DOCSLIB.ORG

Generated by SRI International Pathway Tools Version 25.0, Authors S

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Generated by SRI International Pathway Tools Version 25.0, Authors S Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp 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. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000067205Cyc: Bordetella petrii DSM 12804 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari an amino an amino an amino an amino an amino an amino an amino an amino an amino acid acid acid acid acid acid acid acid acid molybdate glutathione phosphate phosphate spermidine an amino an amino an amino molybdate molybdate ammonium benzoate benzoate phosphate phosphate phosphate phosphate putrescine acid acid acid predicted predicted predicted predicted predicted predicted predicted predicted predicted predicted predicted predicted ABC ABC ABC ABC ABC ABC ABC ABC ABC ABC ABC ABC RS20125 RS15820 RS18345 RS17890 RS26835 transporter transporter transporter transporter transporter RS24045 RS09900 RS09515 transporter RS03665 RS13385 transporter RS07010 RS20170 transporter transporter transporter transporter RS24670 RS24550 transporter of an of an of an of an of an of molybdate of glutathione of an of an of an of an of phosphate amino acid amino acid amino acid amino acid amino acid amino acid amino acid amino acid amino acid spermidine phosphate molybdate molybdate ammonium benzoate benzoate an amino an amino phosphate phosphate phosphate phosphate an amino putrescine acid acid acid glutathione molybdate an amino an amino an amino an amino phosphate an amino an amino an amino an amino an amino acid acid acid acid acid acid acid acid acid Amino Acid Degradation Hormone Biosynthesis Aminoacyl-tRNA Charging gln Macromolecule Modification tRNA-uridine 2-thiolation glutaminyl-tRNA Carbohydrate Degradation 6 γ N -(3-methylbut- a mature peptidoglycan UDP-N-acetyl-α-D- a [DNA]-3'- a 5'-phospho- UDP-N-acetyl- L-alanyl-γ-D- L-alanyl- -D- UDP-N-acetyl- a [protein]-L- a [protein]-L- a [protein]-L- biosynthesis via transamidation and selenation (bacteria) + L(or D)-O- an L-glutamyl- an L-asparaginyl- L-valine degradation I a sulfurated NAD meso- α glutamyl-meso- α a lipid II glutamate-O 5 N-acetyl- Polyprenyl Biosynthesis 2-en-1-yl)- (meso-diaminopimelate muramoyl-L-alanyl- hydroxyl -D-muramoyl-L- glutamyl-meso-2,6- UDP-N-acetyl- -D-muramoyl- Gln β-isoaspartate glu ala Asn methionine indole-3-acetate Amine and Polyamine Biosynthesis L-isoleucine degradation I L-leucine degradation I L-tyrosine degradation I L-tryptophan degradation to L-histidine degradation I [sulfur carrier] [DNA] diaminopimelate phosphoserine [tRNA ] L-citrulline [tRNA ] glycogen degradation II adenosine 37 containing) γ-D-glutamyl-meso- UDP-N-acetyl- diaminopimelate α γ protein-L- -methyl-ester peptide- biosynthesis 2-amino-3-carboxymuconate D-alanyl-D-alanine alanyl-D-glutamate diaminopimeloyl- -D-muramate L-alanyl- -D- bifunctional Asp-tRNA(Asn) glu cys in tRNA 2,6-diaminopimelate α-D-muramate isoaspartate O- methionine di-trans,poly-cis IV (bacteria) val semialdehyde D-alanine glutamyl-meso-2,6- penicillin- phosphoserine /Glu-tRNA(Gln) ectoine biosynthesis DNA methyltransferase: (S)-S-oxide octaprenyl (indole-3-yl) spermidine putrescine ile leu tyr his a glycogen lytic murein