Human Gene FDPS (uc001fkc.2) Description and Page Index
  Description: Homo sapiens farnesyl diphosphate synthase (FDPS), transcript variant 1, mRNA.
RefSeq Summary (NM_002004): This gene encodes an enzyme that catalyzes the production of geranyl pyrophosphate and farnesyl pyrophosphate from isopentenyl pyrophosphate and dimethylallyl pyrophosphate. The resulting product, farnesyl pyrophosphate, is a key intermediate in cholesterol and sterol biosynthesis, a substrate for protein farnesylation and geranylgeranylation, and a ligand or agonist for certain hormone receptors and growth receptors. Drugs that inhibit this enzyme prevent the post-translational modifications of small GTPases and have been used to treat diseases related to bone resorption. Multiple pseudogenes have been found on chromosomes 1, 7, 14, 15, 21 and X. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2008].
Transcript (Including UTRs)
   Position: hg19 chr1:155,278,539-155,290,457 Size: 11,919 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr1:155,279,581-155,290,400 Size: 10,820 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:155,278,539-155,290,457)mRNA (may differ from genome)Protein (419 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: FPPS_HUMAN
DESCRIPTION: RecName: Full=Farnesyl pyrophosphate synthase; Short=FPP synthase; Short=FPS; EC=2.5.1.10; AltName: Full=(2E,6E)-farnesyl diphosphate synthase; AltName: Full=Dimethylallyltranstransferase; EC=2.5.1.1; AltName: Full=Farnesyl diphosphate synthase; AltName: Full=Geranyltranstransferase;
FUNCTION: Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids, and ubiquinones. FPP also serves as substrate for protein farnesylation and geranylgeranylation. Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.
CATALYTIC ACTIVITY: Dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate.
CATALYTIC ACTIVITY: Geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)-farnesyl diphosphate.
COFACTOR: Binds 3 magnesium ions per subunit.
ENZYME REGULATION: Inactivated by interferon-induced RSAD2. This inactivation may result of disruption of lipid rafts at the plasma membrane, and thus have an antiviral effect since many enveloped viruses need lipid rafts to bud efficiently out of the cell.
PATHWAY: Isoprenoid biosynthesis; farnesyl diphosphate biosynthesis; farnesyl diphosphate from geranyl diphosphate and isopentenyl diphosphate: step 1/1.
PATHWAY: Isoprenoid biosynthesis; geranyl diphosphate biosynthesis; geranyl diphosphate from dimethylallyl diphosphate and isopentenyl diphosphate: step 1/1.
SUBUNIT: Homodimer. Interacts with RSAD2. Interacts with HTLV-1 protein p13(II).
SUBCELLULAR LOCATION: Cytoplasm.
SIMILARITY: Belongs to the FPP/GGPP synthase family.
CAUTION: It is uncertain whether Met-1 or Met-67 is the initiator.
SEQUENCE CAUTION: Sequence=AAA52423.1; Type=Erroneous initiation; Sequence=BAA03523.2; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): FDPS
CDC HuGE Published Literature: FDPS

-  MalaCards Disease Associations
  MalaCards Gene Search: FDPS
Diseases sorted by gene-association score: porokeratosis 9, multiple types* (1229), porokeratosis* (197), linear porokeratosis (19), punctate porokeratosis (13), osteonecrosis of the jaw (8), bruxism (8), borna disease (7), osteonecrosis (6), testicular yolk sac tumor (5), adult fibrosarcoma (5), osteogenesis imperfecta, type v (5), hypoprothrombinemia (4), ischemic bone disease (4), osteogenesis imperfecta, type iii (3), osteoporosis (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 77.70 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1141.77 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -85.10219-0.389 Picture PostScript Text
3' UTR -10.5457-0.185 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000092 - Polyprenyl_synt
IPR008949 - Terpenoid_synth

Pfam Domains:
PF00348 - Polyprenyl synthetase

SCOP Domains:
48576 - Terpenoid synthases

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1YQ7
- X-ray MuPIT

1YV5
- X-ray MuPIT

1ZW5
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2F7M - X-ray MuPIT 2F89 - X-ray MuPIT 2F8C - X-ray MuPIT
2F8Z - X-ray MuPIT 2F92 - X-ray MuPIT 2F94 - X-ray MuPIT
2F9K - X-ray MuPIT 2OPM - X-ray MuPIT 2OPN - X-ray MuPIT
2QIS - X-ray MuPIT 2RAH - X-ray MuPIT 2VF6 - X-ray MuPIT
3B7L - X-ray MuPIT 3CP6 - X-ray MuPIT 3N1V - X-ray MuPIT
3N1W - X-ray MuPIT 3N3L - X-ray MuPIT 3N45 - X-ray MuPIT
3N46 - X-ray MuPIT 3N49 - X-ray MuPIT 3N5H - X-ray MuPIT
3N5J - X-ray MuPIT 3N6K - X-ray MuPIT 3RYE - X-ray MuPIT
3S4J - X-ray MuPIT 4DEM - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P14324
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0004161 dimethylallyltranstransferase activity
GO:0004337 geranyltranstransferase activity
GO:0016740 transferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006629 lipid metabolic process
GO:0006694 steroid biosynthetic process
GO:0006695 cholesterol biosynthetic process
GO:0008202 steroid metabolic process
GO:0008203 cholesterol metabolic process
GO:0008299 isoprenoid biosynthetic process
GO:0016032 viral process
GO:0016126 sterol biosynthetic process
GO:0033384 geranyl diphosphate biosynthetic process
GO:0045337 farnesyl diphosphate biosynthetic process
GO:0045540 regulation of cholesterol biosynthetic process

