Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
CAS
PubMed
PubMed Central
Google Scholar
Burschowsky D, Thorbjørnsrud HV, Heim JB, Fahrig-Kamarauskaitė J, Würth-Roderer K, Kast P, Krengel U (2018) Inter-enzyme allosteric regulation of chorismate mutase in corynebacterium glutamicum: structural basis of feedback activation by Trp. Biochemistry 57:557–573. https://doi.org/10.1021/acs.biochem.7b01018
Article
CAS
PubMed
Google Scholar
Cross PJ, Pietersma AL, Allison TM, Wilson-Coutts SM, Cochrane FC, Parker EJ (2013) Neisseria meningitidis expresses a single 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase that is inhibited primarily by phenylalanine. Protein Sci 22:1087–1099. https://doi.org/10.1002/pro.2293
Article
CAS
PubMed
PubMed Central
Google Scholar
Cui Y, Ling C, Zhang Y, Huang J, Liu J (2014) Production of shikimic acid from Escherichia coli through chemically inducible chromosomal evolution and cofactor metabolic engineering. Microb Cell Fact 13:21. https://doi.org/10.1186/1475-2859-13-21
Article
CAS
PubMed
PubMed Central
Google Scholar
Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Humana Press, Totowa, pp 571–607. https://doi.org/10.1385/1-59259-890-0:571
Chapter
Google Scholar
Gosset G, Bonner CA, Jensen RA (2001) Microbial origin of plant-type 2-keto-3-deoxy-d-arabino-heptulosonate 7-phosphate synthases, exemplified by the chorismate- and tryptophan-regulated enzyme from Xanthomonas campestris. J Bacteriol 183:4061–4070. https://doi.org/10.1128/JB.183.13.4061-4070.2001
Article
CAS
PubMed
PubMed Central
Google Scholar
Helmstaedt K, Strittmatter A, Lipscomb WN, Braus GH (2005) Evolution of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase-encoding genes in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci 102:9784–9789. https://doi.org/10.1073/pnas.0504238102
Article
CAS
PubMed
Google Scholar
Herrmann KM (1995) The shikimate pathway as an entry to aromatic secondary metabolism. Plant Physiol 107:7–12. https://doi.org/10.1104/pp.107.1.7
Article
CAS
PubMed
PubMed Central
Google Scholar
Heyes LC, Reichau S, Cross PJ, Jameson GB, Parker EJ (2014) Structural analysis of substrate-mimicking inhibitors in complex with Neisseria meningitidis 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase—the importance of accommodating the active site water. Bioorg Chem 57:242–250. https://doi.org/10.1016/j.bioorg.2014.08.003
Article
CAS
PubMed
Google Scholar
Jensen RA, Xie G, Calhoun DH, Bonner CA (2002) The correct phylogenetic relationship of KdsA (3-deoxy-d-manno-octulosonate 8-phosphate synthase) with one of two independently evolved classes of AroA (3-deoxy-d-arabino-heptulosonate 7-phosphate synthase). J Mol Evol 54:416–423. https://doi.org/10.1007/s00239-001-0031-z
Article
CAS
PubMed
Google Scholar
König V, Pfeil A, Braus GH, Schneider TR (2004) Substrate and metal complexes of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Saccharomyces cerevisiae provide new insights into the catalytic mechanism. J Mol Biol 337:675–690. https://doi.org/10.1016/j.jmb.2004.01.055
Article
CAS
PubMed
Google Scholar
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Article
CAS
PubMed
Google Scholar
Künzler M, Paravicini G, Egli CM, Irniger S, Braus GH (1992) Cloning, primary structure and regulation of the ARO4 gene, encoding the tyrosine-inhibited 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Saccharomyces cerevisiae. Gene 113:67–74. https://doi.org/10.1016/0378-1119(92)90670-K
Article
PubMed
Google Scholar
Leis B, Angelov A, Mientus M, Li H, Pham VTT, Lauinger B, Bongen P, Pietruszka J, Gonalves LG, Santos H, Liebl W (2015) Identification of novel esterase-active enzymes from hot environments by use of the host bacterium Thermus thermophilus. Front Microbiol 6:275. https://doi.org/10.3389/fmicb.2015.00275
Article
PubMed
PubMed Central
Google Scholar
Light SH, Halavaty AS, Minasov G, Shuvalova L, Anderson WF (2012) Structural analysis of a 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase with an N-terminal chorismate mutase-like regulatory domain. Protein Sci 21:887–895. https://doi.org/10.1002/pro.2075
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu YJ, Li PP, Zhao KX, Wang BJ, Jiang CY, Drake HL, Liu SJ (2008) Corynebacterium glutamicum contains 3-deoxy-d-arabino-heptulosonate 7-phosphate synthases that display novel biochemical features. Appl Environ Microbiol 74:5497–5503. https://doi.org/10.1128/AEM.00262-08