UDP-N- diaminopimeloyl- binding phosphatase/ chemotaxis glutamate-- acetylornithine -undecaprenyl IscS subfamily tRNA (N6-isopentenyl ligase bifunctional UDP- amidotransferase aminoacyl- diphosphate biosynthesis I biosynthesis III aspartate/ trp D-alanyl-D-alanine BPET_RS02445 cysteine ligase: deacetylase: reductase phosphate biosynthesis acetonitrilenitrile cysteine branched-chain branched-chain transglycosylase: bifunctional UDP- D: ligD N-acetylmuramoyl- UDP-N- acetylmuramate:L- protein homoserine GatCAB subunit A: response tRNA biosynthesis asp tyrosine/aromatic tryptophan 2,3- adenosine(37)-C2)- protein-L- BPET_RS01975 argE MsrA: msrA (2E,6E)-farnesyl desulfurase: amino acid branched-chain amino acid BPET_RS09485 N-acetylmuramoyl- L-alanyl-D- acetylmuramate:L- alanyl-gamma-D- 2: mrdA phosphotransferase BPET_RS07165 regulator protein- hydrolase: IPP hydratase: aminotransferase: methylthiotransferase NAD- diphosphate (2E,6E)-farnesyl SAM arg transaminase: amino acid transaminase: dioxygenase: urocanate [+ 5 isozymes] L-alanyl-D- glutamate--2, 6- alanyl-gamma-D- glutamyl- meso- penicillin- ThrH: thrH isoaspartate(D- glutamate glutamate-- acetylornithine arfB peptide- an L-glutamyl- IPP (indol-3-yl)nthB nthA aspartate kinase: BPET_RS14065 3-(4- BPET_RS14085 MiaB: miaB dependent D-alanyl-D-alanine Asp-tRNA(Asn) Gln diphosphate an [L-cysteine transaminase: BPET_RS04645 kynA α glutamyl- meso- diaminopimelate aspartate) O- methylesterase: cysteine ligase: deacetylase: methionine [tRNA ] BPET_RS17500 arginase: BPET_RS04645 hydroxyphenyl) N-Formyl-L- an -limit dextrin glutamate--2, 6- DNA ligase diaminopimelate binding carboxypeptidase/ phosphoserine /Glu-tRNA(Gln) aminoacyl- acetamide desulfurase]-S- BPET_RS04645 succinate diaminopimelate ligase: mpl methyltransferase: BPET_RS10685 BPET_RS23825 argE (S)-S-oxide di-trans,poly-cis- L-aspartyl- rocF branched-chain branched-chain pyruvate kynurenine a mature peptidoglycan a mature peptidoglycan diaminopimelate LigA: ligA ligase MurE/UDP- protein D-alanyl-D-alanine- phosphatase amidotransferase: tRNA Asp-tRNA(Asn) amidase: sulfanyl-L-cysteine 4-alpha- dehydrogenase, ligase: mpl BPET_RS12875 reductase decaprenylcistransferase: octaprenyl- 4-phosphate L-ornithine amino acid branched-chain amino acid arylformamidase: L-proline degradation I with (L-alanyl-γ-D- strand (non- ligase MurE/UDP- N-acetylmuramoyl- 2: mrdA endopeptidase: dacB SerB: serB gatB gatA gatC a protein L-β- hydrolase: /Glu-tRNA(Gln) diphosphate BPET_RS11310 4-hydroxyphenylpyruvate glucanotransferase: hydrophobic an L-glutaminyl- MsrA: msrA gln uppS aminotransferase: amino acid aminotransferase: kynB 4-imidazolone- glutamyl-meso-2,6- reducing terminus) N-acetylmuramoyl- tripeptide--D- UDP-N-acetyl- D-alanyl-D-alanine serine isoaspartate a [protein]-α- γ pth a protein-L- amidotransferase [+ 6 isozymes] aspartate- dioxygenase: hppD malQ membrane anchor Gln MeOH -L-glutamyl- synthase: putrescine dAdoMet aminotransferase: BPET_RS08740 5-propanoate diaminopimeloyl-D- tripeptide--D- [DNA] NMN alanyl-D-alanine UDP-N-acetylmuramoyl- α-D-muramoyl- carboxypeptidase/ [tRNA ] α-methyl ester L-glutamate acetate L-citrulline GatCAB subunit A: semialdehyde arginine/lysine/ BPET_RS08740 4-methyl-2- a debranched protein: sdhD a N- D-alanine methionine- di-trans,octa-cis BPET_RS21420 a [TusA