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF206172 - JP 2014500723-A/13675: Polycomb-Associated Non-Coding RNAs.
AK021828 - Homo sapiens cDNA FLJ11766 fis, clone HEMBA1005732, moderately similar to Human mRNA for KIAA1293 gene.
AK022841 - Homo sapiens cDNA FLJ12779 fis, clone NT2RP2001748, moderately similar to FARNESYL PYROPHOSPHATE SYNTHETASE.
AK291084 - Homo sapiens cDNA FLJ76177 complete cds, highly similar to Homo sapiens farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase) (FDPS), mRNA.
D14697 - Homo sapiens KIAA1293 mRNA.
BC010004 - Homo sapiens farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase), mRNA (cDNA clone MGC:15352 IMAGE:4132071), complete cds.
JD170252 - Sequence 151276 from Patent EP1572962.
AB384173 - Synthetic construct DNA, clone: pF1KSDA1293, Homo sapiens FDPS gene for farnesyl pyrophosphate synthetase, complete cds, without stop codon, in Flexi system.
DQ893471 - Synthetic construct clone IMAGE:100006101; FLH193022.01X; RZPDo839B1178D farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase) (FDPS) gene, encodes complete protein.
DQ895943 - Synthetic construct Homo sapiens clone IMAGE:100010403; FLH193018.01L; RZPDo839B1168D farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase) (FDPS) gene, encodes complete protein.
KJ891154 - Synthetic construct Homo sapiens clone ccsbBroadEn_00548 FDPS gene, encodes complete protein.
J05262 - Human farnesyl pyrophosphate synthetase mRNA, complete cds.
LF352185 - JP 2014500723-A/159688: Polycomb-Associated Non-Coding RNAs.
M29863 - Human farnesyl pyrophosphate synthetase mRNA (hpt807), 3' end.
LF352184 - JP 2014500723-A/159687: Polycomb-Associated Non-Coding RNAs.
JD021439 - Sequence 2463 from Patent EP1572962.
LF352182 - JP 2014500723-A/159685: Polycomb-Associated Non-Coding RNAs.
JD025597 - Sequence 6621 from Patent EP1572962.
JD031655 - Sequence 12679 from Patent EP1572962.
LF360357 - JP 2014500723-A/167860: Polycomb-Associated Non-Coding RNAs.
LF352181 - JP 2014500723-A/159684: Polycomb-Associated Non-Coding RNAs.
JD034700 - Sequence 15724 from Patent EP1572962.
LF352180 - JP 2014500723-A/159683: Polycomb-Associated Non-Coding RNAs.
LF211905 - JP 2014500723-A/19408: Polycomb-Associated Non-Coding RNAs.
LF360355 - JP 2014500723-A/167858: Polycomb-Associated Non-Coding RNAs.
JD023068 - Sequence 4092 from Patent EP1572962.
LF352178 - JP 2014500723-A/159681: Polycomb-Associated Non-Coding RNAs.
JD030339 - Sequence 11363 from Patent EP1572962.
MA587762 - JP 2018138019-A/159688: Polycomb-Associated Non-Coding RNAs.
MA587761 - JP 2018138019-A/159687: Polycomb-Associated Non-Coding RNAs.
MA587759 - JP 2018138019-A/159685: Polycomb-Associated Non-Coding RNAs.
MA587758 - JP 2018138019-A/159684: Polycomb-Associated Non-Coding RNAs.
MA587757 - JP 2018138019-A/159683: Polycomb-Associated Non-Coding RNAs.
MA587755 - JP 2018138019-A/159681: Polycomb-Associated Non-Coding RNAs.
MA441749 - JP 2018138019-A/13675: Polycomb-Associated Non-Coding RNAs.
MA595934 - JP 2018138019-A/167860: Polycomb-Associated Non-Coding RNAs.
MA447482 - JP 2018138019-A/19408: Polycomb-Associated Non-Coding RNAs.
MA595932 - JP 2018138019-A/167858: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00900 - Terpenoid backbone biosynthesis
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
PWY-5123 - trans, trans-farnesyl diphosphate biosynthesis
PWY66-5 - superpathway of cholesterol biosynthesis

Reactome (by CSHL, EBI, and GO)

Protein P14324 (Reactome details) participates in the following event(s):

R-HSA-191303 Another isopentenyl pyrophosphate is added to geranyl pyrophosphate
R-HSA-191322 Addition of isopentenyl pyrophosphate to DMAPP
R-HSA-2426168 Activation of gene expression by SREBF (SREBP)
R-HSA-1655829 Regulation of cholesterol biosynthesis by SREBP (SREBF)
R-HSA-8957322 Metabolism of steroids
R-HSA-556833 Metabolism of lipids
R-HSA-191273 Cholesterol biosynthesis
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: D3DV91, FPPS_HUMAN, FPS, KIAA1293, NM_002004, NP_001229754, P14324, Q96G29
UCSC ID: uc001fkc.2
RefSeq Accession: NM_002004
Protein: P14324 (aka FPPS_HUMAN)
CCDS: CCDS1110.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002004.3
exon count: 11CDS single in 3' UTR: no RNA size: 1555
ORF size: 1260CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2717.00frame shift in genome: no % Coverage: 98.78
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.