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Prenyltransferase PDB id
1fps
Jmol
Contents
Protein chain
348 a.a. *
Waters ×79
* Residue conservation analysis
PDB id:
1fps
Name: Prenyltransferase
Title: Crystal structure of recombinant farnesyl diphosphate syntha angstroms resolution
Structure: Farnesyl diphosphate synthase. Chain: a. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.194    
Authors: L.C.Tarshis,M.Yan,C.D.Poulter,J.C.Sacchettini
Key ref:
L.C.Tarshis et al. (1994). Crystal structure of recombinant farnesyl diphosphate synthase at 2.6-A resolution. Biochemistry, 33, 10871-10877. PubMed id: 8086404 DOI: 10.1021/bi00202a004
Date:
30-Jun-94     Release date:   10-Jul-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08836  (FPPS_CHICK) -  Farnesyl pyrophosphate synthase
Seq:
Struc: 		367 a.a.
348 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.2.5.1.1  - Dimethylallyltranstransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Terpenoid biosynthesis
      Reaction: Dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate
Dimethylallyl diphosphate
 + isopentenyl diphosphate
 = diphosphate
 + geranyl diphosphate
   Enzyme class 2: E.C.2.5.1.10  - (2E,6E)-farnesyl diphosphate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: Geranyl diphosphate + isopentenyl diphosphate = diphosphate + (2E,6E)- farnesyl diphosphate
Geranyl diphosphate
 + isopentenyl diphosphate
 = diphosphate
 + (2E,6E)- farnesyl diphosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     lipid biosynthetic process   5 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi00202a004 Biochemistry 33:10871-10877 (1994)
PubMed id: 8086404  
 
 
Crystal structure of recombinant farnesyl diphosphate synthase at 2.6-A resolution.
L.C.Tarshis, M.Yan, C.D.Poulter, J.C.Sacchettini.
 