sulfur- BPET_RS08740 pro alanine) tetrapeptide alanyl-D-alanine AMP ligase MurF: murF L-alanyl-γ-D- L-alanyl-γ-D- D-alanyl-D-alanine- Asp-tRNA(Asn) BPET_RS07165 (indol-3-yl)acetate dehydrogenase: ornithine 3-methyl-2- oxopentanoate homogentisate L-kynurenine α-limit dextrin D-ala acetylglucosamine- (S)-S-oxide -undecaprenyl 6 ligase MurF: murF glutamyl-meso-2,6- Asn /Glu-tRNA(Gln) octaprenyl spermidine decarboxylase: carrier protein]-S- oxobutanoate (3S)-3-methyl-2- trifunctional N -(3-methylbut- glutamyl-meso-2,6- endopeptidase: dacB -N-acetylmuramyl- asn tRNA Asp-tRNA(Asn) diphosphate asd homogentisate an unsulfurated diaminopimelate amidotransferase diphosphate synthase: BPET_RS20755 sulfanyl-L-cysteine oxopentanoate transcriptional 5'-deoxyadenosine 2-en-1-yl)-2- met UDP-N-acetyl- diaminopimeloyl- (tetrapeptide) /Glu-tRNA(Gln) undecaprenyl- L-aspartate 4- 1,2-dioxygenase: [sulfur carrier] GatCAB subunit A: synthase: BPET_RS16275 regulator/proline N-formimino- (methylsulfanyl) UDP-N-acetyl-α-D- α-D-muramoyl- D-alanine UDP-N- pyrophosphoryl- amidotransferase: diphosphate semialdehyde putrescine 3-methylbutanoyl- 37 BPET_RS07165 BPET_RS23660 BPET_RS20390 dehydrogenase/L- L-glutamate α adenosine L-alanyl-γ-D- undecaprenol gatB gatA gatC phosphatase: spermidine -D- muramoyl-L-alanyl- D-ala acetylmuramoyl- diaminobutyrate- CoA 4-maleyl- 3-hydroxy- glutamate gamma- D-glucopyranose in tRNA γ γ [+ 8 isozymes] a 5-phosphooxy- synthase: a [TusD sulfur- isobutanoyl-CoA (2S)-2- formimidoylglutamase: glucopyranose -D-glutamyl-meso- glutamyl-meso-2,6- L-alanyl- -D- BPET_RS17540 all-trans- -2-oxoglutarate isovaleryl-CoA acetoacetate L-kynurenine semialdehyde L-glutamyl- di-trans,octa-cis BPET_RS16615 carrier protein]-S- methylbutanoyl- BPET_RS12605 1-phosphate 2,6-diaminopimeloyl- diaminopimelate glutamyl-meso-2,6- ammonium octaprenyl transaminase: ectB dehydrogenase: dehydrogenase: Gln -undecaprenyl sulfanyl-L-cysteine CoA maleylacetoacetate D-alanyl-D-alanine diaminopimeloyl- [tRNA ] diphosphate kynureninase: phosphate L-2,4- BPET_RS00295 isomerase: maiA (S)-1-pyrroline-putA phosphomannomutase/ D-alanine spermidine kynU glu Asp-tRNA(Asn) diaminobutanoate isovaleryl-CoA maleylacetoacetate 5-carboxylate phosphoglucomutase: methylacrylyl-CoA dehydrogenase: BPET_RS20415 /Glu-tRNA(Gln) a [TusE sulfur isomerase: maiA 3-hydroxyanthranilate an O 4 - α α diaminobutyrate (E)-2- ditrans,octacis- a peptidoglycan with a single a peptidoglycan dimer (meso a [protein]- ditrans,octacis- Nα,Nε-diacetyl-lysyl- a [bis(guanylyl a 6-(N-acetyl- - queuosine at N-acetyl- - 4-methyl-3- amidotransferase BPET_RS09935 4-fumaryl- NADPH NAD + an L-aspartyl- N-formyl- an L-cysteinyl- acetyltransferase:
Load more

Recommended publications
  • Heterologous Expression and Identification of the Genes Involved
    Heterologous Expression and Identification of the Genes Involved in Anaerobic Degradation of 1,3-Dihydroxybenzene (Resorcinol) in Azoarcus anaerobiusᰔ Paula I. Darley,1† Jutta A. Hellstern,1†‡ Javier I. Medina-Bellver,2 Silvia Marque´s,2 Bernhard Schink,1 and Bodo Philipp1* Fachbereich Biologie, Universita¨t Konstanz, D-78457 Constance, Germany,1 and Estacio´n Experimental del Zaidı´n, C/. Profesor Albareda 1, E-18008 Granada, Spain2 Received 9 November 2006/Accepted 9 March 2007 Azoarcus anaerobius, a strictly anaerobic, gram-negative