DOCSLIB.ORG

Table 2. Annotation of G. Thermodenitrificans NG80-2 Genome Gene ID Gene Name Gene Product COG Functional Category

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Table 2. Annotation of G. Thermodenitrificans NG80-2 Genome Gene ID Gene Name Gene Product COG Functional Category Table 2. Annotation of G. thermodenitrificans NG80-2 genome Gene ID Gene Gene product COG functional category name GT0001 dnaA DnaA COG0592, Replication, recombination and repair GT0002 gt2 DNA polymerase III, beta subunit COG0592, Replication, recombination and repair GT0003 gt3 Conserved hypothetical protein COG2501, Function unknown GT0004 recF RecF COG1195, Replication, recombination and repair GT0005 gt5 DNA gyrase subunit B COG0187, Replication, recombination and repair GT0006 gt6 DNA gyrase subunit A COG0188, Replication, recombination and repair GT0007 gt7 Conserved hypothetical protein COG2206, Signal transduction mechanism GT0008 yaaC YaaC GT0009 guaB Inosine-monophosphate dehydrogenase COG0516, Nucleotide transport and metabolism GT0010 gt10 D-alanine carboxypeptidase COG1686, Cell wall/membrane biogenesis GT0011 gt11 Pyridoxine biosynthesis protein COG0214, Coenzyme transport and metabolism GT0012 gt12 Glutamine amidotransferase Sno family COG0311, Coenzyme transport and metabolism GT0013 gt13 Seryl-tRNA synthetase COG0172, Translation GT0014 gt14 Spore peptidoglycan hydrolase, N-acetylglucosaminidase COG3858, General function prediction only GT0015 gt15 Cytosine deaminase COG0590, Nucleotide transport and metabolism GT0016 dnaZX DnaZX COG2812, Replication, recombination and repair GT0017 gt17 Conserved hypothetical protein COG0718, Function unknown GT0018 recR RecR COG0353, Replication, recombination and repair GT0019 gt19 Hypothetical cytosolic protein Gene ID Gene Gene product COG functional category name GT0020 gt20 Inhibitor of the pro-sigma K processing machinery GT0021 csfB CsfB GT0022 gt22 Similar to lysine decarboxylase COG1982, Amino acid transport and metabolism GT0023 tmk Thymidylate kinase COG0125, Nucleotide transport and metabolism GT0024 gt24 DNA polymerase III delta subunit COG0470, Replication, recombination and repair GT0025 gt25 Signal peptidase II COG1774, Function unknown GT0026 gt26 Conserved hypothetical protein COG4467, Function unknown GT0027 gt27 Methyltransferase COG4123, General function prediction only GT0028 gt28 Corrin/porphyrin methyltransferase COG0313, General function prediction only GT0029 gt29 Transition state regulator COG2002, Transcription GT0030 gt30 Methionine-tRNA ligase/methionyl-tRNA synthetase COG0143, Translation GT0031 gt31 Deoxyribonuclease TatD family COG0084, Replication, recombination and repair GT0032 gt32 Conserved hypothetical protein COG3583, Function unknown GT0033 gt33 Unknown GT0034 gt34 Ribonuclease M5 COG1658, Replication, recombination and repair GT0035 gt35 Dimethyladenosine transferase COG0030, Translation GT0036 yabG Sporulation-specific protease YabG GT0037 gt37 Conserved hypothetical protein COG4466, Function unknown GT0038 gt38 Small acid-soluble spore protein, minoralpha/beta-type SASP GT0039 gt39 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase COG1947, Lipid transport and metabolism GT0040 gt40 Transcriptional regulator COG0503, Nucleotide transport and metabolism Gene ID Gene Gene product COG functional category name GT0041 gt41 Translation initiation inhibitor COG0251, Translation GT0042 gt42 Stage V sporulation protein G COG2088, Cell wall/membrane biogenesis GT0043 gt43 Glucosamine-1-phosphate acetyltransferase COG1207, Cell wall/membrane biogenesis GT0044 gt44 Phosphoribosyl diphosphate synthetase/ribose-phosphate COG0462, Nucleotide transport and metabolism pyrophosphokinase GT0045 gt45 General stress protein COG1825, Translation GT0046 gt46 