DOCSLIB.ORG

Classification I Classification II Subsystem Functional Role

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Classification I Classification II Subsystem Functional Role Classification I Classification II Subsystem Functional Role Occurrence Amino Acids and Derivatives Alanine, serine, and glycine Alanine Biosynthesis Cysteine desulfurase (EC 4.4.1.-) 2 Amino Acids and Derivatives Alanine, serine, and glycine Glycine cleavage system Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2) 4 Amino Acids and Derivatives Alanine, serine, and glycine Glycine cleavage system Dihydrolipoamide dehydrogenase (EC 1.8.1.4) 3 Amino Acids and Derivatives Alanine, serine, and glycine Glycine cleavage system Aminomethyltransferase (glycine cleavage system T protein) (EC:2.1.2.10) 1 Amino Acids and Derivatives Alanine, serine, and glycine Glycine synthesis Serine hydroxymethyltransferase (EC 2.1.2.1) 2 Amino Acids and Derivatives Alanine, serine, and glycine Glycine synthesis Low- specificity L-threonine aldolase (EC 4.1.2.5) 2 Amino Acids and Derivatives Alanine, serine, and glycine Serine Biosynthesis Phosphoserine aminotransferase (EC 2.6.1.52) 1 Amino Acids and Derivatives Alanine, serine, and glycine Serine Biosynthesis Phosphoserine phosphatase (EC 3.1.3.3) 1 Amino Acids and Derivatives Alanine, serine, and glycine Serine Biosynthesis Serine hydroxymethyltransferase (EC 2.1.2.1) 2 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Urease accessory protein UreF 3 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Agmatine deiminase (EC 3.5.3.12) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation 4-aminobutyrate aminotransferase (EC 2.6.1.19) 4 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Arginine decarboxylase (EC 4.1.1.19) 9 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Urease accessory protein UreE 7 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Ornithine aminotransferase (EC 2.6.1.13) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation 3-polyprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Ornithine carbamoyltransferase (EC 2.1.3.3) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Arginine Putrescine and 4- aminobutyrate degradation Urease alpha subunit (EC 3.5.1.5) 9 Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Spermidine Putrescine ABC transporter permease component potC (TC_3.A.1.11.1) 2 Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Arginine decarboxylase (EC 4.1.1.19) 9 Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Putrescine transport system permease protein potH (TC 3.A.1.11.2) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Spermidine Putrescine ABC transporter permease component potB (TC_3.A.1.11.1) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Polyamine Metabolism Ornithine decarboxylase (EC 4.1.1.17) 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urea ABC transporter, permease protein UrtC 6 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urease alpha subunit (EC 3.5.1.5) 9 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urease accessory protein UreF 3 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urea ABC transporter, permease protein UrtB 2 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urea ABC transporter, ATPase protein UrtD 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urea carboxylase 2 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urea ABC transporter, urea binding protein 1 Amino Acids and Derivatives Arginine; urea cycle, polyamines Urea decomposition Urease accessory protein UreE 7 Amino Acids and Derivatives Aromatic amino acids and derivatives Central meta-cleavage pathway of aromatic compound degradation 2-hydroxymuconic semialdehyde hydrolase (EC 3.7.1.9) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis 3- phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) 10 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Prephenate dehydrogenase (EC 1.3.1.12) 7 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Shikimate kinase (EC 2.7.1.71) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Shikimate 5-dehydrogenase (EC 1.1.1.25) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) 5 https://static-content.springer.com/esm/art%3A10.1186%2F1471-2164-7-57/MediaObjects/12864_2005_440_MOESM3_ESM.txt[9/25/2019 2:46:04 PM] Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Chorismate mutase (EC 5.4.99.5) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis 3- dehydroquinate synthase (EC 4.2.3.4) 5 Amino Acids and Derivatives Aromatic amino acids and derivatives Chorismate Synthesis Chorismate synthase (EC 4.2.3.5) 2 Amino Acids and Derivatives Aromatic amino acids and derivatives Phenylalanine synthesis Aspartate aminotransferase (EC 2.6.1.1) 6 Amino Acids and Derivatives Aromatic amino acids and derivatives Phenylalanine synthesis Chorismate mutase (EC 5.4.99.5) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Tryptophan