bacterium, utilizes resorcinol as a sole carbon and energy source with nitrate as an electron acceptor. Previously, we showed that resorcinol degradation by this bacterium is initiated by two oxidative steps, both catalyzed by membrane-associated enzymes that lead to the formation of hydroxyhydroquinone (HHQ; 1,2,4-benzenetriol) and 2-hydroxy-1,4-benzoquinone (HBQ). This study presents evidence for the further degradation of HBQ in cell extracts to form acetic and malic acids. To identify the A. anaerobius genes required for anaerobic resorcinol catabolism, a cosmid library with genomic DNA was constructed and transformed into the phylogenetically related species Thauera aromatica, which cannot grow with resorcinol. By heterologous complementation, a transconjugant was identified that gained the ability to metabolize resorcinol. Its cosmid, designated R؉, carries a 29.88-kb chromosomal DNA fragment containing 22 putative genes. In cell extracts of T. aromatica transconjugants, resorcinol was degraded to HHQ, HBQ, and acetate, suggesting that cosmid R؉ carried all of the genes necessary for resorcinol degradation. On the basis of the physiological characterization of T. aromatica transconjugants carrying transposon insertions -in different genes of cosmid R؉, eight open reading frames were found to be essential for resorcinol miner alization.
    [Show full text]
  • Phospholipid:Diacylglycerol Acyltransferase: an Enzyme That Catalyzes the Acyl-Coa-Independent Formation of Triacylglycerol in Yeast and Plants
    Phospholipid:diacylglycerol acyltransferase: An enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants Anders Dahlqvist*†‡, Ulf Ståhl†§, Marit Lenman*, Antoni Banas*, Michael Lee*, Line Sandager¶, Hans Ronne§, and Sten Stymne¶ *Scandinavian Biotechnology Research (ScanBi) AB, Herman Ehles Va¨g 2 S-26831 Svaloˆv, Sweden; ¶Department of Plant Breeding Research, Swedish University of Agricultural Sciences, Herman Ehles va¨g 2–4, S-268 31 Svalo¨v, Sweden; and §Department of Plant Biology, Uppsala Genetic Center, Swedish University of Agricultural Sciences, Box 7080, S-750 07 Uppsala, Sweden Edited by Christopher R. Somerville, Carnegie Institution of Washington, Stanford, CA, and approved March 31, 2000 (received for review February 15, 2000) Triacylglycerol (TAG) is known to be synthesized in a reaction that acid) and epoxidated fatty acid (vernolic acid) in TAG in castor uses acyl-CoA as acyl donor and diacylglycerol (DAG) as acceptor, bean (Ricinus communis) and the hawk’s-beard Crepis palaestina, and which is catalyzed by the enzyme acyl-CoA:diacylglycerol respectively. Furthermore, a similar enzyme is shown to be acyltransferase. We have found that some plants and yeast also present in the yeast Saccharomyces cerevisiae, and the gene have an acyl-CoA-independent mechanism for TAG synthesis, encoding this enzyme, YNR008w, is identified. which uses phospholipids as acyl donors and DAG as acceptor. This reaction is catalyzed by an enzyme that we call phospholipid:dia- Materials and Methods cylglycerol acyltransferase, or PDAT. PDAT was characterized in Yeast Strains and Plasmids. The wild-type yeast strains used were microsomal preparations from three different oil seeds: sunflower, either FY1679 (MAT␣ his3-⌬200 leu2-⌬1 trp1-⌬6 ura3-52) (9) or castor bean, and Crepis palaestina.
