3hlc: Difference between revisions

Latest revision as of 10:00, 21 February 2024

Simvastatin Synthase (LovD) from Aspergillus terreus, S5 mutant, unliganded

Structural highlights

3hlc is a 1 chain structure with sequence from Aspergillus terreus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	GOL, PG4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LOVD_ASPTE Monacolin J acid methylbutanoyltransferase; part of the gene cluster that mediates the biosynthesis of lovastatin (also known as mevinolin, mevacor or monacolin K), a hypolipidemic inhibitor of (3S)-hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR) (PubMed:10334994, PubMed:12929390, PubMed:21495633). The first step in the biosynthesis of lovastatin is the production of dihydromonacolin L acid by the lovastatin nonaketide synthase lovB and the trans-acting enoyl reductase lovC via condensation of one acetyl-CoA unit and 8 malonyl-CoA units (PubMed:10334994, PubMed:10381407, PubMed:19900898, PubMed:22733743). Dihydromonacolin L acid is released from lovB by the thioesterase lovG (PubMed:23653178). Next, dihydromonacolin L acid is oxidized by the dihydromonacolin L monooxygenase lovA twice to form monacolin J acid (PubMed:12929390, PubMed:21495633). The 2-methylbutyrate moiety of lovastatin is synthesized by the lovastatin diketide synthase lovF via condensation of one acetyl-CoA unit and one malonyl-CoA unit (PubMed:19530726, PubMed:21069965). Finally, the covalent attachment of this moiety to monacolin J acid is catalyzed by the transesterase lovD to yield lovastatin (PubMed:10334994, PubMed:17113998, PubMed:18988191, PubMed:19875080, PubMed:24727900). LovD has broad substrate specificity and can also convert monacolin J to simvastatin using alpha-dimethylbutanoyl-S-methyl-3-mercaptopropionate (DMB-S-MMP) as the thioester acyl donor, and can also catalyze the reverse reaction and function as hydrolase in vitro (PubMed:19875080). LovD has much higher activity with LovF-bound 2-methylbutanoate than with free diketide substrates (PubMed:21069965).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Kennedy J, Auclair K, Kendrew SG, Park C, Vederas JC, Hutchinson CR. Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science. 1999 May 21;284(5418):1368-72. PMID:10334994
↑ Hendrickson L, Davis CR, Roach C, Nguyen DK, Aldrich T, McAda PC, Reeves CD. Lovastatin biosynthesis in Aspergillus terreus: characterization of blocked mutants, enzyme activities and a multifunctional polyketide synthase gene. Chem Biol. 1999 Jul;6(7):429-39. doi: 10.1016/s1074-5521(99)80061-1. PMID:10381407 doi:https://dx.doi.org/10.1016/s1074-5521(99)80061-1
↑ Sorensen JL, Auclair K, Kennedy J, Hutchinson CR, Vederas JC. Transformations of cyclic nonaketides by Aspergillus terreus mutants blocked for lovastatin biosynthesis at the lovA and lovC genes. Org Biomol Chem. 2003 Jan 7;1(1):50-9. doi: 10.1039/b207721c. PMID:12929390 doi:https://dx.doi.org/10.1039/b207721c
↑ Xie X, Watanabe K, Wojcicki WA, Wang CC, Tang Y. Biosynthesis of lovastatin analogs with a broadly specific acyltransferase. Chem Biol. 2006 Nov;13(11):1161-9. PMID:17113998 doi:10.1016/j.chembiol.2006.09.008
↑ Xie X, Pashkov I, Gao X, Guerrero JL, Yeates TO, Tang Y. Rational improvement of simvastatin synthase solubility in Escherichia coli leads to higher whole-cell biocatalytic activity. Biotechnol Bioeng. 2009 Jan 1;102(1):20-8. PMID:18988191 doi:10.1002/bit.22028