synthesis Tryptophan synthase beta chain like (EC 4.2.1.20) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Tryptophan synthesis Indole-3-glycerol phosphate synthase (EC 4.1.1.48) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Tryptophan synthesis Anthranilate synthase, aminase component (EC 4.1.3.27) 2 Amino Acids and Derivatives Aromatic amino acids and derivatives Tryptophan synthesis Tryptophan synthase beta chain (EC 4.2.1.20) 3 Amino Acids and Derivatives Aromatic amino acids and derivatives Tyrosine synthesis Chorismate mutase (EC 5.4.99.5) 1 Amino Acids and Derivatives Aromatic amino acids and derivatives Tyrosine synthesis Aspartate aminotransferase (EC 2.6.1.1) 5 Amino Acids and Derivatives Aromatic amino acids and derivatives Tyrosine synthesis Prephenate dehydrogenase (EC 1.3.1.12) 7 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis Dihydroxy-acid dehydratase (EC 4.2.1.9) 6 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 3-isopropylmalate dehydrogenase (EC 1.1.1.85) 3 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis Acetolactate synthase large subunit (EC 2.2.1.6) 4 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 2-isopropylmalate synthase (EC 2.3.3.13) 12 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis Threonine dehydratase (EC 4.3.1.19) 1 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33) 1 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis Ketol-acid reductoisomerase (EC 1.1.1.86) 3 Amino Acids and Derivatives Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis Branched-chain amino acid aminotransferase (EC 2.6.1.42) 45 Amino Acids and Derivatives Branched-chain amino acids HMG CoA Synthesis Isovaleryl- CoA dehydrogenase (EC 1.3.99.10) 2 Amino Acids and Derivatives Branched-chain amino acids HMG CoA Synthesis Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) 1 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Branched- chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4) 5 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Dihydrolipoamide dehydrogenase (EC 1.8.1.4) 3 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation 3- hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) 1 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Branched- chain amino acid aminotransferase (EC 2.6.1.42) 45 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Branched- chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4) 2 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Acyl-CoA dehydrogenase (EC 1.3.99.3) 1 Amino Acids and Derivatives Branched-chain amino acids Isoleucine degradation Enoyl-CoA hydratase (EC 4.2.1.17) 1 Amino Acids and Derivatives Branched-chain amino
Load more

Recommended publications
  • Lignite Coal Burning Seam in the Remote Altai Mountains Harbors A
    www.nature.com/scientificreports OPEN Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic Received: 20 September 2017 Accepted: 17 April 2018 microbial community Published: xx xx xxxx Vitaly V. Kadnikov1, Andrey V. Mardanov1, Denis A. Ivasenko2, Dmitry V. Antsiferov2, Alexey V. Beletsky1, Olga V. Karnachuk2 & Nikolay V. Ravin1 Thermal ecosystems associated with underground coal combustion sites are rare and less studied than geothermal features. Here we analysed microbial communities of near-surface ground layer and bituminous substance in an open quarry heated by subsurface coal fre by metagenomic DNA sequencing. Taxonomic classifcation revealed dominance of only a few groups of Firmicutes. Near- complete genomes of three most abundant species, ‘Candidatus Carbobacillus altaicus’ AL32, Brockia lithotrophica AL31, and Hydrogenibacillus schlegelii AL33, were assembled. According to the genomic data, Ca. Carbobacillus altaicus AL32 is an aerobic heterotroph, while B. lithotrophica AL31 is a chemolithotrophic anaerobe assimilating CO2 via the Calvin cycle. H. schlegelii AL33 is an aerobe capable of both growth on organic compounds and carrying out CO2 fxation via the Calvin cycle. Phylogenetic analysis of the large subunit of RuBisCO of B. lithotrophica AL31 and H. schlegelii AL33 showed that it belongs to the type 1-E. All three Firmicutes species can gain energy from aerobic or anaerobic oxidation of molecular hydrogen, produced as a result of underground coal combustion along with other coal gases. We propose that thermophilic Firmicutes, whose spores can spread from their original geothermal habitats over long distances, are the frst colonizers of this recently formed thermal ecosystem. Studies of thermophilic microorganisms that survive and develop at temperatures that are extreme for ordi- nary life have broadened our understanding of the diversity of microorganisms and their evolution, the mech- anisms of adaptation to environmental conditions.
    [Show full text]
  • Generated by SRI International Pathway Tools Version 25.0, Authors S
    An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility.
