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PDBsum entry 5eat
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Isoprenoid synthase PDB id
5eat

 

 

 

 

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Contents
Protein chain
532 a.a. *
Ligands
FHP
Metals
_MG ×3
Waters ×157
* Residue conservation analysis
PDB id:
5eat
Name: Isoprenoid synthase
Title: 5-epi-aristolochene synthase from nicotiana tabacum with substrate analog farnesyl hydroxyphosphonate
Structure: 5-epi-aristolochene synthase. Chain: a. Synonym: 5-epi-aristolochene cyclase. Engineered: yes
Source: Nicotiana tabacum. Common tobacco. Organism_taxid: 4097. Strain: nk326. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.80Å     R-factor:   0.240     R-free:   0.280
Authors: C.M.Starks,K.Back,J.Chappell,J.P.Noel
Key ref:
C.M.Starks et al. (1997). Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase. Science, 277, 1815-1820. PubMed id: 9295271 DOI: 10.1126/science.277.5333.1815
Date:
24-Jul-97     Release date:   12-Nov-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q40577  (5EAS_TOBAC) -  5-epi-aristolochene synthase from Nicotiana tabacum
Seq:
Struc: 		 
Seq:
Struc: 		548 a.a.
532 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.2.3.61  - 5-epiaristolochene synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (2E,6E)-farnesyl diphosphate = +-5-epi-aristolochene + diphosphate
(2E,6E)-farnesyl diphosphate
Bound ligand (Het Group name = FHP)
matches with 57.14% similarity 		= (+)-5-epi-aristolochene
 + diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1126/science.277.5333.1815 Science 277:1815-1820 (1997)
PubMed id: 9295271  
 
 
Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase.
C.M.Starks, K.Back, J.Chappell, J.P.Noel.
 
  ABSTRACT  
 
Terpene cyclases catalyze the synthesis of cyclic terpenes with 10-, 15-, and 20-carbon acyclic isoprenoid diphosphates as substrates. Plants have been a source of these natural products by providing a homologous set of terpene synthases. The crystal structures of 5-epi-aristolochene synthase, a sesquiterpene cyclase from tobacco, alone and complexed separately with two farnesyl diphosphate analogs were analyzed. These structures reveal an unexpected enzymatic mechanism for the synthesis of the bicyclic product, 5-epi-aristolochene, and provide a basis for understanding the stereochemical selectivity displayed by other cyclases in the biosynthesis of pharmacologically important cyclic terpenes. As such, these structures provide templates for the engineering of novel terpene cyclases.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereo views of the TEAS active site. Blue dashed lines are hydrogen bonds; green dashed lines are coordination bonds. The^ top panel illustrates the TEAS·FHP complex. FHP is emphasized^ with dark gray bonds. The lower panel illustrates the TEAS·F[3]FPP complex. The diphosphate moiety is emphasized with dark bonds. The rest of the F[3]-FPP molecule, which exhibits weak electron density, is indicated with dashed bonds. Figure was prepared with MOLSCRIPT (24) and RASTER3D (24). 		Figure 3.
Fig. 3. Proposed catalytic mechanisms of TEAS and HVS based on the TEAS crystal structures. (A) through (F) are reaction steps common to both TEAS and HVS. (G[1]) through (I[1]) are specific to TEAS, and (G[2]) through (I[2]) are^ specific to HVS. Carbocations are yellow, protons are light blue, and aromatic quadrupoles are indicated with purple lines. Intermediate^ structures are numbered according to the acyclic precursor, FPP (A). Figure was generated with Chem3D (CambridgeSoft).
 
