Editing Vancomycin (section)

==Biosynthesis==
Vancomycin is made by the soil bacterium ''[[Amycolatopsis orientalis]]''.<ref name=AHFS2015/>
[[Image:Vancomycin Modules.png|thumb|left|Figure 1: Modules and domains of vancomycin assembly]]
Vancomycin biosynthesis occurs primarily via three [[Nonribosomal peptide synthetase|nonribosomal protein synthases]] (NRPSs) VpsA, VpsB, and VpsC.<ref name="pmid18414736">{{cite journal | vauthors = Samel SA, Marahiel MA, Essen LO | title = How to tailor non-ribosomal peptide products--new clues about the structures and mechanisms of modifying enzymes | journal = Molecular BioSystems | volume = 4 | issue = 5 | pages = 387–93 | date = May 2008 | pmid = 18414736 | doi = 10.1039/b717538h }}</ref> The [[enzymes]] determine the amino acid sequence during its assembly through its 7 [[Protein domain|modules]]. Before vancomycin is assembled through NRPS, the non-proteinogenic [[amino acids]] are first synthesized. <small>L</small>-tyrosine is modified to become the [[β-hydroxytyrosine]] (β-HT) and 4-hydroxyphenylglycine (4-Hpg) residues. 3,5-dihydroxyphenylglycine ring (3,5-DPG) is derived from acetate.<ref name="isbn0-471-49641-3">{{cite book | vauthors = Dewick PM |title=Medicinal natural products: a biosynthetic approach |publisher=Wiley |location=New York |year=2002 |isbn=978-0-471-49641-0}}{{page needed|date=November 2014}}</ref>

[[Image:Linear heptapeptide of Vancomycin.png|class=skin-invert-image|thumb|Figure 2: Linear heptapeptide, which consists of modified aromatic rings]]
Nonribosomal peptide synthesis occurs through distinct modules that can load and extend the [[protein]] by one amino acid per module through the [[amide]] bond formation at the contact sites of the activating domains.<ref name="pmid9545426">{{cite journal | vauthors = van Wageningen AM, Kirkpatrick PN, Williams DH, Harris BR, Kershaw JK, Lennard NJ, Jones M, Jones SJ, Solenberg PJ | title = Sequencing and analysis of genes involved in the biosynthesis of a vancomycin group antibiotic | journal = Chemistry & Biology | volume = 5 | issue = 3 | pages = 155–62 | date = March 1998 | pmid = 9545426 | doi = 10.1016/S1074-5521(98)90060-6 | doi-access = free }}</ref> Each module typically consists of an [[Adenylylation|adenylation]] (A) domain, a [[peptidyl carrier protein]] (PCP) domain, and a condensation (C) domain. In the A domain, the specific amino acid is activated by converting into an aminoacyl adenylate enzyme complex attached to a [[4'-phosphopantetheine]] cofactor by thioesterification.<ref name="pmid1744112">{{cite journal | vauthors = Schlumbohm W, Stein T, Ullrich C, Vater J, Krause M, Marahiel MA, Kruft V, Wittmann-Liebold B | title = An active serine is involved in covalent substrate amino acid binding at each reaction center of gramicidin S synthetase | journal = The Journal of Biological Chemistry | volume = 266 | issue = 34 | pages = 23135–41 | date = December 1991 | doi = 10.1016/S0021-9258(18)54473-2 | pmid = 1744112 | doi-access = free }}</ref><ref name="pmid8663196">{{cite journal | vauthors = Stein T, Vater J, Kruft V, Otto A, Wittmann-Liebold B, Franke P, Panico M, McDowell R, Morris HR | title = The multiple carrier model of nonribosomal peptide biosynthesis at modular multienzymatic templates | journal = The Journal of Biological Chemistry | volume = 271 | issue = 26 | pages = 15428–35 | date = June 1996 | pmid = 8663196 | doi = 10.1074/jbc.271.26.15428 | doi-access = free }}</ref> The complex is then transferred to the PCP domain with the expulsion of AMP. The PCP domain uses the attached 4'-phosphopantethein prosthetic group to load the growing peptide chain and their precursors.<ref name="pmid12167866">{{cite journal | vauthors = Kohli RM, Walsh CT, Burkart MD | s2cid = 4380296 | title = Biomimetic synthesis and optimization of cyclic peptide antibiotics | journal = Nature | volume = 418 | issue = 6898 | pages = 658–61 | date = August 2002 | pmid = 12167866 | doi = 10.1038/nature00907 | bibcode = 2002Natur.418..658K }}</ref> The organization of the modules necessary to biosynthesize vancomycin is shown in Figure 1. In the biosynthesis of vancomycin, additional modification domains are present, such as the [[epimerization]] (E) domain, which isomerizes the amino acid from one [[stereochemistry]] to another, and a thioesterase domain (TE) is used as a catalyst for cyclization and releases of the molecule via a [[thioesterase]] scission.{{cn|date=March 2023}}

[[Image:Biosynthesis of Vancomycin.png|class=skin-invert-image|thumb|left|Figure 3: Modifications necessary for vancomycin to become biologically active]]
A set of NRPS enzymes (peptide synthase VpsA, VpsB, and VpsC) are responsible for assembling the heptapeptide. (Figure 2).<ref name="pmid9545426"/> VpsA codes for modules 1, 2, and 3. VpsB codes for modules 4, 5, and 6, and VpsC codes for module 7. The vancomycin aglycone contains 4 D-amino acids, although the NRPSs only contain 3 epimerization domains. The origin of D-Leu at residue 1 is unknown. The three peptide syntheses are at the start of the region of the bacterial genome linked with antibiotic biosynthesis, and span 27 kb.<ref name="pmid9545426"/>

