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Authors: Pallavi Subhraveti Ron Caspi Quang Ong 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. Ecol316385Cyc: Escherichia coli K-12 substr. DH10B Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari sn-glycerol met spermidine spermidine 3-phosphate L-tartrate agmatine arg glutamate γ-butyrobetaine a dipeptide a purine O-acetyl-L-serine O-acetyl-L-serine 1-(β-D glutathione Fe 3+ putrescine putrescine D-ala 3-(3- N 6 -(D- D-methionine spermidine enterobactin enterobactin succinate arg 4-aminobutanoate glutamate glutamate sn-glycerol L-carnitine a tripeptide ribonucleoside (R)- glutathione cys cys ribofuranosyl) N-acetyl-D- a polysaccharide α-L- arg spermidine glycine betaine D-serine hydroxyphenyl) N,N'- fructosyl) p-aminobenzoyl a 2,3,4-saturated fatty acid met a sulfonate N-acetylneuraminate D-mannitol D-mannitol putrescine 4-aminobutanoate putrescine putrescine asp asp 2-oxoglutarate 3-phenylpropanoate D-glucarate galactitol D-galactarate pantothenate cys nicotinamide rhamnopyranose putrescine gly gly 3-phosphate predicted -L-lysine glutamate cis-vaccenate predicted muramate predicted predicted propanoate diacetylchitobiose predicted predicted ABC ATP-driven ABC ABC ABC ABC transporter RS00900 transporter RS11675 RS17445 RS17355 UbiB RS17995 RS16955 RS17265 RS17610 RS08800 RS08505 RS09015 RS12430 RS04905 RS13975 RS08525 RS08875 RS04195 RS00245 RS09040 RS00240 RS08785 RS03375 RS02840 RS19710 RS12455 RS00685 RS11605 RS09020 RS04700 RS05160 RS13185 RS21490 RS20860 RS23020 RS16465 RS15760 RS21970 RS15715 RS19245 RS07285 RS08315 RS14375 RS06175 transporter transporter PotG RS11030 ArtP ArtP RS14460 RS22465 RS12205 RS14025 RS13740 RS23570 RS00210 RS09585 RS15030 RS11420 RS16770 FrlA RS19820 RS15655 RS07415 RS07045 RS18650 RS09025 RS22060 NepI RS07495 RS09945 transporter transporter of sn- of L- of spermidine/ of spermidine/ of glutathione of L-arginine glycerol 3- methionine putrescine putrescine phosphate O-acetyl-L-serine O-acetyl-L-serine a polysaccharide α 3+ 6 (R)- glutathione spermidine 1-(β-D enterobactin enterobactin N-acetyl-D- -L- D-mannitol D-mannitol Fe glycine betaine D-ala 3-(3- N,N'- galactitol 1- N -(D- a purine p-aminobenzoyl a 2,3,4-saturated fatty acyl CoA D-methionine N-acetylneuraminate succinate glutamate glutamate sn-glycerol cys cys ribofuranosyl) a sulfonate muramate 6- rhamnopyranose 1-phosphate arg arg 1-phosphate putrescine 4-aminobutanoate 4-aminobutanoate spermidine putrescine putrescine D-serine 2-oxoglutarate 3-phenylpropanoate hydroxyphenyl) L-carnitine diacetylchitobiose D-glucarate phosphate D-galactarate fructosyl) a tripeptide ribonucleoside met pantothenate cys asp asp gly 3-phosphate glutamate cis-vaccenoyl-CoA nicotinamide phosphate L-tartrate agmatine putrescine gly propanoate γ-butyrobetaine -L-lysine a dipeptide glutathione arg glutamate spermidine spermidine met putrescine putrescine sn-glycerol 3-phosphate pro RS05590 pro MdoG a nascent peptidoglycan 1915 2457 a ribonucleoside adenosine 746 a protein a (7Z,10Z,13Z [2Fe-2S] iron-sulfur cluster biosynthesis Cofactor, Prosthetic Group, Electron Carrier, and Vitamin Biosynthesis L-arginine degradation Amino Acid Degradation a purine a pseudouridine a 23S rRNA uridine uridine sn-glycerol α-ribazole superpathway of tetrahydrofolate biosynthesis superpathway of thiamine diphosphate biosynthesis I NAD salvage pathway III bis(guanylyl molybdenum L-phenylalanine L-threonine degradation II with (L-alanyl-γ-D- a purine a purine 1911/1915/1917 2',3'-cyclic 2',3'-cyclic with incorrect ,16Z,19Z)-3- pro RS01840 pro ubiquinol-8 biosynthesis superpathay of heme b 1,4-dihydroxy-2- thiamine diphosphate Fermentation mixed acid fermentation II (AST