  The above figures are reprinted by permission from the AAAs: Science (1997, 277, 1815-1820) copyright 1997.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom.
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21305070 K.Zhou, and R.J.Peters (2011).
Electrostatic effects on (di)terpene synthase product outcome.
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Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis.
  Nature, 469, 116-120.
PDB codes: 3p5p 3p5r
21455271 N.M.Burton, and L.J.Bruce (2011).
Modelling the structure of the red cell membrane.
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20419468 C.Crocoll, J.Asbach, J.Novak, J.Gershenzon, and J.Degenhardt (2010).
Terpene synthases of oregano (Origanum vulgare L.) and their roles in the pathway and regulation of terpene biosynthesis.
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20964856 D.M.Martin, S.Aubourg, M.B.Schouwey, L.Daviet, M.Schalk, O.Toub, S.T.Lund, and J.Bohlmann (2010).
Functional annotation, genome organization and phylogeny of the grapevine (Vitis vinifera) terpene synthase gene family based on genome assembly, FLcDNA cloning, and enzyme assays.
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20643967 E.Leonard, P.K.Ajikumar, K.Thayer, W.H.Xiao, J.D.Mo, B.Tidor, G.Stephanopoulos, and K.L.Prather (2010).
Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control.
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20419721 F.Lopez-Gallego, S.A.Agger, D.Abate-Pella, M.D.Distefano, and C.Schmidt-Dannert (2010).
Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus: catalytic promiscuity and cyclization of farnesyl pyrophosphate geometric isomers.
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21098670 F.Y.Lin, C.I.Liu, Y.L.Liu, Y.Zhang, K.Wang, W.Y.Jeng, T.P.Ko, R.Cao, A.H.Wang, and E.Oldfield (2010).
Mechanism of action and inhibition of dehydrosqualene synthase.
  Proc Natl Acad Sci U S A, 107, 21337-21342.
PDB codes: 3acw 3acx 3acy 3adz 3ae0 3lgz 3npr 3nri
20131801 J.A.Aaron, X.Lin, D.E.Cane, and D.W.Christianson (2010).
Structure of epi-isozizaene synthase from Streptomyces coelicolor A3(2), a platform for new terpenoid cyclization templates.
  Biochemistry, 49, 1787-1797.
PDB codes: 3kb9 3kbk 3lg5 3lgk
  20175559 J.P.Noel, N.Dellas, J.A.Faraldos, M.Zhao, B.A.Hess, L.Smentek, R.M.Coates, and P.E.O'Maille (2010).
Structural elucidation of cisoid and transoid cyclization pathways of a sesquiterpene synthase using 2-fluorofarnesyl diphosphates.
  ACS Chem Biol, 5, 377-392.
PDB codes: 3lz9 3m00 3m01 3m02
20074143 K.G.Zulak, and J.Bohlmann (2010).
Terpenoid biosynthesis and specialized vascular cells of conifer defense.
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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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  20975893 P.Alam, U.Kiran, M.M.Ahmad, Kamaluddin, M.A.Khan, S.Jhanwar, and M.Abdin (2010).
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20602361 R.Cao, Y.Zhang, F.M.Mann, C.Huang, D.Mukkamala, M.P.Hudock, M.E.Mead, S.Prisic, K.Wang, F.Y.Lin, T.K.Chang, R.J.Peters, and E.Oldfield (2010).
Diterpene cyclases and the nature of the isoprene fold.
  Proteins, 78, 2417-2432.  
19858213 B.Zhao, L.Lei, D.G.Vassylyev, X.Lin, D.E.Cane, S.L.Kelly, H.Yuan, D.C.Lamb, and M.R.Waterman (2009).
Crystal structure of albaflavenone monooxygenase containing a moonlighting terpene synthase active site.
  J Biol Chem, 284, 36711-36719.
PDB codes: 3dbg 3el3
19547916 F.Yu, and R.Utsumi (2009).
Diversity, regulation, and genetic manipulation of plant mono- and sesquiterpenoid biosynthesis.
  Cell Mol Life Sci, 66, 3043-3052.  
19489610 H.A.Gennadios, V.Gonzalez, L.Di Costanzo, A.Li, F.Yu, D.J.Miller, R.K.Allemann, and D.W.Christianson (2009).
Crystal structure of (+)-delta-cadinene synthase from Gossypium arboreum and evolutionary divergence of metal binding motifs for catalysis.
  Biochemistry, 48, 6175-6183.
PDB codes: 3g4d 3g4f
19201430 K.Zhou, and R.J.Peters (2009).
Investigating the conservation pattern of a putative second terpene synthase divalent metal binding motif in plants.
  Phytochemistry, 70, 366-369.  
19181671 S.Green, C.J.Squire, N.J.Nieuwenhuizen, E.N.Baker, and W.Laing (2009).
