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Email [email protected] Description O75828 Thu Apr 26 09:31:29 BST Date 2012 Unique Job a4625e2a2da66506 ID Detailed template information # Template Alignment Coverage 3D Model Confidence % i.d. Template Information Fold:NAD(P)-binding Rossmann-fold domains 1 d1wmaa1 Alignment 100.0 72 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases Fold:NAD(P)-binding Rossmann-fold domains 2 d1n5da_ Alignment 100.0 70 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: A: PDB Molecule:salutaridine reductase; 3 c3o26A_ 100.0 28 Alignment PDBTitle: the structure of salutaridine reductase from papaver somniferum. PDB header:oxidoreductase Chain: A: PDB Molecule:dehydrogenase with different 4 c3cxtA_ Alignment 100.0 23 specificities; PDBTitle: quaternary complex structure of gluconate 5- dehydrogenase from2 streptococcus suis type 2 Fold:NAD(P)-binding Rossmann-fold domains 5 d1snya_ Alignment 100.0 18 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: A: PDB Molecule:3-oxoacyl-(acyl-carrier protein) 6 c2c07A_ 100.0 23 Alignment reductase; PDBTitle: oxoacyl-acp reductase of plasmodium falciparum Fold:NAD(P)-binding Rossmann-fold domains 7 d2c07a1 Alignment 100.0 23 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: C: PDB Molecule:carveol dehydrogenase; 8 c3t7cC_ 100.0 28 Alignment PDBTitle: crystal structure of carveol dehydrogenase from mycobacterium avium2 bound to nad PDB header:oxidoreductase Chain: B: PDB Molecule:oxidoreductase, short chain 9 c3i1jB_ Alignment 100.0 27 dehydrogenase/reductase family; PDBTitle: structure of a putative short chain dehydrogenase from pseudomonas2 syringae PDB header:oxidoreductase Chain: A: PDB Molecule:short chain dehydrogenase; 10 c3imfA_ 100.0 23 Alignment PDBTitle: 1.99 angstrom resolution crystal structure of a short chain2 dehydrogenase from bacillus anthracis str. 'ames ancestor' PDB header:oxidoreductase Chain: A: PDB Molecule:l-xylulose reductase; 11 c4egfA_ 100.0 26 Alignment PDBTitle: crystal structure of a l-xylulose reductase from mycobacterium2 smegmatis Fold:NAD(P)-binding Rossmann-fold domains 12 d1h5qa_ Alignment 100.0 25 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: C: PDB Molecule:short chain dehydrogenase; 13 c3e03C_ 100.0 24 Alignment PDBTitle: crystal structure of a putative dehydrogenase from2 xanthomonas campestris Fold:NAD(P)-binding Rossmann-fold domains 14 d1yxma1 Alignment 100.0 30 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: B: PDB Molecule:d-beta-hydroxybutyrate dehydrogenase; 15 c3v2hB_ 100.0 26 Alignment PDBTitle: the crystal structure of d-beta-hydroxybutyrate dehydrogenase from2 sinorhizobium meliloti Fold:NAD(P)-binding Rossmann-fold domains 16 d1w6ua_ Alignment 100.0 23 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase 17 c3awdD_ Alignment 100.0 26 Chain: D: PDB Molecule:putative polyol dehydrogenase; PDBTitle: crystal structure of gox2181 PDB header:antibiotic biosynthesis 18 c1w4zA_ Alignment 100.0 28 Chain: A: PDB Molecule:ketoacyl reductase; PDBTitle: structure of actinorhodin polyketide (actiii) reductase PDB header:oxidoreductase Chain: D: PDB Molecule:short chain dehydrogenase; 19 c3o38D_ 100.0 25 Alignment PDBTitle: crystal structure of a short chain dehydrogenase from mycobacterium2 smegmatis PDB header:oxidoreductase Chain: B: PDB Molecule:short chain oxidoreductase q9hya2; 20 c3lf2B_ Alignment 100.0 25 PDBTitle: nadph bound structure of the short chain oxidoreductase q9hya2 from2 pseudomonas aeruginosa pao1 containing an atypical catalytic center PDB header:oxidoreductase Chain: C: PDB Molecule:short chain oxidoreductase; 21 c3rkrC_ not modelled 100.0 27 Alignment PDBTitle: crystal structure of a metagenomic short-chain oxidoreductase (sdr) in2 complex with nadp Fold:NAD(P)-binding Rossmann-fold domains 22 d1fmca_ Alignment not modelled 100.0 27 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: G: PDB Molecule:short chain dehydrogenase; 23 c3toxG_ not modelled 100.0 28 Alignment PDBTitle: crystal structure of a short chain dehydrogenase in complex with2 nad(p) from sinorhizobium meliloti 