    [Show full text]
  • Supplementary Table S1. Table 1. List of Bacterial Strains Used in This Study Suppl
    Supplementary Material Supplementary Tables: Supplementary Table S1. Table 1. List of bacterial strains used in this study Supplementary Table S2. List of plasmids used in this study Supplementary Table 3. List of primers used for mutagenesis of P. intermedia Supplementary Table 4. List of primers used for qRT-PCR analysis in P. intermedia Supplementary Table 5. List of the most highly upregulated genes in P. intermedia OxyR mutant Supplementary Table 6. List of the most highly downregulated genes in P. intermedia OxyR mutant Supplementary Table 7. List of the most highly upregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Table 8. List of the most highly downregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Figures: Supplementary Figure 1. Comparison of the genomic loci encoding OxyR in Prevotella species. Supplementary Figure 2. Distribution of SOD and glutathione peroxidase genes within the genus Prevotella. Supplementary Table S1. Bacterial strains Strain Description Source or reference P. intermedia V3147 Wild type OMA14 isolated from the (1) periodontal pocket of a Japanese patient with periodontitis V3203 OMA14 PIOMA14_I_0073(oxyR)::ermF This study E. coli XL-1 Blue Host strain for cloning Stratagene S17-1 RP-4-2-Tc::Mu aph::Tn7 recA, Smr (2) 1 Supplementary Table S2. Plasmids Plasmid Relevant property Source or reference pUC118 Takara pBSSK pNDR-Dual Clonetech pTCB Apr Tcr, E. coli-Bacteroides shuttle vector (3) plasmid pKD954 Contains the Porpyromonas gulae catalase (4)
    [Show full text]
  • Distribution in Different Organisms of Amino Acid Oxidases with FAD Or a Quinone As Cofactor and Their Role As Antimicrobial Proteins in Marine Bacteria
    Supplementary Materials: Distribution in Different Organisms of Amino Acid Oxidases with FAD or a Quinone As Cofactor and Their Role as Antimicrobial Proteins in Marine Bacteria Jonatan C. Campillo‐Brocal, Patricia Lucas‐Elío and Antonio Sanchez‐Amat * Table S1. Amino acid oxidases (AAOs) from microbial sources. Marine microorganisms are shown in bold. * cofactor and/or activity attributed for high similarity with LodA. ND, not determined. NA, not accessible. LAAOs, L‐amino acid oxidases. DAAOs, D‐amino acid oxidases. LASPOs, L‐aspartate oxidases. CTQ, cysteine tryptophilquinone. Microorganism Oligomeric Structure/Mass Accession Activity (Main Substrate) Cofactor Various Reference (Enzyme Name) Molecular Number AAOs with Quinone Cofactor (LodA‐Like Proteins) Marinomonas Homotetramer (80.9 × 4 kDa). Antimicrobial. Biofilms mediterranea MMB‐1 L‐Lysine ε‐oxidase (L‐Lys) CTQ Crystal structure solved, PDB AAY33849 [1,2] dispersion. Extracellular (LodA) ID: 2YMW Marinomonas Other substrates: Gly ethyl mediterranea MMB‐1 Glycine oxidase (Gly) CTQ 76.2 kDa ADZ90918 [3,4] ester (GoxA) Pseudoalteromonas Antimicrobial. Biofilms L‐Lysine ε‐oxidase (L‐Lys) * CTQ 110 kDa Q7X0I8 [5,6] tunicata D2 (AlpP) dispersion Chromobacterium Antimicrobial. Biofilms ND ND ND AAQ60932 [6] violaceum dispersion Antimicrobial. Biofilms Caulobacter crescentus ND ND ND NP_419374 [6] dispersion Pseudoalteromonas flavipulchra JG1 * L‐Lysine ε‐oxidase (* L‐Lys) * CTQ 77 kDa Antimicrobial. pI = 4.6 AFB71049 [7] (PfaP) Broad spectrum oxidase Antimicrobial. pI = 9.4. It Pseudoalteromonas (L‐Lys > L‐Met > L‐Glu > L‐Leu > L‐ ND 60 kDa contains a 9‐residues peptide NA [8] flavipulchra C2 Gln > L‐Tyr > L‐Phe) similar to AlpP S1 Table S1. Cont. Broad spectrum oxidase Pseudoalteromonas (L‐Met > L‐Gln > L‐Leu > L‐Phe > L‐ ND Oligomer (110 kDa) Antimicrobial NA [9] luteoviolacea Glu > L‐Trp) Antimicrobial.