β-hydroxytyrosine (β-HT) is synthesized before incorporation into the heptapeptide backbone. L-tyrosine is activated and loaded on the NRPS VpsD, hydroxylated by OxyD, and released by the thioesterase Vhp.<ref name="pmid15342578">{{cite journal | vauthors = Puk O, Bischoff D, Kittel C, Pelzer S, Weist S, Stegmann E, Süssmuth RD, Wohlleben W | title = Biosynthesis of chloro-beta-hydroxytyrosine, a nonproteinogenic amino acid of the peptidic backbone of glycopeptide antibiotics | journal = Journal of Bacteriology | volume = 186 | issue = 18 | pages = 6093–100 | date = September 2004 | pmid = 15342578 | pmc = 515157 | doi = 10.1128/JB.186.18.6093-6100.2004 }}</ref> The timing of the chlorination by halogenase VhaA during biosynthesis is undetermined, but is proposed to occur before the complete assembly of the heptapeptide.<ref name="pmid24756572">{{cite journal | vauthors = Schmartz PC, Zerbe K, Abou-Hadeed K, Robinson JA | title = Bis-chlorination of a hexapeptide-PCP conjugate by the halogenase involved in vancomycin biosynthesis | journal = Organic & Biomolecular Chemistry | volume = 12 | issue = 30 | pages = 5574–7 | date = August 2014 | pmid = 24756572 | doi = 10.1039/C4OB00474D | url = http://www.zora.uzh.ch/id/eprint/103226/1/manuscript.pdf | doi-access = free | access-date = 2 February 2024 | archive-date = 2 February 2024 | archive-url = https://web.archive.org/web/20240202143359/https://www.zora.uzh.ch/id/eprint/103226/1/manuscript.pdf | url-status = live }}</ref>

After the linear heptapeptide molecule is synthesized, vancomycin must undergo further modifications, such as oxidative cross-linking and [[glycosylation]], in trans{{Clarify|date=August 2011}} by distinct enzymes, referred to as tailoring enzymes, to become biologically active (Figure 3). To convert the linear heptapeptide to cross-linked, glycosylated vancomycin, six enzymes are required. The enzymes OxyA, OxyB, OxyC, and OxyD are cytochrome P450 enzymes. OxyB catalyzes oxidative cross-linking between residues 4 and 6, OxyA between residues 2 and 4, and OxyC between residues 5 and 7. This cross-linking occurs while the heptapeptide is covalently bound to the PCP domain of the 7th NRPS module. These P450s are recruited by the X domain in the 7th NRPS module, which is unique to glycopeptide antibiotic biosynthesis.<ref name="pmid25686610">{{cite journal | vauthors = Haslinger K, Peschke M, Brieke C, Maximowitsch E, Cryle MJ | s2cid = 4466657 | title = X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis | journal = Nature | volume = 521 | issue = 7550 | pages = 105–9 | date = May 2015 | pmid = 25686610 | doi = 10.1038/nature14141 | bibcode = 2015Natur.521..105H | url = http://www.nature.com/articles/nature14141 | url-access = subscription | access-date = 23 June 2020 | archive-date = 24 February 2021 | archive-url = https://web.archive.org/web/20210224172657/https://www.nature.com/articles/nature14141 | url-status = live }}</ref> The cross-linked heptapeptide is then released by the action of the TE domain, and methyltransferase Vmt then ''N''-methylates the terminal leucine residue. GtfE then joins D-glucose to the phenolic oxygen of residue 4, followed by the addition of [[vancosamine]] catalyzed by GtfD.{{cn|date=March 2023}}

Some of the glycosyltransferases capable of glycosylating vancomycin and related nonribosomal peptides display notable permissivity and have been used to generate libraries of differentially glycosylated analogs through [[glycorandomization]].<ref name="pmid14608364">{{cite journal | vauthors = Fu X, Albermann C, Jiang J, Liao J, Zhang C, Thorson JS | s2cid = 2469387 | title = Antibiotic optimization via in vitro glycorandomization | journal = Nature Biotechnology | volume = 21 | issue = 12 | pages = 1467–9 | date = December 2003 | pmid = 14608364 | doi = 10.1038/nbt909 }}</ref><ref name="pmid15816740">{{cite journal | vauthors = Fu X, Albermann C, Zhang C, Thorson JS | title = Diversifying vancomycin via chemoenzymatic strategies | journal = Organic Letters | volume = 7 | issue = 8 | pages = 1513–5 | date = April 2005 | pmid = 15816740 | doi = 10.1021/ol0501626 }}</ref><ref name="pmid22984807">{{cite journal | vauthors = Peltier-Pain P, Marchillo K, Zhou M, Andes DR, Thorson JS | title = Natural product disaccharide engineering through tandem glycosyltransferase catalysis reversibility and neoglycosylation | journal = Organic Letters | volume = 14 | issue = 19 | pages = 5086–9 | date = October 2012 | pmid = 22984807 | pmc = 3489467 | doi = 10.1021/ol3023374 }}</ref>
{{clear}}