1021 Fold:NAD(P)-binding Rossmann-fold domains 24 d1xhla_ Alignment not modelled 100.0 22 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: A: PDB Molecule:putative oxidoreductase protein; 25 c4e3zA_ not modelled 100.0 27 Alignment PDBTitle: crystal structure of a oxidoreductase from rhizobium etli cfn 42 Fold:NAD(P)-binding Rossmann-fold domains 26 d2rhca1 Alignment not modelled 100.0 28 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase 27 c2z1nA_ Alignment not modelled 100.0 19 Chain: A: PDB Molecule:dehydrogenase; PDBTitle: crystal structure of ape0912 from aeropyrum pernix k1 PDB header:oxidoreductase Chain: B: PDB Molecule:3-oxoacyl-(acyl-carrier-protein) 28 c3lylB_ Alignment not modelled 100.0 29 reductase; PDBTitle: structure of 3-oxoacyl-acylcarrier protein reductase, fabg2 from francisella tularensis PDB header:oxidoreductase Chain: A: PDB Molecule:3-oxoacyl-[acyl-carrier-protein] 29 c2p68A_ not modelled 100.0 25 Alignment reductase; PDBTitle: crystal structure of aq_1716 from aquifex aeolicus vf5 PDB header:oxidoreductase Chain: A: PDB Molecule:short-chain type 30 c3svtA_ Alignment not modelled 100.0 24 dehydrogenase/reductase; PDBTitle: structure of a short-chain type dehydrogenase/reductase from2 mycobacterium ulcerans Fold:NAD(P)-binding Rossmann-fold domains 31 d2ae2a_ Alignment not modelled 100.0 25 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: A: PDB Molecule:(3r)-hydroxyacyl-coa dehydrogenase; 32 c2et6A_ not modelled 100.0 26 Alignment PDBTitle: (3r)-hydroxyacyl-coa dehydrogenase domain of candida tropicalis2 peroxisomal multifunctional enzyme type 2 Fold:NAD(P)-binding Rossmann-fold domains 33 d2ew8a1 Alignment not modelled 100.0 23 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: A: PDB Molecule:3-oxoacyl-[acyl-carrier-protein] 34 c3v2gA_ Alignment not modelled 100.0 31 reductase; PDBTitle: crystal structure of a dehydrogenase/reductase from sinorhizobium2 meliloti 1021 PDB header:oxidoreductase Chain: C: PDB Molecule:dehydrogenase/reductase sdr family 35 c2zatC_ not modelled 100.0 28 Alignment member 4; PDBTitle: crystal structure of a mammalian reductase Fold:NAD(P)-binding Rossmann-fold domains 36 d1edoa_ Alignment not modelled 100.0 27 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases Fold:NAD(P)-binding Rossmann-fold domains 37 d1ae1a_ Alignment not modelled 100.0 25 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: A: PDB Molecule:3-oxoacyl-[acyl-carrier-protein] 38 c4dryA_ Alignment not modelled 100.0 19 reductase; PDBTitle: the crystal structure of 3-oxoacyl-[acyl-carrier-protein] reductase2 from rhizobium meliloti PDB header:oxidoreductase Chain: B: PDB Molecule:short chain dehydrogenase or reductase; 39 c3rihB_ not modelled 100.0 20 Alignment PDBTitle: crystal structure of a putative short chain dehydrogenase or reductase2 from mycobacterium abscessus Fold:NAD(P)-binding Rossmann-fold domains 40 d2bgka1 Alignment not modelled 100.0 24 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: A: PDB Molecule:3-oxoacyl-[acyl-carrier-protein] 41 c4dmmA_ Alignment not modelled 100.0 31 reductase; PDBTitle: 3-oxoacyl-[acyl-carrier-protein] reductase from synechococcus2 elongatus pcc 7942 in complex with nadp PDB header:oxidoreductase Chain: A: PDB Molecule:glucose/ribitol dehydrogenase; 42 c3emkA_ not modelled 100.0 28 Alignment PDBTitle: 2.5a crystal structure of glucose/ribitol dehydrogenase2 from brucella melitensis Fold:NAD(P)-binding Rossmann-fold domains 43 d1k2wa_ Alignment not modelled 100.0 25 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: D: PDB Molecule:3-oxoacyl-[acyl-carrier protein] 44 c3ftpD_ Alignment not modelled 100.0 31 reductase; PDBTitle: crystal structure of 3-ketoacyl-(acyl-carrier-protein)2 reductase from burkholderia pseudomallei at 2.05 a3 resolution PDB header:oxidoreductase Chain: A: PDB Molecule:3-oxoacyl-[acyl-carrier-protein] 45 c3osuA_ Alignment not modelled 100.0 30 reductase; PDBTitle: crystal structure of the 3-oxoacyl-acyl carrier protein reductase,2 fabg, from staphylococcus aureus Fold:NAD(P)-binding Rossmann-fold domains 46 d1iy8a_ Alignment not modelled 100.0 21 Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases PDB header:oxidoreductase Chain: B: PDB Molecule:3-ketoacyl-(acyl-carrier-protein) 47 c3llsB_ Alignment not modelled 100.0 27 reductase; PDBTitle: crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase from2 mycobacterium tuberculosis PDB header:oxidoreductase
