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Phyre 2 Results for Q2FV59

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Email [email protected] Description Q2FV59 Tue Jul 17 17:05:54 BST Date 2012 Unique Job 2b2080859139b16d ID Detailed template information # Template Alignment Coverage 3D Model Confidence % i.d. Template Information PDB header:transferase Chain: A: PDB Molecule:dehydrosqualene synthase; 1 c2zcpA_ Alignment 100.0 99 PDBTitle: crystal structure of the c(30) carotenoid dehydrosqualene2 synthase from staphylococcus aureus complexed with3 farnesyl thiopyrophosphate Fold:Terpenoid synthases 2 d1ezfa_ Alignment 100.0 18 Superfamily:Terpenoid synthases Family:Squalene synthase PDB header:transferase Chain: G: PDB Molecule:geranyl diphosphate synthase; 3 c3aq0G_ Alignment 98.4 15 PDBTitle: ligand-bound form of arabidopsis medium/long-chain length prenyl2 pyrophosphate synthase (surface polar residue mutant) Fold:Terpenoid synthases 4 d2q80a1 Alignment 98.0 12 Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases PDB header:transferase Chain: A: PDB Molecule:polyprenyl synthetase; 5 c4dhdA_ 97.9 13 Alignment PDBTitle: crystal structure of isoprenoid synthase a3msh1 (target efi-501992)2 from pyrobaculum calidifontis PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate 6 c1wy0A_ Alignment 97.9 13 synthetase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthetase from2 pyrococcus horikoshii ot3 Fold:Terpenoid synthases 7 d1v4ea_ Alignment 97.8 15 Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases PDB header:transferase Chain: D: PDB Molecule:farnesyl-diphosphate synthase; 8 c3m9uD_ 97.7 10 Alignment PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase2 from lactobacillus brevis atcc 367 PDB header:transferase Chain: B: PDB Molecule:decaprenyl diphosphate synthase; 9 c3mzvB_ 97.7 11 Alignment PDBTitle: crystal structure of a decaprenyl diphosphate synthase from2 rhodobacter capsulatus PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate synthase; 10 c3n3dB_ 97.6 13 Alignment PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase from2 lactobacillus brevis atcc 367 PDB header:transferase Chain: B: PDB Molecule:trans-isoprenyl diphosphate synthase; 11 c3oyrB_ Alignment 97.4 11 PDBTitle: crystal structure of polyprenyl synthase from caulobacter crescentus2 cb15 complexed with calcium and isoprenyl diphosphate PDB header:transferase Chain: A: PDB Molecule:putative polyprenyl synthetase; 12 c3nf2A_ 97.3 14 Alignment PDBTitle: crystal structure of polyprenyl synthetase from streptomyces2 coelicolor a3(2) PDB header:transferase Chain: B: PDB Molecule:octaprenyl-diphosphate synthase; 13 c3rmgB_ 97.2 10 Alignment PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase from2 bacteroides thetaiotaomicron PDB header:transferase Chain: D: PDB Molecule:component b of hexaprenyl diphosphate 14 c3aqbD_ Alignment 97.1 15 synthase; PDBTitle: m. luteus b-p 26 heterodimeric hexaprenyl diphosphate synthase in2 complex with magnesium PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate 15 c2e8xB_ Alignment 97.0 16 synthetase; PDBTitle: s. cerevisiae geranylgeranyl pyrophosphate synthase in2 complex with magnesium and gpp PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthase; 16 c3lmdA_ 96.6 8 Alignment PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase2 from corynebacterium glutamicum atcc 13032 PDB header:transferase Chain: A: PDB Molecule:octaprenyl pyrophosphate synthase; 17 c3tc1A_ 96.6 15 Alignment PDBTitle: crystal structure of octaprenyl pyrophosphate synthase from2 helicobacter pylori Fold:Terpenoid synthases 18 d1rtra_ Alignment 96.4 11 Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; 19 c3ts7B_ 96.2 12 Alignment PDBTitle: crystal structure of farnesyl diphosphate synthase (target efi-501951)2 from methylococcus capsulatus PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthase; 20 c3lk5A_ 95.7 12 Alignment PDBTitle: crystal structure of putative geranylgeranyl pyrophosphate synthase2 from corynebacterium glutamicum PDB header:transferase Chain: A: PDB Molecule:trans-isoprenyl diphosphate synthase; 21 c3oyrA_ Alignment not modelled 95.4 10 PDBTitle: crystal structure of polyprenyl synthase from caulobacter crescentus2 cb15 complexed with calcium and isoprenyl diphosphate PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; 22 c3ucaB_ not modelled 95.3 15 Alignment PDBTitle: crystal structure of isoprenoid synthase (target efi- 501974) from2 clostridium perfringens PDB header:transferase Chain: B: PDB Molecule:farnesyl diphosphate synthase; 23 c3m0gB_ not modelled 94.8 18 Alignment PDBTitle: crystal structure of putative farnesyl diphosphate synthase from2 rhodobacter