    [Show full text]
  • Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
    ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co.
    [Show full text]
  • Peroxisomal Fatty Acid Beta-Oxidation in Relation to the Accumulation Of
    Peroxisomal fatty acid beta-oxidation in relation to the accumulation of very long chain fatty acids in cultured skin fibroblasts from patients with Zellweger syndrome and other peroxisomal disorders. R J Wanders, … , A W Schram, J M Tager J Clin Invest. 1987;80(6):1778-1783. https://doi.org/10.1172/JCI113271. Research Article The peroxisomal oxidation of the long chain fatty acid palmitate (C16:0) and the very long chain fatty acids lignocerate (C24:0) and cerotate (C26:0) was studied in freshly prepared homogenates of cultured skin fibroblasts from control individuals and patients with peroxisomal disorders. The peroxisomal oxidation of the fatty acids is almost completely dependent on the addition of ATP, coenzyme A (CoA), Mg2+ and NAD+. However, the dependency of the oxidation of palmitate on the concentration of the cofactors differs markedly from that of the oxidation of lignocerate and cerotate. The peroxisomal oxidation of all three fatty acid substrates is markedly deficient in fibroblasts from patients with the Zellweger syndrome, the neonatal form of adrenoleukodystrophy and the infantile form of Refsum disease, in accordance with the deficiency of peroxisomes in these patients. In fibroblasts from patients with X-linked adrenoleukodystrophy the peroxisomal oxidation of lignocerate and cerotate is impaired, but not that of palmitate. Competition experiments indicate that in fibroblasts, as in rat liver, distinct enzyme systems are responsible for the oxidation of palmitate on the one hand and lignocerate and cerotate on the other hand. Fractionation studies indicate that in rat liver activation of cerotate and lignocerate to cerotoyl-CoA and lignoceroyl-CoA, respectively, occurs in two subcellular fractions, the endoplasmic reticulum and the peroxisomes but not in the mitochondria.
    [Show full text]
  • Table S1-Final.Xlsx
    Table S1. Functional gene families covered on the GeoChip 5.0. No. of sequence‐ No. of group‐ No. of total No. of covered No. of total Category Subcategory Subcategory 2 Gene Encoded Enzyme specific probesa specific probesa probes on 5M CDSa probes on 5S Categories for Geochemical Cycling Carbon Cycling Carbon Degradation Agar beta_agarase Agarase 42 79 217 121 Agar Total 42 79 0 217 121 Alginate alginase Alginase 45 200 512 245 Alginate Total 45 200 0 512 245 Cellulose Endoglucanase Endoglucanase 198 248 446 740 343 Cellulose Total 198 248 446 740 343 Chitin Acetylglucosaminidase Acetylglucosaminidase 119 976 1095 3088 1116 Chitinase Chitinase 649 1231 1880 3285 1411 endochitinase Endochitinase 213 334 1104 547 exochitinase Exochitinase 14 55 259 69 Chitin Total 995 2596 2975 7736 3143 Glyoxylate cycle AceA Isocitrate lyase 69 373 442 887 0 AceB Malate synthase A 90 610 700 1457 0 Glyoxylate cycle Total 159 983 1142 2344 0 Hemicellulose Ara Arabinofuranosidase 172 543 715 1367 827 Mannanase Mannanase 159 238 397 639 478 Xylanase Xylanase 150 653 803 1739 858 Hemicellulose Total 481 1434 1915 3745 2163 Heparin heparinase Heparinase 7 53 166 60 Heparin Total 7 53 0 166 60 Hyaluronic acid hyaluronidase Hyaluronidase 880 383 88 Hyaluronidase Total 8 80 0 383 88 Lignin Glx Glyoxal oxidase 103 40 143 178 125 Mnp Manganese peroxidase 50 13 63 74 66 Phenol_oxidase Laccase or phenol oxidase 188 372 560 1009 677 Lignin Total 341 425 766 1261 868 Pectin Pectinase (pectate_lyase) Pectate lyase 53 252 305 827 321 Pme Pectin methylesterase 25 240 265