Peptidyl-tRNA hydrolase COG0193, Translation GT0047 gt47 Conserved hypothetical protein GT0048 gt48 Transcription-repair coupling factor COG1197, Replication, recombination and repair GT0049 gt49 Stage V sporulation protein T COG2002, Transcription GT0050 gt50 Similar to stage V sporulation protein B COG2244, General function prediction only GT0051 gt51 Tetrapyrrole methylase family protein, MazG family protein COG3956, General function prediction only GT0052 gt52 Heat shock protein 15 COG1188, Translation GT0053 gt53 Conserved hypothetical protein GT0054 gt54 Spore cortex biosynthesis protein GT0055 gt55 Cell-division initiation protein COG2919, Cell cycle control, mitosis and meiosis GT0056 gt56 Polyribonucleotide nucleotidyltransferase COG1098, Translation GT0057 gt57 Serine phosphatase COG2208, Signal transduction mechanisms GT0058 gt58 Conserved hypothetical protein GT0059 gt59 Serine/threonine-protein kinase COG0515, General function prediction only GT0060 mesJ Cell cycle protein MesJ COG0037, Cell cycle control, mitosis and meiosis Gene ID Gene Gene product COG functional category name GT0061 gt61 Hypoxanthine-guanine phosphoribosyltransferase COG0634, Nucleotide transport and metabolism GT0062 gt62 Cell-division protein and general stress protein(class III heat-shock) COG0465, Posttranslational modification, protein turnover, chaperones GT0063 coaA Pantothenate kinase COG1521, Transcription GT0064 gt64 Putative 30 kDa replication protein COG1281, Posttranslational modification, protein turnover, chaperones GT0065 gt65 O-acetyl-L-serine sulfhydrylase COG0031, Amino acid transport and metabolism GT0066 gt66 P-aminobenzoate synthase COG0147, Amino acid transport and metabolism GT0067 gt67 Anthranilate synthase component II COG0512, Amino acid transport and metabolism GT0068 gt68 4-amino-4-deoxychorismate lyase COG0115, Amino acid transport and metabolism GT0069 gt69 Dihydropteroate synthase, dihydropteroatepyrophosphorylase COG0294, Coenzyme transport and metabolism GT0070 gt70 Dihydroneopterin aldolase COG1539, Coenzyme transport and metabolism GT0071 gt71 2-amino-4-hydroxy-6- COG0801, Coenzyme transport and metabolism hydroxymethyldihydropteridinepyrophosphokinase GT0072 gt72 Transcriptional regulator Xre family COG1476, Transcription GT0073 gt73 Transcriptional regulator involved in nitrogen regulation, COG0042, Translation NifR3/Smm1 family GT0074 gt74 Lysyl-tRNA synthetase COG1190, Translation GT0075 gt75 Transcriptional regulator COG4463, Transcription GT0076 gt76 ClpC ATPase COG3880, Function unknown GT0077 gt77 Arginine kinase COG3869, Amino acid transport and metabolism GT0078 gt78 Negative regulator of genetic competence ClpC/MecB COG0542, Posttranslational modification, protein turnover, chaperones GT0079 gt79 DNA repair protein homolog COG1066, Posttranslational modification, protein turnover, chaperones Gene ID Gene Gene product COG functional category name GT0080 gt80 Hypothetical membrane associated protein COG4956, General function prediction only GT0081 gt81 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase COG1211, Lipid transport and metabolism GT0082 gt82 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase COG0245, Lipid transport and metabolism GT0083 gt83 Transfer RNA-Gln synthetase COG0008, Translation GT0084 gt84 Serine acetyltransferase COG1045, Amino acid transport and metabolism GT0085 gt85 Cysteine-tRNA ligase COG0215, Translation GT0086 gt86 Conserved hypothetical protein COG1939, Function unknown GT0087 gt87 23S rRNA methyltransferase COG0566, Translation GT0088 gt88 Hypothetical cytosolic protein COG3688, General function prediction only GT0089 gt89 RNA polymerase sigma-30 factor COG1595, Transcription GT0090 rpmG 50S ribosomal protein L33 COG0267,Translation GT0091 gt91 Preprotein translocase