    [Show full text]
  • Yeast Genome Gazetteer P35-65
    gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal
    [Show full text]
  • Progress Toward Understanding the Contribution of Alkali Generation in Dental Biofilms to Inhibition of Dental Caries
    International Journal of Oral Science (2012) 4, 135–140 ß 2012 WCSS. All rights reserved 1674-2818/12 www.nature.com/ijos REVIEW Progress toward understanding the contribution of alkali generation in dental biofilms to inhibition of dental caries Ya-Ling Liu1, Marcelle Nascimento2 and Robert A Burne1 Alkali production by oral bacteria is believed to have a major impact on oral microbial ecology and to be inibitory to the initiation and progression of dental caries. A substantial body of evidence is beginning to accumulate that indicates the modulation of the alkalinogenic potential of dental biofilms may be a promising strategy for caries control. This brief review highlights recent progress toward understanding molecular genetic and physiologic aspects of important alkali-generating pathways in oral bacteria, and the role of alkali production in the ecology of dental biofilms in health and disease. International Journal of Oral Science (2012) 4, 135–140; doi:10.1038/ijos.2012.54; published online 21 September 2012 Keywords: arginine; biofilm; dental caries; microbial ecology; urea INTRODUCTION via the arginine deiminase system (ADS).15–18 Urea is provided con- Dental biofilms, the microbial communities that colonize the surfaces tinuously in salivary secretions and gingival exudates at concentra- of the teeth, exist in a dynamic equilibrium with host defenses and are tions roughly equivalent to those in serum, which range from about 3 generally compatible with the integrity of the tissues they colonize.1–4 to10 mmol?L21 in healthy humans. Urea is rapidly converted to A strong correlation is evident between the compositional and meta- ammonia and CO2 by bacterial ureases (Figure 1), which are produced bolic changes of the dental biofilms and the transition from oral health by a small subset of oral bacteria that includes Streptococcus salivarius, 2,5 to disease states, including dental caries and periodontal disease.
    [Show full text]
  • Paul R Thompson
    Paul R Thompson Department of Biochemistry and Molecular Pharmacology Voice: (508) 856-8492 UMass Medical School FAX: (508) 856-6215 Worcester, MA, 01605 Email: [email protected] PROFESSIONAL PREPARATION Institution Major Area Degree & Year McMaster University Biochemistry Honors B.S.c. – 1994 McMaster University Biochemistry Ph.D. – 2000 Johns Hopkins University SOM Pharmacology PDF – 2000-2003 PROFESSIONAL EXPERIENCE Dates Title Institution Department 2014-present Professor and Director University of Massachusetts Biochemistry and of Chemical Biology Medical School Molecular with tenure Pharmacology 2010-2014 Associate Professor The Scripps Research Chemistry with tenure Institute, Scripps Florida 2009-2010 Associate Professor University of South Carolina Chemistry with Tenure 2004-2008 Assistant Professor University of South Carolina Chemistry 2003-2004 Visiting Assistant Professor University of South Carolina Chemistry 2000-2003 Postdoctoral Fellow Johns University SOM Pharmacology 1994-2000 Teaching and McMaster University Biochemistry Research Assistant 1993-1994 Teaching Assistant McMaster University Chemistry HONORS, AWARDS AND OTHER SIGNIFICANT ACTIVITIES • Consultant to Disarm Therapeutics, 2018 to present • Chair, Bioorganic Chemistry Gordon Research Conference 2017 • Permanent Member, Synthetic Biological Chemistry B (SBCB) Study Section, NIH October 2016- present. • Consultant to Celgene, 2018 to present. • Associate Chair, Bioorganic Chemistry Gordon Research Conference 2017 • Consultant to Bristol Myers Squibb,
    [Show full text]
  • Letters to Nature
    letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997).
    [Show full text]
  • Leeds Thesis Template
    Determining the Link Between Genome Integrity and Seed Quality Robbie Michael Gillett Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds Faculty of Biological Sciences School of Biology January, 2017 - ii - The candidate confirms that the work submitted is his own and that appropriate credit has been given where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. The right of Robbie M. Gillett to be identified as Author of this work has been asserted by him in accordance with the Copyright, Designs and Patents Act 1988. © 2016 The University of Leeds and Robbie Michael Gillett - iii - Acknowledgements I would like to thank my supervisor Dr Christopher West and co-supervisor Dr. Wanda Waterworth for all of their support, expertise and incredible patience and for always being available to help. I would like to thank Aaron Barrett, James Cooper, Valérie Tennant, and all my other friends at university for their help throughout my PhD. Thanks to Vince Agboh and Grace Hoysteed for their combined disjointedness and to Ashley Hines, Daniel Johnston and Darryl Ransom for being a source of entertainment for many years. I would like to thank my international Sona friends, Lindsay Hoffman and Jan Maarten ten Katen. Finally unreserved thanks to my loving parents who supported me throughout the tough times and to my Grandma and Granddad, Jean and Dennis McCarthy, who were always very vocal with their love, support and pride.
