324 FPPS_HUMAN Dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate. Geranyl diphosphate + isopentenyl diphosphate = diphosphate + trans,trans-farnesyl diphosphate. Homodimer. Interacts with RSAD2. Interacts with HTLV-1 protein p13(II). Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00100 Biosynthesis of steroids 2.5.1.1 2.5.1.10
MAP00900 Terpenoid biosynthesis 2.5.1.1 2.5.1.10

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C02148 C00235 C00341 C00129 C00013 C00341 C00448
E.C. 2.5.1.1
2.5.1.10
2.5.1.1
2.5.1.10
2.5.1.1
2.5.1.10
2.5.1.1
2.5.1.10
Compound Divalent metal Dimethylallyl diphosphate Geranyl diphosphate Isopentenyl diphosphate Pyrophosphate Geranyl diphosphate Trans,trans-Farnesyl diphosphate Carbocation and eliminated pyrophosphate in transition-state
Type divalent metal (Ca2+, Mg2+) lipid,phosphate group/phosphate ion lipid,phosphate group/phosphate ion lipid,phosphate group/phosphate ion phosphate group/phosphate ion lipid,phosphate group/phosphate ion lipid,phosphate group/phosphate ion
ChEBI 16057
 16057
 		17211
 17211
 		16584
 16584
 		29888
 29888
 		17211
 17211
 		17407
 17407
PubChem 647
 647
 		445995
 445995
 		1195
 1195
 		1023
 21961011
 1023
 21961011
 		445995
 445995
 		445713
 445713
1fpsA Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ubvA Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ubwA Bound:2x_MG Unbound Bound:GPP Unbound Unbound Unbound Unbound Unbound
1ubxA Bound:_MG Unbound Analogue:FPP Unbound Unbound Unbound Unbound Unbound
1ubyA Bound:2x_MG Bound:DMA Unbound Unbound Unbound Unbound Unbound Unbound
1yq7A Bound:3x_MG Unbound Unbound Analogue:PO4-PO4 Unbound Unbound Unbound Transition-state-analogue:RIS
1yv5A Bound:3x_MG Unbound Unbound Analogue:PO4-PO4 Unbound Unbound Unbound Transition-state-analogue:RIS
1zw5A Bound:3x_MG Unbound Unbound Bound:IPR Unbound Unbound Unbound Transition-state-analogue:ZOL
2f7mF Unbound Unbound Unbound Analogue:PO4 Unbound Unbound Unbound Unbound
2f89F Bound:3x_MN Unbound Unbound Unbound Unbound Unbound Unbound Transition-state-analogue:210
2f8cF Bound:3x_MG Unbound Unbound Analogue:PO4 Unbound Unbound Unbound Transition-state-analogue:ZOL
2f8zF Bound:3x_MG Unbound Unbound Bound:IPE Unbound Unbound Unbound Transition-state-analogue:ZOL
2f92F Analogue:3x_ZN Unbound Unbound Analogue:PO4 Unbound Unbound Unbound Transition-state-analogue:AHD
2f94F Analogue:3x_ZN Unbound Unbound Analogue:PO4 Unbound Unbound Unbound Transition-state-analogue:BFQ
2f9kF Analogue:3x_ZN Unbound Unbound Analogue:PO4 Unbound Unbound Unbound Transition-state-analogue:ZOL

Reference for Active-site residues
resource references E.C.