SecE subunit COG0690, Intracellular trafficking and secretion GT0092 gt92 Transcription antitermination factor COG0250, Transcription GT0093 gt93 Ribosomal protein L11 COG0080, Translation GT0094 gt94 LSU ribosomal protein L1P COG0081, Translation GT0095 gt95 Ribosomal protein L10 COG0244, Translation GT0096 gt96 LSU ribosomal protein L12P (L7/L12) COG0222, Translation GT0097 gt97 16S rRNA m(2)G 1207 methyltransferase COG2813, Translation GT0098 gt98 DNA-directed RNA polymerase beta subunit COG0085, Transcription GT0099 gt99 RNA polymerase beta subunit COG0086, Transcription GT0100 gt100 LSU ribosomal protein L7AE COG1358, Translation Gene ID Gene Gene product COG functional category name GT0101 gt101 Ribosomal protein S12 COG0048, Translation GT0102 gt102 SSU ribosomal protein S7P COG0049, Translation GT0103 gt103 Translation elongation factor G, EF-G COG0480, Translation GT0104 gt104 EF-Tu COG0050, Translation GT0105 gt105 SSU ribosomal protein S10P COG0051, Translation GT0106 gt106 Ribosomal protein L3 COG0087, Translation GT0107 gt107 Ribosomal protein L4 COG0088, Translation GT0108 gt108 Ribosomal protrein L23 COG0089, Translation GT0109 gt109 Ribosomal protein L2 COG0090, Translation GT0110 gt110 Ribosomal protein S19 COG0185, Translation GT0111 gt111 Ribosomal protein L22 COG0091, Translation GT0112 gt112 Ribosomal protein S3 COG0092, Translation GT0113 gt113 50S ribosomal protein L16 COG0197, Translation GT0114 gt114 Ribosomal protein L29 COG0255, Translation GT0115 gt115 Ribosomal protein L17 COG0186, Translation GT0116 gt116 Ribosomal protein L14 COG0093, Translation GT0117 gt117 Ribosomal protein L5 COG0094, Translation GT0118 gt118 SSU ribosomal protein S14P COG0199, Translation GT0119 gt119 SSU ribosomal protein S8P COG0096, Translation GT0120 gt120 Ribosomal protein L6 COG0097, Translation GT0121 gt121 Ribosomal protein L18 COG0256, Translation Gene ID Gene Gene product COG functional category name GT0122 gt122 Ribosomal protein S5 COG0098, Translation GT0123 gt123 50S ribosomal protein L30 COG1841, Translation GT0124 gt124 Ribosomal protein L15 COG0200, Translation GT0125 secY SecY COG0201, Intracellular trafficking and secretion GT0126 adk Adenylate kinase COG0563, Nucleotide transport and metabolism GT0127 gt127 Methionine aminopeptidase COG0024,
Load more

Recommended publications
  • Comparison of Strand-Specific Transcriptomes Of
    Landstorfer et al. BMC Genomics 2014, 15:353 http://www.biomedcentral.com/1471-2164/15/353 RESEARCH ARTICLE Open Access Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces Richard Landstorfer1, Svenja Simon2, Steffen Schober3, Daniel Keim2, Siegfried Scherer1 and Klaus Neuhaus1* Abstract Background: Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 (EHEC) are known, including animal products, fruit and vegetables. The ecology of this pathogen outside its human host is largely unknown and one third of its annotated genes are still hypothetical. To identify genetic determinants expressed under a variety of environmental factors, we applied strand-specific RNA-sequencing, comparing the SOLiD and Illumina systems. Results: Transcriptomes of EHEC were sequenced under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes in strain EDL933 (genome and plasmid), a surprising minority of only 144 had null sequencing reads under all conditions. We therefore developed a statistical method to distinguish weakly transcribed genes from background transcription. We find that 96% of all genes and 91.5% of the hypothetical genes exhibit a significant transcriptional signal under at least one condition. Comparing SOLiD and Illumina systems, we find a high correlation between both approaches for fold-changes of the induced or repressed genes. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics.