Defining the potassium binding region in an apple terpene synthase.
  J Biol Chem, 284, 8661-8669.  
19635410 S.Y.Kim, P.Zhao, M.Igarashi, R.Sawa, T.Tomita, M.Nishiyama, and T.Kuzuyama (2009).
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  Chem Biol, 16, 736-743.  
18198275 C.I.Keeling, S.Weisshaar, R.P.Lin, and J.Bohlmann (2008).
Functional plasticity of paralogous diterpene synthases involved in conifer defense.
  Proc Natl Acad Sci U S A, 105, 1085-1090.  
18493792 D.Köpke, R.Schröder, H.M.Fischer, J.Gershenzon, M.Hilker, and A.Schmidt (2008).
Does egg deposition by herbivorous pine sawflies affect transcription of sesquiterpene synthases in pine?
  Planta, 228, 427-438.  
18249199 D.W.Christianson (2008).
Unearthing the roots of the terpenome.
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18385128 E.Y.Shishova, F.Yu, D.J.Miller, J.A.Faraldos, Y.Zhao, R.M.Coates, R.K.Allemann, D.E.Cane, and D.W.Christianson (2008).
X-ray crystallographic studies of substrate binding to aristolochene synthase suggest a metal ion binding sequence for catalysis.
  J Biol Chem, 283, 15431-15439.
PDB codes: 3bnx 3bny 3cke
18476870 J.Bohlmann, and C.I.Keeling (2008).
Terpenoid biomaterials.
  Plant J, 54, 656-669.  
18663389 J.Kirby, and J.D.Keasling (2008).
Metabolic engineering of microorganisms for isoprenoid production.
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  Annu Rev Biochem, 77, 521-555.  
18347585 M.B.Austin, P.E.O'Maille, and J.P.Noel (2008).
Evolving biosynthetic tangos negotiate mechanistic landscapes.
  Nat Chem Biol, 4, 217-222.  
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Identification and functional analysis of genes controlling biosynthesis of 2-methylisoborneol.
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Molecular analysis of a 4-dimethylallyltryptophan synthase from Malbranchea aurantiaca.
  J Biol Chem, 283, 16068-16076.  
17440821 C.C.van Schie, M.A.Haring, and R.C.Schuurink (2007).
Tomato linalool synthase is induced in trichomes by jasmonic acid.
  Plant Mol Biol, 64, 251-263.  
17372193 D.C.Hyatt, B.Youn, Y.Zhao, B.Santhamma, R.M.Coates, R.B.Croteau, and C.Kang (2007).
Structure of limonene synthase, a simple model for terpenoid cyclase catalysis.
  Proc Natl Acad Sci U S A, 104, 5360-5365.
PDB codes: 2ong 2onh
17261032 E.Y.Shishova, L.Di Costanzo, D.E.Cane, and D.W.Christianson (2007).
X-ray crystal structure of aristolochene synthase from Aspergillus terreus and evolution of templates for the cyclization of farnesyl diphosphate.
  Biochemistry, 46, 1941-1951.
PDB codes: 2e4o 2oa6
17925960 F.Yu, D.J.Miller, and R.K.Allemann (2007).
Probing the reaction mechanism of aristolochene synthase with 12,13-difluorofarnesyl diphosphate.
  Chem Commun (Camb), (), 4155-4157.  
17886322 J.A.Faraldos, Y.Zhao, P.E.O'Maille, J.P.Noel, and R.M.Coates (2007).
Interception of the enzymatic conversion of farnesyl diphosphate to 5-epi-aristolochene by using a fluoro substrate analogue: 1-fluorogermacrene A from (2E,6Z)-6-fluorofarnesyl diphosphate.
  Chembiochem, 8, 1826-1833.  
17873868 J.Jiang, X.He, and D.E.Cane (2007).
Biosynthesis of the earthy odorant geosmin by a bifunctional Streptomyces coelicolor enzyme.
  Nat Chem Biol, 3, 711-715.  
17456599 M.Xu, P.R.Wilderman, and R.J.Peters (2007).
Following evolution's lead to a single residue switch for diterpene synthase product outcome.
  Proc Natl Acad Sci U S A, 104, 7397-7401.  
17653361 S.Schulz, and J.S.Dickschat (2007).
Bacterial volatiles: the smell of small organisms.
  Nat Prod Rep, 24, 814-842.  
17115212 S.T.Withers, and J.D.Keasling (2007).
Biosynthesis and engineering of isoprenoid small molecules.
  Appl Microbiol Biotechnol, 73, 980-990.  
17013941 S.Takahashi, Y.Yeo, B.T.Greenhagen, T.McMullin, L.Song, J.Maurina-Brunker, R.Rosson, J.P.Noel, and J.Chappell (2007).
Metabolic engineering of sesquiterpene metabolism in yeast.
  Biotechnol Bioeng, 97, 170-181.  
16785438 B.T.Greenhagen, P.E.O'Maille, J.P.Noel, and J.Chappell (2006).
Identifying and manipulating structural determinates linking catalytic specificities in terpene synthases.
  Proc Natl Acad Sci U S A, 103, 9826-9831.  
16684230 C.I.Keeling, and J.Bohlmann (2006).