literature [14], [27], [29]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1fpsA ARG 126;LYS 214;THR 215;PHE 253;GLN 254;LYS 271 ASP 117;ASP 121(Magnesium-1 & -2);ASP 257(Magnesium-3) LYS 214
1ubvA ARG 126;LYS 214;THR 215;PHE 253;GLN 254; ASP 117;ASP 121(Magnesium-1 & -2);ASP 257(Magnesium-3) LYS 214 mutant F112A, F113S, K271A
1ubwA ARG 126;LYS 214;THR 215;PHE 253;GLN 254; ASP 117;ASP 121(Magnesium-1 & -2);ASP 257(Magnesium-3) LYS 214 mutant F112A, F113S, K271A
1ubxA ARG 126;LYS 214;THR 215;PHE 253;GLN 254;LYS 271 ASP 117;ASP 121(Magnesium-1 & -2);ASP 257(Magnesium-3) LYS 214 mutant F112A, F113S
1ubyA ARG 126;LYS 214;THR 215;PHE 253;GLN 254; ASP 117;ASP 121(Magnesium-1 & -2);ASP 257(Magnesium-3) LYS 214 mutant F112A, F113S, K271A
1yq7A ARG 126;LYS 214;THR 215;PHE 253;GLN 254;LYS 271 ASP 117;ASP 121(Magnesium-1 & -2);ASP 257(Magnesium-3) LYS 214
1yv5A ARG 126;LYS 214;THR 215;PHE 253;GLN 254;LYS 271 ASP 117;ASP 121(Magnesium-1 & -2);ASP 257(Magnesium-3) LYS 214
1zw5A ARG 126;LYS 214;THR 215;PHE 253;GLN 254;LYS 271 ASP 117;ASP 121(Magnesium-1 & -2);ASP 257(Magnesium-3) LYS 214
2f7mF ARG 112;LYS 200;THR 201;PHE 239;GLN 240;LYS 257 ASP 103;ASP 107(Magnesium-1 & -2);ASP 243(Magnesium-3) LYS 200
2f89F ARG 112;LYS 200;THR 201;PHE 239;GLN 240;LYS 257 ASP 103;ASP 107(Magnesium-1 & -2);ASP 243(Magnesium-3) LYS 200
2f8cF ARG 112;LYS 200;THR 201;PHE 239;GLN 240;LYS 257 ASP 103;ASP 107(Magnesium-1 & -2);ASP 243(Magnesium-3) LYS 200
2f8zF ARG 112;LYS 200;THR 201;PHE 239;GLN 240;LYS 257 ASP 103;ASP 107(Magnesium-1 & -2);ASP 243(Magnesium-3) LYS 200
2f92F ARG 112;LYS 200;THR 201;PHE 239;GLN 240;LYS 257 ASP 103;ASP 107(Magnesium-1 & -2);ASP 243(Magnesium-3) LYS 200
2f94F ARG 112;LYS 200;THR 201;PHE 239;GLN 240;LYS 257 ASP 103;ASP 107(Magnesium-1 & -2);ASP 243(Magnesium-3) LYS 200
2f9kF ARG 112;LYS 200;THR 201;PHE 239;GLN 240;LYS 257 ASP 103;ASP 107(Magnesium-1 & -2);ASP 243(Magnesium-3) LYS 200

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig. 4, p.30753-30754
[3]
p.3344-3346, Fig.9
[9]
Fig.4, p.999-1000
[13]
p.10876
[14]
[16]
Fig.5, p.15021-15023
[17]
[27]
Fig.3, p.8527-8528
[29]
p.7830-7831

References
[1]
Resource
Comments
Medline ID
PubMed ID 8003978
Journal Protein Sci
Year 1994
Volume 3
Pages 600-7
Authors Chen A, Kroon PA, Poulter CD
Title Isoprenyl diphosphate synthases: protein sequence comparisons, a phylogenetic tree, and predictions of secondary structure.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8940054
Journal J Biol Chem
Year 1996
Volume 271
Pages 30748-54
Authors Ohnuma S, Narita K, Nakazawa T, Ishida C, Takeuchi Y, Ohto C, Nishino T
Title A role of the amino acid residue located on the fifth position before the first aspartate-rich motif of farnesyl diphosphate synthase on determination of the final product.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 12135472
Journal Eur J Biochem
Year 2002
Volume 269
Pages 3339-54
Authors Liang PH, Ko TP, Wang AH
Title Structure, mechanism and function of prenyltransferases.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 12769708
Journal Curr Top Med Chem
Year 2003
Volume 3
Pages 1043-74
Authors Kale TA, Hsieh SA, Rose MW, Distefano MD
Title Use of synthetic isoprenoid analogues for understanding protein prenyltransferase mechanism and structure.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 15456258
Journal J Med Chem
Year 2004
Volume 47
Pages 5149-58
Authors Cheng F, Oldfield E
Title Inhibition of isoprene biosynthesis pathway enzymes by phosphonates, bisphosphonates, and diphosphates.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 84684
Journal Biochemistry
Year 1979
Volume 18
Pages 860-4
Authors Brems DN, Rilling HC
Title Photoaffinity labeling of the catalytic site of prenyltransferase
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 7259201
Journal Arch Biochem Biophys
Year 1981
Volume 208
Pages 508-11
Authors Saito A, Rilling HC
Title The formation of cyclic sesquiterpenes from farnesyl pyrophosphate by prenyltransferase
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 7272273