capsulatus PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; 24 c3ipiA_ not modelled 94.5 11 Alignment PDBTitle: crystal structure of a geranyltranstransferase from the2 methanosarcina mazei PDB header:transferase Chain: A: PDB Molecule:farnesyl pyrophosphate synthetase; 25 c3cp6A_ not modelled 94.4 15 Alignment PDBTitle: crystal structure of human farnesyl diphosphate synthase (t201a2 mutant) complexed with mg and biphosphonate inhibitor PDB header:lyase Chain: A: PDB Molecule:isoprene synthase; 26 c3n0fA_ not modelled 94.4 14 Alignment PDBTitle: crystal structure of isoprene synthase from grey poplar leaves2 (populus x canescens) PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate 27 c2azjB_ Alignment not modelled 94.4 12 synthetase; PDBTitle: crystal structure for the mutant d81c of sulfolobus2 solfataricus hexaprenyl pyrophosphate synthase PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl diphosphate synthetase; 28 c1wmwA_ Alignment not modelled 94.3 17 28 c1wmwA_ not modelled 94.3 17 Alignment PDBTitle: crystal structure of geranulgeranyl diphosphate synthase from thermus2 thermophilus PDB header:lyase Chain: A: PDB Molecule:epi-isozizaene synthase; 29 c3lg5A_ not modelled 93.9 11 Alignment PDBTitle: f198a epi-isozizaene synthase: complex with mg, inorganic2 pyrophosphate and benzyl triethyl ammonium cation Fold:Terpenoid synthases 30 d1fpsa_ Alignment not modelled 93.2 13 Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases PDB header:transferase Chain: A: PDB Molecule:farnesyl pyrophosphate synthase; 31 c1yhlA_ not modelled 93.0 17 Alignment PDBTitle: structure of the complex of trypanosoma cruzi farnesyl diphosphate2 synthase with risedronate, dmapp and mg+2 PDB header:lyase 32 c1hx9A_ Alignment not modelled 93.0 15 Chain: A: PDB Molecule:5-epi-aristolochene synthase; PDBTitle: crystal structure of teas w273s form 1 Fold:Terpenoid synthases 33 d5easa2 Alignment not modelled 92.2 15 Superfamily:Terpenoid synthases Family:Terpenoid cyclase C-terminal domain PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate 34 c2j1pB_ Alignment not modelled 92.1 16 synthetase; PDBTitle: geranylgeranyl diphosphate synthase from sinapis alba in2 complex with ggpp Fold:Terpenoid synthases 35 d1rqja_ Alignment not modelled 91.5 13 Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases PDB header:lyase Chain: B: PDB Molecule:(+)-delta-cadinene synthase isozyme xc1; 36 c3g4dB_ not modelled 91.3 17 Alignment PDBTitle: crystal structure of (+)-delta-cadinene synthase from gossypium2 arboreum and evolutionary divergence of metal binding motifs for3 catalysis PDB header:isomerase Chain: A: PDB Molecule:(+)-bornyl diphosphate synthase; 37 c1n20A_ not modelled 90.5 15 Alignment PDBTitle: (+)-bornyl diphosphate synthase: complex with mg and 3-aza-2 2,3-dihydrogeranyl diphosphate Fold:Terpenoid synthases 38 d1n1ba2 Alignment not modelled 90.3 14 Superfamily:Terpenoid synthases Family:Terpenoid cyclase C-terminal domain PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative farnesyl pyrophosphate 39 c2o1oB_ Alignment not modelled 90.1 14 synthase; PDBTitle: cryptosporidium parvum putative polyprenyl pyrophosphate2 synthase (cgd4_2550) in complex with risedronate. PDB header:lyase Chain: A: PDB Molecule:farnesyl pyrophosphate synthase, putative; 40 c3ez3A_ not modelled 89.9 13 Alignment PDBTitle: crystal structure of plasmodium vivax geranylgeranylpyrophosphate2 synthase pvx_092040 with zoledronate and ipp bound PDB header:transferase Chain: F: PDB Molecule:farnesyl diphosphate synthase; 41 c2f94F_ not modelled 88.7 15 Alignment PDBTitle: crystal structure of human fpps in complex with ibandronate PDB header:transferase Chain: B: PDB Molecule:geranyl diphosphate synthase small 42 c3qkcB_ Alignment not modelled 87.8 13 subunit; PDBTitle: crystal structure of geranyl diphosphate synthase small subunit from2 antirrhinum majus Fold:Terpenoid synthases 43 d1ps1a_ Alignment not modelled 86.9 7 Superfamily:Terpenoid synthases Family:Aristolochene/pentalenene synthase PDB header:lyase Chain: B: PDB Molecule:1,8-cineole synthase; 44 c2j5cB_ Alignment not modelled 85.0 14 PDBTitle: rational conversion of substrate and product specificity2 in a monoterpene synthase. structural insights into the3 molecular basis of rapid evolution. PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; 45 c3p8rA_ not modelled 84.7 14 Alignment PDBTitle: crystal structure of polyprenyl synthase from vibrio cholerae PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; 46 c3p8lB_ not modelled 84.5 13 Alignment PDBTitle:
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  • Developmental Changes in Scots Pine Transcriptome During Heartwood Formation