pathway) L-proline degradation glycine cleavage a tRNA precursor CTP ATP arsenate in 23S rRNA uridine in 23S rRNA in 23S rRNA 3-phosphate 5'-phosphate RS12270 cofactor) biosynthesis Aldehyde Degradation glutamyl-meso-2,6- lipid II (meso ribonucleoside adenosylcobinamide ribonucleoside 23S rRNA ribonucleoside ribosomal large ribosomal large phosphate monophosphate 23S rRNA disulfide bonds oxodocosa- (prokaryotic) biosynthesis from glutamate naphthoate biosynthesis biosynthesis degradation II (anaerobic) 2',3'-cyclic-nucleotide multifunctional CCA glycerol-3-phosphate thiol:disulfide adenosylcobalamin/ a [glycine- diaminopimelate 5'-triphosphate multifunctional CCA purine-nucleoside (pseudouridine(1915)- purine-nucleoside L-cysteine desulfurase all-trans- + MoO - phosphoenol diaminopimeloyl- adenosylcobinamide subunit pseudouridine subunit pseudouridine pseudouridine acyltransferase: interchange 7,10,13,16,19- II (Bacillus) NADP 2 arg containing) phosphorylase: 2'-phosphodiesterase/ tRNA nucleotidyl alpha-ribazole beta- cys pro cleavage complex thr methylglyoxal degradation I D-alanyl-D-alanine) monofunctional kinase/ tRNA nucleotidyl N(3))-methyltransferase phosphorylase: synthase D: synthase D: synthase F: pentaenoyl-[acp] serine serine GTP 4-hydroxybenzoate octaprenyl Glu chorismate alkaline phosphatase: molybdopterin pyruvate phe L-lactaldehyde 3'-nucleotidase: transferase/2'3'-cyclic ECDH10B_RS16445 protein DsbG: phosphatase: ketoacyl- RS16600 HMP-PP arginine N- H protein] N 6 - P-protein: L-threonine 3- biosynthetic ECDH10B_RS23180 ECDH10B_RS23180 cysteine desulfurase: 4-hydroxybenzoatediphosphate isochorismate cofactor bis(molybdenum bifunctional proline pentapeptide adenosylcobinamide transferase/2'3'-cyclic RlmH: ECDH10B_RS14065 ECDH10B_RS14065 ECDH10B_RS22490 ECDH10B_RS21460 ECDH10B_RS02910 ECDH10B_RS03080 ACP thr thr glutamate--tRNA ligase: thiamine phosphate cysteine desulfurase: ECDH10B_RS01745 succinyltransferase: aromatic amino acid dehydrogenase: degradation (anaerobic) purine-nucleoside phosphodiesterase/ glycerol-3-phosphate ECDH10B_RS09290 synthase EntC: pyruvate kinase I: phosphoenolpyruvate dehydrogenase/L- lipoyl-L-lysine ECDH10B_RS14085 peptidoglycan phosphate phosphodiesterase/ ECDH10B_RS03070 purine-nucleoside 23S rRNA RS04435 GTP cyclohydrolase octaprenyltransferase: ECDH10B_RS09290 acid phosphatase cofactor) ECDH10B_RS09640 aminotransferase: L-serine degradation ECDH10B_RS19335 methylglyoxal a nascent peptidoglycan bifunctional tRNA bifunctional tRNA multifunctional CCA 2'nucleotidase/ 1-O-acyltransferase: thiol:disulfide adenosylcobalamin/ a (3R,7Z,10reductase:Z ECDH10B_RS13030 synthase: carboxylase: N 2 -succinyl- glutamate gamma- gcv system: L-2-amino-3- transglycosylase: guanyltransferase: 2'nucleotidase/ phosphorylase: phosphorylase: cysteine I FolE: ECDH10B_RS21570 an L-glutamyl- ECDH10B_RS02850 synthase: mobA ECDH10B_RS09270 ECDH10B_RS21640 dihydrolipoyl lactoylglutathione (S)-lactaldehyde γ 23S rRNA pseudouridine(32) pseudouridine(32) phosphatase: pseudouridine ECDH10B_RS21575 interchange ,13Z,16Z,19ZfabG)-3- 3-octaprenyl-4- ECDH10B_RS21305 cysteine AphA: bis(molybdenum keto- ECDH10B_RS00485 withECDH10B_RS17180 (L-alanyl- -D- phosphatase: ECDH10B_RS13070 ECDH10B_RS13070 tRNA nucleotidyl 1-[18- alpha-ribazole L-homoserine L-homoserine Glu ECDH10B_RS21110 L-arginine semialdehyde oxobutanoate di-trans,octa-cis a purine ECDH10B_RS10910adenosyl- synthase E: desulfurase CsdA: ECDH10B_RS11740 [tRNA ] [+ 2 isozymes] thiamine ECDH10B_RS21650 pyruvate kinase II: dehydrogenase: lyase: lactaldehyde glutamyl-meso-2,6- (pseudouridine(1915)- α-D-ribose- synthase/ribosomal synthase/ribosomal transferase/2'3'-cyclic ECDH10B_RS16430 protein DsbG: phosphatase: hydroxydocosa- RS04530 7,8- hydroxybenzoate superpathway of pyridoxal 5'-phosphate biosynthesis and salvage desulfurase CsdA: cofactor) dehydrogenase: phenylpyruvate a tRNA ECDH10B_RS16430 hydroxyoleyl]- thr thr ECDH10B_RS15140 isochorismate phosphate NAD + ECDH10B_RS10225 N-succinylarginine ECDH10B_RS00485 ser 2-amino-3-ketobutyrate ECDH10B_RS09140 reductase: -undecaprenyl ribonucleoside cobinamide ribose-1-arsenate a purine base N(3))-methyltransferase a purine base large subunit large subunit ECDH10B_RS06225 ECDH10B_RS03445 7,10,13,16,19- 3-octaprenyl-4- glutamyl-tRNA ECDH10B_RS15140 molybdenum cofactor (R)-S- diaminopimeloyl- 1-phosphate phosphodiesterase/ 2',3'-cyclic-nucleotide 746 2-lyso- a protein ECDH10B_RS03615 dihydroneopterin dihydrolase: putA CoA ligase: ECDH10B_RS15085 diphosphate 5'-diphosphate phosphate containing a RlmH: pseudouridine pseudouridine a pseudouridine RS04140 an S-sulfanyl-[L- thiamine- an [L-cysteine guanylyltransferase: oxaloacetate (S)-1-pyrroline- a [glycine- L-serine dehydratase lactoylglutathione D-alanyl-D-alanine) 2'nucleotidase/ 2'-phosphodiesterase/ phosphatidate with correct α-ribazole pentaenoyl-[acp] 3'-triphosphate hydroxybenzoate reductase: 2-succinyl-6-hydroxy- D-erythrose NADH ECDH10B_RS09630 a [glycine-cleavage (S)-propane- 3' CCA end ECDH10B_RS03605 in 23S rRNA flavin biosynthesis I (bacteria and plants) desulfurase]-S- 5-carboxylate 1: ECDH10B_RS09990 ECDH10B_RS19340 3 synthase RluA: synthase RluA: cysteine desulfurase] monophosphate mobA pyruvate cleavage complex 6 pentapeptide phosphatase: decarboxylase: ECDH10B_RS06510 2, 4-cyclohexadiene-1- 4-phosphate 2 hydroxyacylglutathione 1,2-diol an N - 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    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).
  • Dissimilation of Cysteate Via 3-Sulfolactate Sulfo-Lyase and a Sulfate Exporter in Paracoccus Pantotrophus NKNCYSA

    Dissimilation of Cysteate Via 3-Sulfolactate Sulfo-Lyase and a Sulfate Exporter in Paracoccus Pantotrophus NKNCYSA

    Microbiology (2005), 151, 737–747 DOI 10.1099/mic.0.27548-0 Dissimilation of cysteate via 3-sulfolactate sulfo-lyase and a sulfate exporter in Paracoccus pantotrophus NKNCYSA Ulrike Rein,1 Ronnie Gueta,1 Karin Denger,1 Ju¨rgen Ruff,1 Klaus Hollemeyer2 and Alasdair M. Cook1 Correspondence 1Department of Biology, The University, D-78457 Konstanz, Germany Alasdair Cook 2Institute of Biochemical Engineering, Saarland University, Box 50 11 50, D-66041 [email protected] Saarbru¨cken, Germany Paracoccus pantotrophus NKNCYSA utilizes (R)-cysteate (2-amino-3-sulfopropionate) as a sole source of carbon and energy for growth, with either nitrate or molecular oxygen as terminal electron acceptor, and the specific utilization rate of cysteate is about 2 mkat (kg protein)”1. The initial degradative reaction is catalysed by an (R)-cysteate : 2-oxoglutarate aminotransferase, which yields 3-sulfopyruvate. The latter was reduced to 3-sulfolactate by an NAD-linked sulfolactate dehydrogenase [3?3 mkat (kg protein)”1]. The inducible desulfonation reaction was not detected initially in cell extracts. However, a strongly induced protein with subunits of 8 kDa (a) and 42 kDa (b) was found and purified. The corresponding genes had similarities to those encoding altronate dehydratases, which often require iron for activity. The purified enzyme could then be shown to convert 3-sulfolactate to sulfite and pyruvate and it was termed sulfolactate sulfo-lyase (Suy). A high level of sulfite dehydrogenase was also induced during growth with cysteate, and the organism excreted sulfate. A putative regulator, OrfR, was encoded upstream of suyAB on the reverse strand. Downstream of suyAB was suyZ, which was cotranscribed with suyB.