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu S, Xiao M, Zhang L, Xu J, Ding Z, Gu Z, Shi G (2013) Production of l-phenylalanine from glucose by metabolic engineering of wild type Escherichia coli W3110. Process Biochem 48:413–419. https://doi.org/10.1016/j.procbio.2013.02.016
Article
CAS
Google Scholar
Ma N, Wei L, Fan Y, Hua Q (2012) Heterologous expression and characterization of soluble recombinant 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Actinosynnema pretiosum ssp. auranticum ATCC31565 through co-expression with Chaperones in Escherichia coli. Protein Expr Purif 82:263–269. https://doi.org/10.1016/j.pep.2012.01.013
Article
CAS
PubMed
Google Scholar
Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Geer LY, Bryant SH (2017) CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45:D200–D203. https://doi.org/10.1093/nar/gkw1129
Article
CAS
PubMed
Google Scholar
Mewis K, Armstrong Z, Song YC, Baldwin SA, Withers SG, Hallam SJ (2013) Biomining active cellulases from a mining bioremediation system. J Biotechnol 167:462–471. https://doi.org/10.1016/j.jbiotec.2013.07.015
Article
CAS
PubMed
Google Scholar
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791. https://doi.org/10.1002/jcc.21256
Article
CAS
PubMed
PubMed Central
Google Scholar
Nazmi AR, Schofield LR, Dobson RCJ, Jameson GB, Parker EJ (2014) Destabilization of the homotetrameric assembly of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from the hyperthermophile pyrococcus furiosus enhances enzymatic activity. J Mol Biol 426:656–673. https://doi.org/10.1016/j.jmb.2013.11.008
Article
CAS
PubMed
Google Scholar
Nazmi AR, Lang EJM, Bai Y, Allison TM, Othman MH, Panjikar S, Arcus VL, Parker EJ (2016) Interdomain conformational changes provide allosteric regulation en route to chorismate. J Biol Chem 291:21836–21847. https://doi.org/10.1074/jbc.M116.741637
Article
CAS
PubMed
PubMed Central
Google Scholar
Niehaus F, Gabor E, Wieland S, Siegert P, Maurer KH, Eck J (2011) Enzymes for the laundry industries: tapping the vast metagenomic pool of alkaline proteases. Microb Biotechnol 4:767–776. https://doi.org/10.1111/j.1751-7915.2011.00279.x
Article
PubMed
PubMed Central
Google Scholar
Pratap S, Dev A, Kumar V, Yadav R, Narwal M, Tomar S, Kumar P (2017) Structure of chorismate mutase-like domain of DAHPS from Bacillus subtilis complexed with novel inhibitor reveals conformational plasticity of active site. Sci Rep 7:6364. https://doi.org/10.1038/s41598-017-06578-1
Article
CAS
PubMed
PubMed Central
Google Scholar
Ray JM, Bauerle R (1991) Purification and properties of tryptophan-sensitive 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. J Bacteriol 173:1894–1901. https://doi.org/10.1128/jb.173.6.1894-1901.1991
Article
CAS
PubMed
PubMed Central
Google Scholar
Schofield LR, Patchett ML, Parker EJ (2004) Expression, purification, and characterization of 3-deoxy-d-arabino- heptulosonate 7-phosphate synthase from Pyrococcus furiosus. Protein Expr Purif 34:17–27. https://doi.org/10.1016/j.pep.2003.11.008
Article
CAS
PubMed
Google Scholar
Schofield LR, Anderson BF, Patchett ML, Norris GE, Jameson GB, Parker EJ (2005) Substrate ambiguity and crystal structure of Pyrococcus furiosus 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase: an ancestral 3-deoxyald-2-ulosonate-phosphate synthase? Biochemistry 44:11950–11962. https://doi.org/10.1021/bi050577z
Article
CAS
PubMed
Google Scholar
Schoner R, Herrmann KM (1976) 3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase. Purification, properties, and kinetics of the tyrosine-sensitive isoenzyme from Escherichia coli. J Biol Chem 251:5440–5447
CAS
PubMed
Google Scholar
Seow KT, Meurer G, Gerlitz M, Wendt-Pienkowski E, Hutchinson CR, Davies J (1997) A study of iterative type II polyketide synthases, using bacterial genes cloned from soil DNA: a means to access and use genes from uncultured microorganisms. J Bacteriol 179:7360–7368. https://doi.org/10.1128/jb.179.23.7360-7368.1997
Article
CAS
PubMed
PubMed Central
Google Scholar