    [Show full text]
  • Maleylacetate Reductase from Trichosporon Cutaneum
    Biochem. J. (1980) 185, 783-786 783 Printed in Great Britain Maleylacetate Reductase from Trichosporon cutaneum Andras B. GAAL and Halina Y. NEUJAHR Department ofBiochemistry and Biochemical Technology, The Royal Institute of Technology, S 100 44 Stockholm, Sweden (Received 12 November 1979) The enzyme catalysing the reduction of maleylacetate to 3-oxoadipate was purified 150-fold from Trichosporon cutaneum, induced for aromatic metabolism by growth with resorcinol as a major carbon source. The enzyme separated upon electrofocusing into three species with pI values 4.6, 5.1 and 5.6. They had similar catalytic properties and the same molecular weight. Our group has previously reported that the yeast fer, pH 7.6, 0.2pmol of maleylacetate, 0.2,mol of Trichosporon cutaneum can be induced to metabol- NADPH and 50-200#ug of enzyme protein. Under ize phenol and resorcinol, both phenols being these conditions 1 enzyme unit corresponds to an attacked by the same hydroxylating enzyme and the absorbance decrease of 6.1 A340 units/min. same ring-cleavage enzyme (Neujahr & Varga, Determination of molecular weight. Molecular 1970; Varga & Neujahr, 1970). We have since weight was determined by gel filtration (Andrews, demonstrated that both phenol and resorcinol are 1965) on a Sephadex G-150 column metabolized to 3-oxoadipate (Gaal & Neujahr, (2.5cm x 85cm) equilibrated with 50mM-Tris/ 1979). The metabolism of resorcinol goes through H2SO4 buffer, pH 7.6. Alcohol dehydrogenase 1,2,4-trihydroxybenzene and maleylacetate. The (mol.wt. 150000), lactate dehydrogenase (mol.wt. enzyme catalysing the reduction of maleylacetate to 136000), hexokinase (mol.wt. 105000) and avidin 3-oxoadipate was enriched from crude extracts (mol.wt.
    [Show full text]
  • (10) Patent No.: US 8119385 B2
    US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides.
    [Show full text]
  • Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT)
    International Journal of Molecular Sciences Review Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT) Abu Iftiaf Md Salah Ud-Din 1, Alexandra Tikhomirova 1 and Anna Roujeinikova 1,2,* 1 Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia; [email protected] (A.I.M.S.U.-D.); [email protected] (A.T.) 2 Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia * Correspondence: [email protected]; Tel.: +61-3-9902-9194; Fax: +61-3-9902-9222 Academic Editor: Claudiu T. Supuran Received: 30 May 2016; Accepted: 20 June 2016; Published: 28 June 2016 Abstract: General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) catalyze the transfer of an acyl moiety from acyl coenzyme A (acyl-CoA) to a diverse group of substrates and are widely distributed in all domains of life. This review of the currently available data acquired on GNAT enzymes by a combination of structural, mutagenesis and kinetic methods summarizes the key similarities and differences between several distinctly different families within the GNAT superfamily, with an emphasis on the mechanistic insights obtained from the analysis of the complexes with substrates or inhibitors. It discusses the structural basis for the common acetyltransferase mechanism, outlines the factors important for the substrate recognition, and describes the mechanism of action of inhibitors of these enzymes. It is anticipated that understanding of the structural basis behind the reaction and substrate specificity of the enzymes from this superfamily can be exploited in the development of novel therapeutics to treat human diseases and combat emerging multidrug-resistant microbial infections.