    [Show full text]
  • Paul R Thompson
    Paul R Thompson Department of Chemistry Voice: (561) 228-2860 The Scripps Research Institute FAX: (561) 228-2918 Jupiter, FL, 33458 Email: [email protected] PROFESSIONAL PREPARATION Institution Major Area Degree & Year McMaster University Biochemistry Honors B.S.c. – 1994 McMaster University Biochemistry Ph.D. – 2000 Johns Hopkins University SOM Pharmacology PDF – 2000-2003 PROFESSIONAL EXPERIENCE Dates Title Institution Department 2010-present Associate Professor The Scripps Research Chemistry with tenure Institute, Scripps Florida 2009-2010 Associate Professor University of South Carolina Chemistry with Tenure 2004-2008 Assistant Professor University of South Carolina Chemistry 2003-2004 Visiting Assistant Professor University of South Carolina Chemistry 2000-2003 Postdoctoral Fellow Johns University SOM Pharmacology 1994-2000 Teaching and McMaster University Biochemistry Research Assistant 1993-1994 Teaching Assistant McMaster University Chemistry HONORS, AWARDS AND OTHER SIGNIFICANT ACTIVITIES Chair, Enzymes, Coenzymes & Metabolic Pathways Gordon Research Conference 2014 Associate Chair, Enzymes, Coenzymes & Metabolic Pathways Gordon Research Conference 2013 Symposium Chair, Chemical Biology: Chemical Answers to Biological Questions, SERMACS 2012 Session Leader, FASEB Conference entitled: "Biological Methylation: From DNA to Histones" 2010 South Carolina Governor’s Young Scientist Award for Excellence in Scientific Research Cofounder Arginomix, 2009 Mail in reviewer, NIH Challenge Grants, June 2009 Camille Dreyfus Teacher Scholar
    [Show full text]
  • The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
    Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota.
    [Show full text]
  • Style Specifications Thesis
    Structural Studies of Salvage Enzymes in Nucleotide Biosynthesis Martin Welin Faculty of Natural Resources and Agricultural Sciences Department of Molecular Biology Uppsala Doctoral thesis Swedish University of Agricultural Sciences Uppsala 2007 Acta Universitatis Agriculturae Sueciae 2007:21 ISSN 1652-6880 ISBN 978-91-576-7320-6 © 2007 Martin Welin, Uppsala Tryck: SLU Service/Repro, Uppsala 2007 Abstract Welin, M., 2007. Structural Studies of Salvage Enzymes in Nucleotide Biosynthesis. Doctoral dissertation. ISSN 1652-6880, ISBN 978-91-576-7320-6 There are two routes to produce deoxyribonucleoside triphosphates (dNTPs) precursors for DNA synthesis, the de novo and the salvage pathways. Deoxyribonucleoside kinases (dNKs) perform the initial phosphorylation of deoxyribonucleosides (dNs). Furthermore, they can act as activators for several medically important nucleoside analogs (NAs) for treatment against cancer or viral infections. Several disorders are characterized by mutations in enzymes involved in the nucleotide biosynthesis, such as Lesch-Nyhan disease that is linked to hypoxanthine guanine phosphoribosyltransferase (HPRT). In this thesis, the structures of human thymidine kinase 1 (TK1), a mycoplasmic deoxyadenosine kinase (Mm-dAK), and phosphoribosyltransferase domain containing 1 (PRTFDC1) are presented. Furthermore, a structural investigation of Drosophila melanogaster dNK (Dm-dNK) N64D mutant was carried out. The obtained structural information reveals the basis for substrate specificity for TKs and the bacterial dAKs. The TK1 revealed a structure different from other known dNK structures, containing an α/β domain similar to the RecA-F1ATPase family, and a lasso-like domain stabilized by a structural zinc. The Mm-dAK structure was similar to its human counterparts, but with some alterations in the proximity of the active site.
    [Show full text]