    [Show full text]
  • Part One Amino Acids As Building Blocks
    Part One Amino Acids as Building Blocks Amino Acids, Peptides and Proteins in Organic Chemistry. Vol.3 – Building Blocks, Catalysis and Coupling Chemistry. Edited by Andrew B. Hughes Copyright Ó 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978-3-527-32102-5 j3 1 Amino Acid Biosynthesis Emily J. Parker and Andrew J. Pratt 1.1 Introduction The ribosomal synthesis of proteins utilizes a family of 20 a-amino acids that are universally coded by the translation machinery; in addition, two further a-amino acids, selenocysteine and pyrrolysine, are now believed to be incorporated into proteins via ribosomal synthesis in some organisms. More than 300 other amino acid residues have been identified in proteins, but most are of restricted distribution and produced via post-translational modification of the ubiquitous protein amino acids [1]. The ribosomally encoded a-amino acids described here ultimately derive from a-keto acids by a process corresponding to reductive amination. The most important biosynthetic distinction relates to whether appropriate carbon skeletons are pre-existing in basic metabolism or whether they have to be synthesized de novo and this division underpins the structure of this chapter. There are a small number of a-keto acids ubiquitously found in core metabolism, notably pyruvate (and a related 3-phosphoglycerate derivative from glycolysis), together with two components of the tricarboxylic acid cycle (TCA), oxaloacetate and a-ketoglutarate (a-KG). These building blocks ultimately provide the carbon skeletons for unbranched a-amino acids of three, four, and five carbons, respectively. a-Amino acids with shorter (glycine) or longer (lysine and pyrrolysine) straight chains are made by alternative pathways depending on the available raw materials.
    [Show full text]
  • Review Article RNA Degradation in Staphylococcus Aureus: Diversity of Ribonucleases and Their Impact
    Hindawi Publishing Corporation International Journal of Genomics Volume 2015, Article ID 395753, 12 pages http://dx.doi.org/10.1155/2015/395753 Review Article RNA Degradation in Staphylococcus aureus: Diversity of Ribonucleases and Their Impact Rémy A. Bonnin and Philippe Bouloc Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, UniversiteParis-Sud,Universit´ eParis-Saclay,91400Orsay,France´ Correspondence should be addressed to Remy´ A. Bonnin; [email protected] Received 6 January 2015; Accepted 4 March 2015 Academic Editor: Martine A. Collart Copyright © 2015 R. A. Bonnin and P. Bouloc. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The regulation of RNA decay is now widely recognized as having a central role in bacterial adaption to environmental stress.Here we present an overview on the diversity of ribonucleases (RNases) and their impact at the posttranscriptional level in the human pathogen Staphylococcus aureus. RNases in prokaryotes have been mainly studied in the two model organisms Escherichia coli and Bacillus subtilis. Based on identified RNases in these two models, putative orthologs have been identified in S. aureus.Themain staphylococcal RNases involved in the processing and degradation of the bulk RNA are (i) endonucleases RNase III and RNase Y and (ii) exonucleases RNase J1/J2 and PNPase, having 5 to 3 and 3 to 5 activities, respectively. The diversity and potential roles of each RNase and of Hfq and RppH are discussed in the context of recent studies, some of which are based on next-generation sequencing technology.