    [Show full text]
  • Catalytic Mechanism of Perosamine N-Acetyltransferase Revealed by High-Resolution X-Ray Crystallographic Studies and Kinetic Analyses James B
    Article pubs.acs.org/biochemistry Catalytic Mechanism of Perosamine N-Acetyltransferase Revealed by High-Resolution X-ray Crystallographic Studies and Kinetic Analyses James B. Thoden,† Laurie A. Reinhardt,† Paul D. Cook,‡ Patrick Menden,§ W. W. Cleland,*,† and Hazel M. Holden*,† † Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, United States ‡ Department of Chemistry and Biochemistry, University of Mount Union, Alliance, Ohio 44601, United States § McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, United States ABSTRACT: N-Acetylperosamine is an unusual dideoxysugar found in the O-antigens of some Gram-negative bacteria, including the pathogenic Escherichia coli strain O157:H7. The last step in its biosynthesis is catalyzed by PerB, an N-acetyltransferase belonging to the left-handed β-helix superfamily of proteins. Here we describe a combined structural and functional investigation of PerB from Caulobacter crescentus. For this study, three structures were determined to 1.0 Å resolution or better: the enzyme in complex with CoA and GDP-perosamine, the protein with bound CoA and GDP-N-acetylperosamine, and the enzyme containing a tetrahedral transition state mimic bound in the active site. Each subunit of the trimeric enzyme folds into two distinct regions. The N-terminal domain is globular and dominated by a six-stranded mainly parallel β-sheet. It provides most of the interactions between the protein and GDP-perosamine. The C-terminal domain consists of a left-handed β-helix, which has nearly seven turns. This region provides the scaffold for CoA binding. On the basis of these high-resolution structures, site-directed mutant proteins were constructed to test the roles of His 141 and Asp 142 in the catalytic mechanism.
    [Show full text]
  • Supplementary Informations SI2. Supplementary Table 1
    Supplementary Informations SI2. Supplementary Table 1. M9, soil, and rhizosphere media composition. LB in Compound Name Exchange Reaction LB in soil LBin M9 rhizosphere H2O EX_cpd00001_e0 -15 -15 -10 O2 EX_cpd00007_e0 -15 -15 -10 Phosphate EX_cpd00009_e0 -15 -15 -10 CO2 EX_cpd00011_e0 -15 -15 0 Ammonia EX_cpd00013_e0 -7.5 -7.5 -10 L-glutamate EX_cpd00023_e0 0 -0.0283302 0 D-glucose EX_cpd00027_e0 -0.61972444 -0.04098397 0 Mn2 EX_cpd00030_e0 -15 -15 -10 Glycine EX_cpd00033_e0 -0.0068175 -0.00693094 0 Zn2 EX_cpd00034_e0 -15 -15 -10 L-alanine EX_cpd00035_e0 -0.02780553 -0.00823049 0 Succinate EX_cpd00036_e0 -0.0056245 -0.12240603 0 L-lysine EX_cpd00039_e0 0 -10 0 L-aspartate EX_cpd00041_e0 0 -0.03205557 0 Sulfate EX_cpd00048_e0 -15 -15 -10 L-arginine EX_cpd00051_e0 -0.0068175 -0.00948672 0 L-serine EX_cpd00054_e0 0 -0.01004986 0 Cu2+ EX_cpd00058_e0 -15 -15 -10 Ca2+ EX_cpd00063_e0 -15 -100 -10 L-ornithine EX_cpd00064_e0 -0.0068175 -0.00831712 0 H+ EX_cpd00067_e0 -15 -15 -10 L-tyrosine EX_cpd00069_e0 -0.0068175 -0.00233919 0 Sucrose EX_cpd00076_e0 0 -0.02049199 0 L-cysteine EX_cpd00084_e0 -0.0068175 0 0 Cl- EX_cpd00099_e0 -15 -15 -10 Glycerol EX_cpd00100_e0 0 0 -10 Biotin EX_cpd00104_e0 -15 -15 0 D-ribose EX_cpd00105_e0 -0.01862144 0 0 L-leucine EX_cpd00107_e0 -0.03596182 -0.00303228 0 D-galactose EX_cpd00108_e0 -0.25290619 -0.18317325 0 L-histidine EX_cpd00119_e0 -0.0068175 -0.00506825 0 L-proline EX_cpd00129_e0 -0.01102953 0 0 L-malate EX_cpd00130_e0 -0.03649016 -0.79413596 0 D-mannose EX_cpd00138_e0 -0.2540567 -0.05436649 0 Co2 EX_cpd00149_e0
    [Show full text]
  • Biochemical Studies on Redox Regulation in Different Dormancy Models of Mycobacteria