    Developmental Changes in Scots Pine Transcriptome During Heartwood Formation

    Developmental changes in Scots pine transcriptome during heartwood formation Kean-Jin Lim, Tanja Paasela, Teemu Teeri University of Helsinki Anni Harju, Martti Venäläinen, Katri Kärkkäinen Luke Punkaharju, June 2016 Heartwood of Scots pine (Pinus sylvestris) is naturally decay resistant Variation in wood extractives correlates with decay resistance — Variation in wood extractives is large and mostly genetic Trees higest in heartwood extractives are most decay resistant. Harju & Venäläinen 2006. Can J. For Res. Heartwood — Does not contain living cells — Reserve materials (e.g. starch) have been converted to ”heartwood substances” — May have different color, lower permeability and increased decay resistance than sapwood — In conifers, heartwood is usually dryer than sapwood Robinia Pinus Picea Heartwood formation Magel 2000 — Type 1 heartwood: Accumulation of (phenolic) extractives takes place in tissue between sapwood and heartwood (transition zone). — Type 2 heartwood: Precursors to phenolics accumulate gradually in ageing sapwood. — Pine heartwood is thought to be of Type 2. Heartwood formation — Much evidence in literature summarizes that heartwood formation takes place during the dormant season. — Pine — From midsummer to autumn (Fukuzawa et al. 1980) — From midsummer to dormant season (Shain and Mackay 1973) — No specific period for heartwood formation (Bergström et al. 1999) Heartwood extractives in Scots pine — Resin acids abietic acid — 50% of heartwood extractives — Stilbenes — 15% of heartwood extractives — Free fatty acids
  • Combining Metabolic and Protein Engineering of a Terpenoid Biosynthetic Pathway for Overproduction and Selectivity Control

    Combining Metabolic and Protein Engineering of a Terpenoid Biosynthetic Pathway for Overproduction and Selectivity Control

    Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control Effendi Leonarda,1, Parayil Kumaran Ajikumara,1, Kelly Thayerb,c,d,3, Wen-Hai Xiaoa, Jeffrey D. Moa, Bruce Tidorb,c,d, Gregory Stephanopoulosa, and Kristala L. J. Prathera,2 aDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; bComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139; cDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; and dDepartment of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139 Edited* by Arnold L. Demain, Drew University, Madison, NJ, and approved June 22, 2010 (received for review May 4, 2010) A common strategy of metabolic engineering is to increase the en- Sequence analysis of these enzymes showed that they are para- dogenous supply of precursor metabolites to improve pathway logous proteins evolved through gene duplications that subse- productivity. The ability to further enhance heterologous produc- quently diverged in functional roles to catalyze the formation tion of a desired compound may be limited by the inherent capacity of different terpenoid structures (16, 17, 19). Particularly, terpe- of the imported pathway to accommodate high precursor supply. noid synthases generate enzyme-bound carbocation intermedi- Here, we present engineered diterpenoid biosynthesis as a case ates that undergo a cascade of rearrangements and quenchings of where insufficient downstream pathway capacity limits high- carbocations to create structural diversity (20). These enzymes level levopimaradiene production in Escherichia coli. To increase are highly promiscuous (21), and the functional promiscuity is levopimaradiene synthesis, we amplified the flux toward isopen- often associated with unwanted product formation and poor cat- tenyl diphosphate and dimethylallyl diphosphate precursors and alytic properties (22).