Journal Biochemistry
Year 1981
Volume 20
Pages 3711-8
Authors Brems DN, Bruenger E, Rilling HC
Title Isolation and characterization of a photoaffinity-labeled peptide from the catalytic site of prenyltransferase
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 4092833
Journal Biochem Soc Trans
Year 1985
Volume 13
Pages 997-1003
Authors Rilling HC
Title The mechanism of the condensation reactions of cholesterol biosynthesis. Fourth Morton lecture
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 3519603
Journal J Biochem (Tokyo)
Year 1986
Volume 99
Pages 1327-37
Authors Fujisaki S, Nishino T, Katsuki H
Title Isoprenoid synthesis in Escherichia coli. Separation and partial purification of four enzymes involved in the synthesis
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 2541701
Journal Biochem Biophys Res Commun
Year 1989
Volume 160
Pages 448-52
Authors Yoshida I, Koyama T, Ogura K
Title Formation of a stable and catalytically active complex of the two essential components of hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 8411181
Journal J Mol Biol
Year 1993
Volume 233
Pages 787-8
Authors Nakane H, Koyama T, Obata S, Osabe M, Takeshita A, Nishino T, Ogura K, Miki K
Title Crystallization and preliminary X-ray diffraction studies of Bacillus stearothermophilus farnesyl diphosphate synthase expressed in Escherichia coli
Related PDB
Related UniProtKB
[13]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 20-367.
Medline ID
PubMed ID 8086404
Journal Biochemistry
Year 1994
Volume 33
Pages 10871-7
Authors Tarshis LC, Yan M, Poulter CD, Sacchettini JC
Title Crystal structure of recombinant farnesyl diphosphate synthase at 2.6-A resolution
Related PDB 1fps
Related UniProtKB P08836
[14]
Resource
Comments
Medline ID
PubMed ID 7626083
Journal Biochem Biophys Res Commun
Year 1995
Volume 212
Pages 681-6
Authors Koyama T, Tajima M, Nishino T, Ogura K
Title Significance of Phe-220 and Gln-221 in the catalytic mechanism of farnesyl diphosphate synthase of Bacillus stearothermophilus
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 8639752
Journal Plant Mol Biol
Year 1996
Volume 30
Pages 935-46
Authors Adiwilaga K, Kush A
Title Cloning and characterization of cDNA encoding farnesyl diphosphate synthase from rubber tree (Hevea brasiliensis)
Related PDB
Related UniProtKB
[16]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 20-367.
Medline ID
PubMed ID 8986756
Journal Proc Natl Acad Sci U S A
Year 1996
Volume 93
Pages 15018-23
Authors Tarshis LC, Proteau PJ, Kellogg BA, Sacchettini JC, Poulter CD
Title Regulation of product chain length by isoprenyl diphosphate synthases
Related PDB 1ubv 1ubw 1ubx 1uby
Related UniProtKB P08836
[17]
Resource
Comments
Medline ID
PubMed ID 9667899
Journal Curr Opin Chem Biol
Year 1997
Volume 1
Pages 570-8
Authors Kellogg BA, Poulter CD
Title Chain elongation in the isoprenoid biosynthetic pathway
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 9324768
Journal Science
Year 1997
Volume 277
Pages 1788-9
Authors Sacchettini JC, Poulter CD
Title Creating isoprenoid diversity
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 10825960
Journal Org Lett
Year 1999
Volume 1
Pages 1071-3
Authors Leyes AE, Baker JA, Poulter CD
Title Biosynthesis of isoprenoids in Escherichia coli
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 10631008
Journal Biochemistry
Year 2000
Volume 39
Pages 463-9
Authors Koyama T, Gotoh Y, Nishino T
Title Intersubunit location of the active site of farnesyl diphosphate synthase
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11112517
Journal Biochemistry
Year 2000
Volume 39
Pages 15316-21
Authors Stanley Fernandez SM, Kellogg BA, Poulter CD
Title Farnesyl diphosphate synthase. Altering the catalytic site to select for geranyl diphosphate activity
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 11027152
Journal Biochemistry
Year 2000
Volume 39
Pages 12717-22
Authors Zhang YW, Li XY, Koyama T
Title Chain length determination of prenyltransferases