Sharma A, Kumar V, Chatrath A, Dev A, Prasad R, Sharma AK, Tomar S, Kumar P (2018) In vitro metal catalyzed oxidative stress in DAH7PS: methionine modification leads to structure destabilization and induce amorphous aggregation. Int J Biol Macromol 106:1089–1106. https://doi.org/10.1016/j.ijbiomac.2017.08.105
Article
CAS
PubMed
Google Scholar
Shumilin IA, Kretsinger RH, Bauerle RH (1999) Crystal structure of phenylalanine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. Structure 7:865–875. https://doi.org/10.1016/S0969-2126(99)80109-9
Article
CAS
PubMed
Google Scholar
Shumilin IA, Bauerle R, Wu J, Woodard RW, Kretsinger RH (2004) Crystal structure of the reaction complex of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Thermotoga maritima refines the catalytic mechanism and indicates a new mechanism of allosteric regulation. J Mol Biol 341:455–466. https://doi.org/10.1016/j.jmb.2004.05.077
Article
CAS
PubMed
Google Scholar
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2014) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. https://doi.org/10.1038/msb.2011.75
Article
Google Scholar
Sterritt OW, Kessans SA, Jameson GB, Parker EJ (2018) A pseudoisostructural type II DAH7PS enzyme from Pseudomonas aeruginosa: alternative evolutionary strategies to control shikimate pathway flux. Biochemistry 57:2667–2678. https://doi.org/10.1021/acs.biochem.8b00082
Article
CAS
PubMed
Google Scholar
Teshiba S, Furter R, Niederberger P, Braus G, Paravicini G, Hütter R (1986) Cloning of the ARO3 gene of Saccharomyces cerevisiae and its regulation. Mol Gen Genet 205:353–357
Article
CAS
Google Scholar
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46:W296–W303. https://doi.org/10.1093/nar/gky427
Article
PubMed
PubMed Central
Google Scholar
Webby CJ, Baker HM, Lott JS, Baker EN, Parker EJ (2005a) The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type i and type ii enzymes. J Mol Biol 354:927–939. https://doi.org/10.1016/j.jmb.2005.09.093
Article
CAS
PubMed
Google Scholar
Webby CJ, Patchett ML, Parker EJ (2005b) Characterization of a recombinant type II 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from Helicobacter pylori. Biochem J 390:223–230. https://doi.org/10.1042/BJ20050259
Article
CAS
PubMed
PubMed Central
Google Scholar
Webby CJ, Jiao W, Hutton RD, Blackmore NJ, Baker HM, Baker EN, Jameson GB, Parker EJ (2010) Synergistic allostery, a sophisticated regulatory network for the control of aromatic amino acid biosynthesis in Mycobacterium tuberculosis. J Biol Chem 285:30567–30576. https://doi.org/10.1074/jbc.M110.111856
Article
CAS
PubMed
PubMed Central
Google Scholar
Westmann CA, de Alves L, Silva-Rocha R, Guazzaroni M (2018) Mining novel constitutive promoter elements in soil metagenomic libraries in Escherichia coli. Front Microbiol 9:1344. https://doi.org/10.3389/fmicb.2018.01344
Article
PubMed
PubMed Central
Google Scholar
Wu J, Woodard RW (2006) New Insights into the evolutionary links relating to the 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase subfamilies. J Biol Chem 281:4042–4048. https://doi.org/10.1074/jbc.M512223200
Article
CAS
PubMed
Google Scholar
Wu J, Howe DL, Woodard RW (2003) Thermotoga maritima 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthase. J Biol Chem 278:27525–27531. https://doi.org/10.1074/jbc.M304631200
Article
CAS
PubMed
Google Scholar
Wu J, Sheflyan GY, Woodard RW (2005) Bacillus subtilis 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase revisited: resolution of two long-standing enigmas. Biochem J 390:583–590. https://doi.org/10.1042/BJ20050294
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang C, Xia Y, Qu H, Li A, Liu R, Wang Y, Zhang T (2016) Discovery of new cellulases from the metagenome by a metagenomics-guided strategy. Biotechnol Biofuels 9:138. https://doi.org/10.1186/s13068-016-0557-3
Article
CAS
PubMed
PubMed Central
Google Scholar
Yun J, Kang S, Park S, Yoon H, Kim M, Heu S, Ryu S (2004) Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. Appl Environ Microbiol 70:7229–7235. https://doi.org/10.1128/AEM.70.12.7229-7235.2004
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou L, Wu J, Janakiraman V, Shumilin IA, Bauerle R, Kretsinger RH, Woodard RW (2012) Structure and characterization of the 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Aeropyrum pernix. Bioorg Chem 40:79–86. https://doi.org/10.1016/j.bioorg.2011.09.002
Article
CAS
PubMed
Google Scholar