    Biochemical Studies on Redox Regulation in Different Dormancy Models of Mycobacteria Thesis Submitted to Savitribai Phule Pune University For The Degree Of DOCTOR OF PHILOSOPHY IN BIOTECHNOLOGY By Ketaki Dilip Shurpali Research Supervisor Dr. Dhiman Sarkar Combichem Bioresource Center Organic Chemistry Division CSIR-National Chemical Laboratory Pune-411008 India October 2014 Certificate This is to certify that the work incorporated in the thesis entitled “ Biochemical Studies on Redox Regulation in Different Dormancy Models of Mycobacteria ” submitted by Ketaki Dilip Shurpali was carried out under my supervision at Combichem Bioresource Center, Organic Chemistry Division, National Chemical Laboratory, Pune-411008, Maharashtra, India. Materials obtained from other sources have been duly acknowledged in the thesis. Dr. Dhiman Sarkar (Research Guide) I Declaration by Research Scholar I hereby declare that the thesis entitled " Biochemical Studies on Redox Regulation in Different Dormancy Models of Mycobacteria ", submitted for the Degree of Doctor of Philosophy to the Savitribai Phule Pune University, has been carried out by me at Combichem Bioresource Center, Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune-411008, Maharashtra, India, under the supervision of Dr. Dhiman Sarkar (Research supervisor). The work is original and has not been submitted in part or full by me for any other degree or diploma to any other University. Ketaki Dilip Shurpali (Research Scholar) II Dedications This thesis is dedicated to all those people who were always besides me in my good and bad times. First dedication goes to my father Mr. Dilip Shurpali and mother Mrs. Devyani Shurpali who instilled in me the desire to learn new things and confidence to achieve my dreams.
    [Show full text]
  • Bacterial Degradation of Chlorophenols and Their Derivatives Pankaj Kumar Arora and Hanhong Bae*
    Arora and Bae Microbial Cell Factories 2014, 13:31 http://www.microbialcellfactories.com/content/13/1/31 REVIEW Open Access Bacterial degradation of chlorophenols and their derivatives Pankaj Kumar Arora and Hanhong Bae* Abstract Chlorophenols (CPs) and their derivatives are persistent environmental pollutants which are used in the manufacture of dyes, drugs, pesticides and other industrial products. CPs, which include monochlorophenols, polychlorophenols, chloronitrophenols, chloroaminophenols and chloromethylphenols, are highly toxic to living beings due to their carcinogenic, mutagenic and cytotoxic properties. Several physico-chemical and biological methods have been used for removal of CPs from the environment. Bacterial degradation has been considered a cost-effective and eco-friendly method of removing CPs from the environment. Several bacteria that use CPs as their sole carbon and energy sources have been isolated and characterized. Additionally, the metabolic pathways for degradation of CPs have been studied in bacteria and the genes and enzymes involved in the degradation of various CPs have been identified and characterized. This review describes the biochemical and genetic basis of the degradation of CPs and their derivatives. Keywords: Chlorophenol, Environmental pollutants, Bacterial degradation, Biodegradation Introduction human carcinogens [5]. Similarly, the United States Envir- Chlorophenols (CPs) are aromatic ring structures contain- onmental Protection Agency has included several CPs in its ing at least one chlorine atom (−Cl) and one hydroxyl list of priority pollutants. (−OH) group at the benzene rings. Five groups of CPs have Several conventional methods such as adsorption, ion been recognized on the basis of their chemical structures, exchange, liquid–liquid extraction, and chemical oxida- monochlorophenols (MCPs), polychlorophenols (poly- tion and advanced oxidation processes have been used CPs), chloronitrophenols (CNPs), chloroaminophenols for the removal of CPs from wastewater [3,6].
    [Show full text]