    [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]
  • 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]
  • Assembly of an Active Enzyme by the Linkage of Two Protein Modules
    Proc. Natl. Acad. Sci. USA Vol. 94, pp. 1069–1073, February 1997 Biochemistry Assembly of an active enzyme by the linkage of two protein modules A. E. NIXON,M.S.WARREN, AND S. J. BENKOVIC* 152 Davey Laboratory, Department of Chemistry, Pennsylvania State University, University Park, PA 16802-6300 Contributed by S. J. Benkovic, December 9, 1996 ABSTRACT The feasibility of creating new enzyme activ- design enzymes with novel properties. Previous approaches to ities from enzymes of known function has precedence in view the design of proteins with novel activities have included of protein evolution based on the concepts of molecular catalytic antibodies (8, 9); introduction of metal ion binding recruitment and exon shuffling. The enzymes encoded by the sites, such as the one engineered into trypsin to allow either Escherichia coli genes purU and purN, N10-formyltetrahydro- control of the proteolytic activity (10) or to regulate specificity folate hydrolase and glycinamide ribonucleotide (GAR) trans- (11); creation of hybrid enzymes through exchange of subunits formylase, respectively, catalyze similiar yet distinct reactions. to create hybrid oligomers (12); replacement of structural N10-formyltetrahydrofolate hydrolase uses water to cleave elements such as the DNA binding domain of GCN4 with that N10-formyltetrahydrofolate into tetrahydrofolate and for- of CyEBP (13); mutation of multiple individual residues to mate, whereas GAR transformylase catalyses the transfer of change the cofactor specificity of glutathione reductase from formyl from N10-formyltetrahydrofolate to GAR to yield NADPH to NADH (14), modulation of the substrate speci- formyl-GAR and tetrahydrofolate. The two enzymes show ficity of aspartate aminotransferase (15); and changing the significant homology ('60%) in the carboxyl-terminal region specificity of subtilisin (16) and a-lytic protease (17) through which, from the GAR transformylase crystal structure and mutation of single functional groups.
    [Show full text]
  • The Journal of Nutrition 1968 Volume 95 No.1
    THE JOURNAL OF NUTRITION* OFFICIAL ORGAN OF THE AMERICAN INSTITUTE OF NUTRITION R i c h a r d H . B a r n e s , Editor Graduate School of Nutrition Cornell University, Savage Hall Ithaca, New York H a r o l d H . W i l l i a m s E. N e i g e T o d h u n t e r Associate Editor Biographical Editor EDITORIAL BOARD S a m u e l J . F o m o n W i l l i a m N. P e a r s o n M . K . H o r w i t t P a u l M . N e w b e r n e F. H. K r a t z e r K e n d a l l W . K i n g B o y d L. O’D e l l H. N. M u n r o H e r b e r t P . S a r e t t H. E. S a u b e r l i c h D o r i s H o w e s C a l l o w a y G e o r g e G . G r a h a m R o s l y n B . A l f i n -S l a t e r J . M . B e l l W i l l i a m G . H o e k s t r a G e o r g e H .
    [Show full text]
  • Resolution of Carbon Metabolism and Sulfur-Oxidation Pathways of Metallosphaera Cuprina Ar-4 Via Comparative Proteomics
    JOURNAL OF PROTEOMICS 109 (2014) 276– 289 Available online at www.sciencedirect.com ScienceDirect www.elsevier.com/locate/jprot Resolution of carbon metabolism and sulfur-oxidation pathways of Metallosphaera cuprina Ar-4 via comparative proteomics Cheng-Ying Jianga, Li-Jun Liua, Xu Guoa, Xiao-Yan Youa, Shuang-Jiang Liua,c,⁎, Ansgar Poetschb,⁎⁎ aState Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China bPlant Biochemistry, Ruhr University Bochum, Bochum, Germany cEnvrionmental Microbiology and Biotechnology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China ARTICLE INFO ABSTRACT Article history: Metallosphaera cuprina is able to grow either heterotrophically on organics or autotrophically Received 16 March 2014 on CO2 with reduced sulfur compounds as electron donor. These traits endowed the species Accepted 6 July 2014 desirable for application in biomining. In order to obtain a global overview of physiological Available online 14 July 2014 adaptations on the proteome level, proteomes of cytoplasmic and membrane fractions from cells grown autotrophically on CO2 plus sulfur or heterotrophically on yeast extract Keywords: were compared. 169 proteins were found to change their abundance depending on growth Quantitative proteomics condition. The proteins with increased abundance under autotrophic growth displayed Bioleaching candidate enzymes/proteins of M. cuprina for fixing CO2 through the previously identified Autotrophy 3-hydroxypropionate/4-hydroxybutyrate cycle and for oxidizing elemental sulfur as energy Heterotrophy source. The main enzymes/proteins involved in semi- and non-phosphorylating Entner– Industrial microbiology Doudoroff (ED) pathway and TCA cycle were less abundant under autotrophic growth. Also Extremophile some transporter proteins and proteins of amino acid metabolism changed their abundances, suggesting pivotal roles for growth under the respective conditions.