Genes, enzymes and chemicals of terpenoid diversity in the constitutive and induced defence of conifers against insects and pathogens.
  New Phytol, 170, 657-675.  
16547477 D.E.Cane (2006).
How to evolve a silk purse from a sow's ear.
  Nat Chem Biol, 2, 179-180.  
16600670 D.Tholl (2006).
Terpene synthases and the regulation, diversity and biological roles of terpene metabolism.
  Curr Opin Plant Biol, 9, 297-304.  
16555072 R.G.Kerr, A.C.Kohl, and T.A.Ferns (2006).
Elucidation of the biosynthetic origin of the anti-inflammatory pseudopterosins.
  J Ind Microbiol Biotechnol, 33, 532-538.  
16791319 S.Forcat, and R.K.Allemann (2006).
Stabilisation of transition states prior to and following eudesmane cation in aristolochene synthase.
  Org Biomol Chem, 4, 2563-2567.  
16495946 Y.Yoshikuni, T.E.Ferrin, and J.D.Keasling (2006).
Designed divergent evolution of enzyme function.
  Nature, 440, 1078-1082.  
16289312 F.Bouvier, A.Rahier, and B.Camara (2005).
Biogenesis, molecular regulation and function of plant isoprenoids.
  Prog Lipid Res, 44, 357-429.  
15789564 L.A.Wessjohann, E.Ruijter, D.Garcia-Rivera, and W.Brandt (2005).
What can a chemist learn from nature's macrocycles?--a brief, conceptual view.
  Mol Divers, 9, 171-186.  
16171386 L.S.Vedula, D.E.Cane, and D.W.Christianson (2005).
Role of arginine-304 in the diphosphate-triggered active site closure mechanism of trichodiene synthase.
  Biochemistry, 44, 12719-12727.
PDB codes: 2aek 2ael 2aet
15834787 Y.J.Chang, J.Jin, H.Y.Nam, and S.U.Kim (2005).
Point mutation of (+)-germacrene A synthase from Ixeris dentata.
  Biotechnol Lett, 27, 285-288.  
17191831 A.Goeke, D.Mertl, and G.Brunner (2004).
A novel approach to prezizaane sesquiterpenes.
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15113001 D.J.Reinert, G.Balliano, and G.E.Schulz (2004).
Conversion of squalene to the pentacarbocyclic hopene.
  Chem Biol, 11, 121-126.
PDB code: 1ump
15255861 M.Xu, M.L.Hillwig, S.Prisic, R.M.Coates, and R.J.Peters (2004).
Functional identification of rice syn-copalyl diphosphate synthase and its role in initiating biosynthesis of diterpenoid phytoalexin/allelopathic natural products.
  Plant J, 39, 309-318.  
12556563 D.E.Cane, and R.M.Watt (2003).
Expression and mechanistic analysis of a germacradienol synthase from Streptomyces coelicolor implicated in geosmin biosynthesis.
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Attracting friends to feast on foes: engineering terpene emission to make crop plants more attractive to herbivore enemies.
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12432096 D.A.Whittington, M.L.Wise, M.Urbansky, R.M.Coates, R.B.Croteau, and D.W.Christianson (2002).
Bornyl diphosphate synthase: structure and strategy for carbocation manipulation by a terpenoid cyclase.
  Proc Natl Acad Sci U S A, 99, 15375-15380.
PDB codes: 1n1b 1n1z 1n20 1n21 1n22 1n23 1n24
12112869 H.Ishibashi, K.Ishihara, and H.Yamamoto (2002).
Chiral proton donor reagents: tin tetrachloride--coordinated optically active binaphthol derivatives.
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Monoterpene biosynthesis in lemon (Citrus limon). cDNA isolation and functional analysis of four monoterpene synthases.
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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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11827517 M.J.Rynkiewicz, D.E.Cane, and D.W.Christianson (2002).
X-ray crystal structures of D100E trichodiene synthase and its pyrophosphate complex reveal the basis for terpene product diversity.
  Biochemistry, 41, 1732-1741.
PDB codes: 1kiy 1kiz
12135472 P.H.Liang, T.P.Ko, and A.H.Wang (2002).
Structure, mechanism and function of prenyltransferases.
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11805316 R.J.Peters, and R.B.Croteau (2002).
Abietadiene synthase catalysis: mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement.
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12033511 T.Maruyama, D.Saeki, M.Ito, and G.Honda (2002).
Molecular cloning, functional expression and characterization of d-limonene synthase from Agastache rugosa.
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11717417 B.Greenhagen, and J.Chappell (2001).
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