  ABSTRACT  
 
The synthesis of farnesyl diphosphate (FPP), a key intermediate in the isoprenoid biosynthetic pathway required for the synthesis of cholesterol and in the formation of prenylated proteins, is catalyzed by the enzyme farnesyl diphosphate synthase (FPS). The crystal structure of avian recombinant FPS, the first three-dimensional structure for any prenyltransferase, was determined to 2.6-A resolution. The enzyme exhibits a novel fold composed entirely of alpha-helices joined by connecting loops. The enzyme's most prominent structural feature is the arrangement of 10 core helices around a large central cavity. Two aspartate-rich sequences that are highly conserved among the isoprenyl diphosphate synthase family of prenyltransferases, and are essential for enzymatic activity, were found on opposite walls of this cavity, with the aspartate side chains approximately 12 A apart and facing each other. The location and metal ion binding properties of these sequences suggest that the conserved aspartate residues participate in substrate binding of catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21084289 J.D.Artz, A.K.Wernimont, J.E.Dunford, M.Schapira, A.Dong, Y.Zhao, J.Lew, R.G.Russell, F.H.Ebetino, U.Oppermann, and R.Hui (2011).
Molecular characterization of a novel geranylgeranyl pyrophosphate synthase from Plasmodium parasites.
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PDB codes: 3ldw 3mav 3ph7
21160477 M.Köksal, Y.Jin, R.M.Coates, R.Croteau, and D.W.Christianson (2011).
Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis.
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PDB codes: 3p5p 3p5r
19876942 C.H.Huang, S.B.Gabelli, E.Oldfield, and L.M.Amzel (2010).
Binding of nitrogen-containing bisphosphonates (N-BPs) to the Trypanosoma cruzi farnesyl diphosphate synthase homodimer.
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PDB codes: 3kb9 3kbk 3lg5 3lgk
20229191 M.Fujisawa, H.Harada, H.Kenmoku, S.Mizutani, and N.Misawa (2010).
Cloning and characterization of a novel gene that encodes (S)-beta-bisabolene synthase from ginger, Zingiber officinale.
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19309001 A.H.Taban, C.Tittiger, G.J.Blomquist, and W.H.Welch (2009).
Isolation and characterization of farnesyl diphosphate synthase from the cotton boll weevil, Anthonomus grandis.
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PDB codes: 3dbg 3el3
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PDB codes: 3g4d 3g4f
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Characterization and tissue-specific expression of two lepidopteran farnesyl diphosphate synthase homologs: implications for the biosynthesis of ethyl-substituted juvenile hormones.
  Proteins, 65, 742-758.  
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Structure and mechanism of the farnesyl diphosphate synthase from Trypanosoma cruzi: implications for drug design.
  Proteins, 62, 80-88.
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Biogenesis, molecular regulation and function of plant isoprenoids.
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Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products.
  Nature, 435, 983-987.
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  J Bacteriol, 186, 1747-1757.  
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Structural basis for bisphosphonate-mediated inhibition of isoprenoid biosynthesis.
  J Biol Chem, 279, 8526-8529.
PDB codes: 1rqi 1rqj 1rtr
14763823 J.K.Lee, G.Her, S.Y.Kim, and J.H.Seo (2004).
Cloning and functional expression of the dps gene encoding decaprenyl diphosphate synthase from Agrobacterium tumefaciens.
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Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic Thermotoga maritima and mechanism of product chain length determination.
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PDB codes: 1v4e 1v4h 1v4i 1v4j 1v4k
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Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies.
  Protein Sci, 13, 971-978.
PDB code: 1v7u
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An alternative mechanism of product chain-length determination in type III geranylgeranyl diphosphate synthase.
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  Acta Crystallogr D Biol Crystallogr, 59, 2265-2268.  
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Catalytic mechanism revealed by the crystal structure of undecaprenyl pyrophosphate synthase in complex with sulfate, magnesium, and triton.
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PDB code: 1ueh
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Interaction with the small subunit of geranyl diphosphate synthase modifies the chain length specificity of geranylgeranyl diphosphate synthase to produce geranyl diphosphate.
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11756461 C.C.Huang, C.V.Smith, M.S.Glickman, W.R.Jacobs, and J.C.Sacchettini (2002).
Crystal structures of mycolic acid cyclopropane synthases from Mycobacterium tuberculosis.
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  Proc Natl Acad Sci U S A, 99, 15375-15380.
PDB codes: 1n1b 1n1z 1n20 1n21 1n22 1n23 1n24
12426357 D.Umeno, A.V.Tobias, and F.H.Arnold (2002).
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Predicting amino acid residues responsible for enzyme specificity solely from protein sequences.
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Chiral proton donor reagents: tin tetrachloride--coordinated optically active binaphthol derivatives.
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12084056 J.Lücker, M.K.El Tamer, W.Schwab, F.W.Verstappen, L.H.van der Plas, H.J.Bouwmeester, and H.A.Verhoeven (2002).
Monoterpene biosynthesis in lemon (Citrus limon). cDNA isolation and functional analysis of four monoterpene synthases.
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Dolichol biosynthesis in the yeast Saccharomyces cerevisiae: an insight into the regulatory role of farnesyl diphosphate synthase.
  FEMS Yeast Res, 2, 259-265.  
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Oncoviral bovine leukemia virus G4 and human T-cell leukemia virus type 1 p13(II) accessory proteins interact with farnesyl pyrophosphate synthetase.
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12135497 M.Brodelius, A.Lundgren, P.Mercke, and P.E.Brodelius (2002).
Fusion of farnesyldiphosphate synthase and epi-aristolochene synthase, a sesquiterpene cyclase involved in capsidiol biosynthesis in Nicotiana tabacum.
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Structure, mechanism and function of prenyltransferases.
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Molecular scaffolds for chemical wizardry: learning nature's rules for terpene cyclases.
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Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase.
  Proc Natl Acad Sci U S A, 98, 4337-4342.
PDB code: 1f75
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Structure of trichodiene synthase from Fusarium sporotrichioides provides mechanistic inferences on the terpene cyclization cascade.
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PDB codes: 1jfa 1jfg
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Metabolic engineering of isoprenoids.
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11287653 S.B.Rivera, B.D.Swedlund, G.J.King, R.N.Bell, C.E.Hussey, D.M.Shattuck-Eidens, W.M.Wrobel, G.D.Peiser, and C.D.Poulter (2001).
Chrysanthemyl diphosphate synthase: isolation of the gene and characterization of the recombinant non-head-to-tail monoterpene synthase from Chrysanthemum cinerariaefolium.
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Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis.
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PDB code: 1jp3
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Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: site-directed mutagenesis of highly conserved residues.
  Biochemistry, 40, 1734-1740.  
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Geranylgeranyl diphosphate synthase from Scoparia dulcis and Croton sublyratus. Plastid localization and conversion to a farnesyl diphosphate synthase by mutagenesis.
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10688662 D.Vicent, E.Maratos-Flier, and C.R.Kahn (2000).
The branch point enzyme of the mevalonate pathway for protein prenylation is overexpressed in the ob/ob mouse and induced by adipogenesis.
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Squalene synthase: steady-state, pre-steady-state, and isotope-trapping studies.
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Effect of site-directed mutagenesis of the conserved aspartate and glutamate on E. coli undecaprenyl pyrophosphate synthase catalysis.
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Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data.
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Mechanism of product chain length determination for heptaprenyl diphosphate synthase from Bacillus stearothermophilus.
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Farnesyl diphosphate synthase. Altering the catalytic site to select for geranyl diphosphate activity.
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Intersubunit location of the active site of farnesyl diphosphate synthase: reconstruction of active enzymes by hybrid-type heteromeric dimers of site-directed mutants.
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Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase.
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