    [Show full text]
  • The Structure of Allophanate Hydrolase from Granulibacter Bethesdensis Provides Insights Into Substrate Specificity in the Amidase Signature Family
    Marquette University e-Publications@Marquette Biological Sciences Faculty Research and Publications Biological Sciences, Department of 2013 The Structure of Allophanate Hydrolase from Granulibacter bethesdensis Provides Insights into Substrate Specificity in the Amidase Signature Family Yi Lin Marquette University, [email protected] Martin St. Maurice Marquette University, [email protected] Follow this and additional works at: https://epublications.marquette.edu/bio_fac Part of the Biochemistry, Biophysics, and Structural Biology Commons Recommended Citation Lin, Yi and St. Maurice, Martin, "The Structure of Allophanate Hydrolase from Granulibacter bethesdensis Provides Insights into Substrate Specificity in the Amidase Signature Family" (2013). Biological Sciences Faculty Research and Publications. 138. https://epublications.marquette.edu/bio_fac/138 Marquette University e-Publications@Marquette Biological Sciences Faculty Research and Publications/College of Arts and Sciences This paper is NOT THE PUBLISHED VERSION; but the author’s final, peer-reviewed manuscript. The published version may be accessed by following the link in the citation below. Biochemistry, Vol. 54, No. 4 (January 29, 2013): 690-700. DOI. This article is © American Chemical Society Publications and permission has been granted for this version to appear in e- Publications@Marquette. American Chemical Society Publications does not grant permission for this article to be further copied/distributed or hosted elsewhere without the express permission from American Chemical Society Publications. The Structure of Allophanate Hydrolase from Granulibacter bethesdensis Provides Insights into Substrate Specificity in the Amidase Signature Family Yi Lin Department of Biological Sciences, Marquette University, Milwaukee, WI Martin St. Maurice Department of Biological Sciences, Marquette University, Milwaukee, WI Abstract Allophanate hydrolase (AH) catalyzes the hydrolysis of allophanate, an intermediate in atrazine degradation and urea catabolism pathways, to NH3 and CO2.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Enzymatic Synthesis of L-Fucose from L-Fuculose Using a Fucose Isomerase
    Kim et al. Biotechnol Biofuels (2019) 12:282 https://doi.org/10.1186/s13068-019-1619-0 Biotechnology for Biofuels RESEARCH Open Access Enzymatic synthesis of L-fucose from L-fuculose using a fucose isomerase from Raoultella sp. and the biochemical and structural analyses of the enzyme In Jung Kim1†, Do Hyoung Kim1†, Ki Hyun Nam1,2 and Kyoung Heon Kim1* Abstract Background: L-Fucose is a rare sugar with potential uses in the pharmaceutical, cosmetic, and food industries. The enzymatic approach using L-fucose isomerase, which interconverts L-fucose and L-fuculose, can be an efcient way of producing L-fucose for industrial applications. Here, we performed biochemical and structural analyses of L-fucose isomerase identifed from a novel species of Raoultella (RdFucI). Results: RdFucI exhibited higher enzymatic activity for L-fuculose than for L-fucose, and the rate for the reverse reaction of converting L-fuculose to L-fucose was higher than that for the forward reaction of converting L-fucose to L-fuculose. In the equilibrium mixture, a much higher proportion of L-fucose (~ ninefold) was achieved at 30 °C and pH 7, indicating that the enzyme-catalyzed reaction favors the formation of L-fucose from L-fuculose. When biochemical analysis was conducted using L-fuculose as the substrate, the optimal conditions for RdFucI activity were determined to be 40 °C and pH 10. However, the equilibrium composition was not afected by reaction temperature in the range 2 of 30 to 50 °C. Furthermore, RdFucI was found to be a metalloenzyme requiring Mn + as a cofactor. The comparative crystal structural analysis of RdFucI revealed the distinct conformation of α7–α8 loop of RdFucI.
    [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]