11698643 M.J.Rynkiewicz, D.E.Cane, and D.W.Christianson (2001).
Structure of trichodiene synthase from Fusarium sporotrichioides provides mechanistic inferences on the terpene cyclization cascade.
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PDB codes: 1jfa 1jfg
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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Genomic organization of plant terpene synthases and molecular evolutionary implications.
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Molecular cloning, functional expression and characterization of d-limonene synthase from Schizonepeta tenuifolia.
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Molecular cloning, functional expression and characterization of (E)-beta farnesene synthase from Citrus junos.
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Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: site-directed mutagenesis of highly conserved residues.
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Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase.
  EMBO J, 20, 1530-1537.
PDB codes: 1hx3 1hzt
11745124 V.J.Martin, Y.Yoshikuni, and J.D.Keasling (2001).
The in vivo synthesis of plant sesquiterpenes by Escherichia coli.
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Enzyme Mechanisms for Polycyclic Triterpene Formation.
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Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme.
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Structure and regulation of mammalian squalene synthase.
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Isolation of a (+)- delta-cadinene synthase gene CAD1-A and analysis of its expression pattern in seedlings ofGossypium arboreum L.
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Diterpene synthesis in Stevia rebaudiana: recruitment and up-regulation of key enzymes from the gibberellin biosynthetic pathway.
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Use of genomics to identify bacterial undecaprenyl pyrophosphate synthetase: cloning, expression, and characterization of the essential uppS gene.
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Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli.
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Crystal structure of thiamin phosphate synthase from Bacillus subtilis at 1.25 A resolution.
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PDB code: 2tps
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Chain-length determination mechanism of isoprenyl diphosphate synthases and implications for molecular evolution.
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Crystallization and preliminary X-ray diffraction studies of undecaprenyl diphosphate synthase from Micrococcus luteus B-P 26.
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Plant natural products: the molecular genetic basis of biosynthetic diversity.
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Managing and manipulating carbocations in biology: terpenoid cyclase structure and mechanism.
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Truncation of limonene synthase preprotein provides a fully active 'pseudomature' form of this monoterpene cyclase and reveals the function of the amino-terminal arginine pair.
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Plant terpenoid synthases: molecular biology and phylogenetic analysis.
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Terpenoid-based defenses in conifers: cDNA cloning, characterization, and functional expression of wound-inducible (E)-alpha-bisabolene synthase from grand fir (Abies grandis).
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Isoprenoid biosynthesis: manifold chemistry catalyzed by similar enzymes.
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Germacrene C synthase from Lycopersicon esculentum cv. VFNT cherry tomato: cDNA isolation, characterization, and bacterial expression of the multiple product sesquiterpene cyclase.
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Structural studies of natural product biosynthetic proteins.
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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