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 11142508
Journal J Biomol NMR
Year 2000
Volume 18
Pages 183-8
Authors Mueller GA, Choy WY, Skrynnikov NR, Kay LE
Title A method for incorporating dipolar couplings into structure calculations in cases of (near) axial symmetry of alignment
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 11435429
Journal J Biol Chem
Year 2001
Volume 276
Pages 33930-7
Authors Montalvetti A, Bailey BN, Martin MB, Severin GW, Oldfield E, Docampo R
Title Bisphosphonates are potent inhibitors of Trypanosoma cruzi farnesyl pyrophosphate synthase
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 11348105
Journal J Org Chem
Year 2001
Volume 66
Pages 3253-64
Authors Turek TC, Gaon I, Distefano MD, Strickland CL
Title Synthesis of farnesyl diphosphate analogues containing ether-linked photoactive benzophenones and their application in studies of protein prenyltransferases
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 12086477
Journal J Med Chem
Year 2002
Volume 45
Pages 2894-903
Authors Szabo CM, Martin MB, Oldfield E
Title An investigation of bone resorption and Dictyostelium discoideum growth inhibition by bisphosphonate drugs
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 14672944
Journal J Biol Chem
Year 2004
Volume 279
Pages 8526-9
Authors Hosfield DJ, Zhang Y, Dougan DR, Broun A, Tari LW, Swanson RV, Finn J
Title Structural basis for bisphosphonate-mediated inhibition of isoprenoid biosynthesis.
Related PDB 1rqi 1rqj 1rtr
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 16698791
Journal J Biol Chem
Year 2006
Volume [Epub ahead of print]
Pages
Authors Kavanagh KL, Dunford JE, Bunkoczi G, Russell RG, Oppermann U
Title The crystal structure of human geranylgeranyl pyrophosphate synthase reveals a novel hexameric arrangement and inhibitory product binding.
Related PDB 2fvi
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 16684881
Journal Proc Natl Acad Sci U S A
Year 2006
Volume 103
Pages 7829-34
Authors Kavanagh KL, Guo K, Dunford JE, Wu X, Knapp S, Ebetino FH, Rogers MJ, Russell RG, Oppermann U
Title The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs.
Related PDB 1yq7 1yv5 1zw5
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID
Journal ChemMedChem
Year 2006
Volume 1
Pages 267-73
Authors Rondeau J-M, Bitsch F, Bourgier E, Geiser M, Hemmig R, Kroemer M, Lehmann S, Ramage P, Rieffel S, Strauss A, Green JR, Jahnke W
Title Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs.
Related PDB 2f7m 2f89 2f8c 2f8z 2f92 2f94 2f9k
Related UniProtKB

Comments
According to the literature [3] & [9], the reaction of this enzyme proceeds via an ionization-condensation-elimination mechanism.
This enzyme catalyzes the following reactions sequentially:
(A) Elimination of phosphate group from DMAPP (leading to the formation of carbocation and pyrophosphate):
This reaction is rupture of the carbon-oxygen bond of the allylic diphosphate to form a ion pair between the pyrophosphate leaving group and the allylic carboncation.
(B) Addition polymerization between the carbocation intermediate and IPP:
This reaction is alkylation of the C3-C4 double bond of IPP by the carbocation to form a second carbocationic intermediate, leading to stereospecific abstraction of a proton from C2 of the isopentenl unit to produce a new allylic diphosphate.
According to the literature [27] & [29], the reaction proceeds as follows:
(A) Elimination of phosphate group from DMAPP (leading to the formation of carbocation and pyrophosphate):
(A1) The developing negative charge on the eliminated group, pyrophosphate, is stabilized by three magnesium ions, which are bound to acidic residues, along with Arg126, Lys214 and Lys271.
(A2) The mainchain carbonyl group of Lys214, the sidechains of Thr215 and Gln254 stabilize the developing positive charge on the leaving group, allylic group, leading to the formation of carbocation.
(A3) This elimination reaction occurs by E1-like mechanism.

Created Updated
2003-11-12 2009-03-11