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  • Osmotic Stress Response in the Industrially Important Bacterium

    Osmotic Stress Response in the Industrially Important Bacterium

    Osmotic stress response in the industrially important bacterium Gluconobacter oxydans Dissertation to obtain the degree of Doctorate (Dr. rer. nat.) from the Faculty of Mathematics and Natural Sciences of the Rheinische Friedrich-Wilhelms University of Bonn, Germany submitted by Nageena Zahid from Lahore, Pakistan Bonn, November 2016 Finalized with the permission from the Faculty of Mathematics and Natural Sciences of the Rheinische Friedrich-Wilhelms University of Bonn, Germany First Referee: Prof. Dr. Uwe Deppenmeier Second Referee: Prof. Dr. Erwin A. Galinski Day of Promotion: 07.02.2017 Year of Publication: 2017 List of parts of this thesis that have already been published. Zahid N., Schweiger P., Galinski E., Deppenmeier U. (2015). Identification of mannitol as compatible solute in Gluconobacter oxydans. Appl Microbiol Biotechnol 99, 5511- 5521. Zahid N. and Deppenmeier U. (2016). Role of mannitol dehydrogenases in osmoprotection of Gluconobacter oxydans. Appl Microbiol Biotechnol 100, 9967-9978. For my Son TABLE OF CONTENTS 1. INTRODUCTION 1 1.1. Acetic acid bacteria 1 1.2. The genus Gluconobacter 2 1.2.1. Respiratory chain of G. oxydans 3 1.2.2. Intracellular carbohydrate metabolism in G. oxydans 6 1.2.3. Types and function of sugars and polyols metabolizing enzymes in Gluconobacter 7 1.2.4. Biotechnological applications of G. oxydans and its limitations 8 1.3. Aims of the work 10 2. MATERIALS AND METHODS 12 2.1. Chemicals and Enzymes 12 2.2. Bacterial strains, plasmids, primers 12 2.2.1. Bacterial strains 12 2.2.2. Oligonucleotides and Plasmids 13 2.3. Antibiotic stock solutions 18 2.4.
  • Frankincense Essential Oil Prepared from Hydrodistillation of Boswellia

    Frankincense Essential Oil Prepared from Hydrodistillation of Boswellia

    Ni et al. BMC Complementary and Alternative Medicine 2012, 12:253 http://www.biomedcentral.com/1472-6882/12/253 RESEARCH ARTICLE Open Access Frankincense essential oil prepared from hydrodistillation of Boswellia sacra gum resins induces human pancreatic cancer cell death in cultures and in a xenograft murine model Xiao Ni1, Mahmoud M Suhail2, Qing Yang3, Amy Cao4, Kar-Ming Fung3,5,6, Russell G Postier7, Cole Woolley8, Gary Young8, Jingzhe Zhang1* and Hsueh-Kung Lin3* Abstract Background: Regardless of the availability of therapeutic options, the overall 5-year survival for patients diagnosed with pancreatic cancer remains less than 5%. Gum resins from Boswellia species, also known as frankincense, have been used as a major ingredient in Ayurvedic and Chinese medicine to treat a variety of health-related conditions. Both frankincense chemical extracts and essential oil prepared from Boswellia species gum resins exhibit anti-neoplastic activity, and have been investigated as potential anti-cancer agents. The goals of this study are to identify optimal condition for preparing frankincense essential oil that possesses potent anti-tumor activity, and to evaluate the activity in both cultured human pancreatic cancer cells and a xenograft mouse cancer model. Methods: Boswellia sacra gum resins were hydrodistilled at 78°C; and essential oil distillate fractions were collected at different durations (Fraction I at 0–2 h, Fraction II at 8–10 h, and Fraction III at 11–12 h). Hydrodistillation of the second half of gum resins was performed at 100°C; and distillate was collected at 11–12 h (Fraction IV). Chemical compositions were identified by gas chromatography–mass spectrometry (GC-MS); and total boswellic acids contents were quantified by high-performance liquid chromatography (HPLC).