An unusual UMP C-5 methylase in nucleoside antibiotic polyoxin biosynthesis
Received date: 14 Apr 2016
Accepted date: 14 Jun 2016
Published date: 27 Sep 2016
Copyright
Polyoxin is a group of structurally-related peptidyl nucleoside antibiotics bearing C-5 modifications on the nucleoside skeleton. Although the structural diversity and bioactivity preference of polyoxin are, to some extent, affected by such modifications, the biosynthetic logic for their occurence remains obscure. Here we report the identification of PolB in polyoxin pathway as an unusual UMP C-5 methylase with thymidylate synthase activity which is responsible for the C-5 methylation of the nucleoside skeleton. To probe its molecular mechanism, we determined the crystal structures of PolB alone and in complexes with 5-Br UMP and 5-Br dUMP at 2.15 Å, 1.76 Å and 2.28 Å resolutions, respectively. Loop 1 (residues 117–131), Loop 2 (residues 192–201) and the substrate recognition peptide (residues 94–102) of PolB exhibit considerable conformational flexibility and adopt distinct structures upon binding to different substrate analogs. Consistent with the structural findings, a PolB homolog that harbors an identical function from Streptomyces viridochromogenes DSM 40736 was identified. The discovery of UMP C5-methylase opens the way to rational pathway engineering for polyoxin component optimization, and will also enrich the toolbox for natural nucleotide chemistry.
Wenqing Chen , Yan Li , Jie Li , Lian Wu , Yan Li , Renxiao Wang , Zixin Deng , Jiahai Zhou . An unusual UMP C-5 methylase in nucleoside antibiotic polyoxin biosynthesis[J]. Protein & Cell, 2016 , 7(9) : 673 -683 . DOI: 10.1007/s13238-016-0289-y
| 1 |
Blodgett JA, Zhang JK, Metcalf WW (2005) Molecular cloning, sequence analysis, and heterologous expression of the phosphinothricin tripeptide biosynthetic gene cluster from Streptomyces viridochromogenes DSM 40736. Antimicrob Agents Chemother 49:230–240
|
| 2 |
Chen W, Huang T, He X, Meng Q, You D, Bai L, Li J, Wu M, Li R, Xie Z
|
| 3 |
Chen W, Qi J, Wu P, Wan D, Liu J, Feng X, Deng Z (2016) Natural and engineered biosynthesis of nucleoside antibiotics in Actinomycetes. J Ind Microbiol Biotechnol 43:401–417
|
| 4 |
Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D 66:486–501
|
| 5 |
Endo A, Kakiki K, Misato T (1970) Mechanism of action of the antifungal agent polyoxin D. J Bacteriol 104:189–196
|
| 6 |
Endo A, Misato T (1969) Polyoxin D, a competitive inhibitor of UDPN-acetylglucosamine:chitinN-acetylglucosaminyltransferase in Neurospora crassa. Biochem Biophys Res Commun 37:718–722
|
| 7 |
Graziani S, Xia Y, Gurnon JR, Van Etten JL, Leduc D, Skouloubris S, Myllykallio H, Liebl U (2004) Functional analysis of FAD-dependent thymidylate synthase ThyX from Paramecium bursaria Chlorella virus-1. J Biol Chem 279:54340–54347
|
| 8 |
Isono K (1988) Nucleoside antibiotics: structure, biological activity, and biosynthesis. J Antibiot (Tokyo) 41:1711–1739
|
| 9 |
Isono K, Funayama S, Suhadolnik RJ (1975) Biosynthesis of the polyoxins, nucleoside peptide antibiotics: a new metabolic role for L-isoleucine as a precursor for 3-ethylidene-L-azetidine-2-carboxylic acid (polyoximic acid). Biochemistry 14:2992–2996
|
| 10 |
Isono K, Suhadolnik RJ (1976) The biosynthesis of natural and unnatural polyoxins by Streptomyces cacaoi. Arch Biochem Biophys 173:141–153
|
| 11 |
Isono K, Suzuki S (1968) The structures of polyoxins A and B. Tetrahedron Lett 9:1133–1137
|
| 12 |
Isono K, Nagutsu J, Kobinata K, Sasaki K, Suzuki S (1967) Studies on polyoxins antifungal antibiotics, Part V: isolation and characterization of polyoxins C, D, E, F, G, H and I. Agric BiolChem 31:190–199
|
| 13 |
Kieser T, Bibb MJ, Chater KF, Butter MJ, Hopwood DA (2000) Practical Streptomyces genetics. A laboratory manual. John Innes Foundation, Norwich
|
| 14 |
Lorenson MY, Maley GF, Maley F (1967) The purification and properties of thymidylate synthetase from chick embryo extracts. J Biol Chem 242:3332–3344
|
| 15 |
Maley F (1960) The synthesis of 5-methyluridine 5′-phosphate in rat embryo extracts. Proc Natl Acad Sci USA 46:632–636
|
| 16 |
Mathews II, Deacon AM, Canaves JM, McMullan D, Lesley SA, Agarwalla S, Kuhn P (2003) Functional analysis of substrate and cofactor complex structures of a thymidylate synthase-complementing protein. Structure 11:677–690
|
| 17 |
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr 40:658–674
|
| 18 |
Myllykallio H, Lipowski G, Leduc D, Filee J, Forterre P, Liebl U (2002) An alternative flavin-dependent mechanism for thymidylate synthesis. Science 297:105–107
|
| 19 |
Niu G, Tan H (2015) Nucleoside antibiotics: biosynthesis, regulation, and biotechnology. Trends Microbiol 23:110–119
|
| 20 |
Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M, Takahashi Y, Horikawa H, Nakazawa H, Osonoe T
|
| 21 |
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor, Cold Spring Harbor
|
| 22 |
Zhai L, Lin S, Qu D, Hong X, Bai L, Chen W, Deng Z (2012) Engineering of an industrial polyoxin producer for the rational production of hybrid peptidyl nucleoside antibiotics. Metab Eng 14:388–393
|
| 23 |
Zhao C, Huang T, Chen W, Deng Z (2010) Enhancement of the diversity of polyoxins by a thymine-7-hydroxylase homolog outside the polyoxin biosynthesis gene cluster. Appl Environ Microbiol 76:7343–7347
|
/
| 〈 |
|
〉 |