↑ Xie X, Meehan MJ, Xu W, Dorrestein PC, Tang Y. Acyltransferase mediated polyketide release from a fungal megasynthase. J Am Chem Soc. 2009 Jun 24;131(24):8388-9. doi: 10.1021/ja903203g. PMID:19530726 doi:https://dx.doi.org/10.1021/ja903203g
↑ Gao X, Xie X, Pashkov I, Sawaya MR, Laidman J, Zhang W, Cacho R, Yeates TO, Tang Y. Directed evolution and structural characterization of a simvastatin synthase. Chem Biol. 2009 Oct 30;16(10):1064-74. PMID:19875080 doi:10.1016/j.chembiol.2009.09.017
↑ Ma SM, Li JW, Choi JW, Zhou H, Lee KK, Moorthie VA, Xie X, Kealey JT, Da Silva NA, Vederas JC, Tang Y. Complete reconstitution of a highly reducing iterative polyketide synthase. Science. 2009 Oct 23;326(5952):589-92. doi: 10.1126/science.1175602. PMID:19900898 doi:https://dx.doi.org/10.1126/science.1175602
↑ Meehan MJ, Xie X, Zhao X, Xu W, Tang Y, Dorrestein PC. FT-ICR-MS characterization of intermediates in the biosynthesis of the alpha-methylbutyrate side chain of lovastatin by the 277 kDa polyketide synthase LovF. Biochemistry. 2011 Jan 18;50(2):287-99. doi: 10.1021/bi1014776. Epub 2010 Dec 22. PMID:21069965 doi:https://dx.doi.org/10.1021/bi1014776
↑ Barriuso J, Nguyen DT, Li JW, Roberts JN, MacNevin G, Chaytor JL, Marcus SL, Vederas JC, Ro DK. Double oxidation of the cyclic nonaketide dihydromonacolin L to monacolin J by a single cytochrome P450 monooxygenase, LovA. J Am Chem Soc. 2011 Jun 1;133(21):8078-81. doi: 10.1021/ja201138v. Epub 2011 Apr , 15. PMID:21495633 doi:https://dx.doi.org/10.1021/ja201138v
↑ Ames BD, Nguyen C, Bruegger J, Smith P, Xu W, Ma S, Wong E, Wong S, Xie X, Li JW, Vederas JC, Tang Y, Tsai SC. Crystal structure and biochemical studies of the trans-acting polyketide enoyl reductase LovC from lovastatin biosynthesis. Proc Natl Acad Sci U S A. 2012 Jun 25. PMID:22733743 doi:10.1073/pnas.1113029109
↑ Xu W, Chooi YH, Choi JW, Li S, Vederas JC, Da Silva NA, Tang Y. LovG: the thioesterase required for dihydromonacolin L release and lovastatin nonaketide synthase turnover in lovastatin biosynthesis. Angew Chem Int Ed Engl. 2013 Jun 17;52(25):6472-5. doi: 10.1002/anie.201302406., Epub 2013 May 7. PMID:23653178 doi:https://dx.doi.org/10.1002/anie.201302406
↑ Jimenez-Oses G, Osuna S, Gao X, Sawaya MR, Gilson L, Collier SJ, Huisman GW, Yeates TO, Tang Y, Houk KN. The role of distant mutations and allosteric regulation on LovD active site dynamics. Nat Chem Biol. 2014 Jun;10(6):431-6. doi: 10.1038/nchembio.1503. Epub 2014 Apr, 13. PMID:24727900 doi:https://dx.doi.org/10.1038/nchembio.1503

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kennedy J, Auclair K, Kendrew SG, Park C, Vederas JC, Hutchinson CR. Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science. 1999 May 21;284(5418):1368-72. PMID:10334994

[2] Hendrickson L, Davis CR, Roach C, Nguyen DK, Aldrich T, McAda PC, Reeves CD. Lovastatin biosynthesis in Aspergillus terreus: characterization of blocked mutants, enzyme activities and a multifunctional polyketide synthase gene. Chem Biol. 1999 Jul;6(7):429-39. doi: 10.1016/s1074-5521(99)80061-1. PMID:10381407 doi:https://dx.doi.org/10.1016/s1074-5521(99)80061-1

[3] Sorensen JL, Auclair K, Kennedy J, Hutchinson CR, Vederas JC. Transformations of cyclic nonaketides by Aspergillus terreus mutants blocked for lovastatin biosynthesis at the lovA and lovC genes. Org Biomol Chem. 2003 Jan 7;1(1):50-9. doi: 10.1039/b207721c. PMID:12929390 doi:https://dx.doi.org/10.1039/b207721c

[4] Xie X, Watanabe K, Wojcicki WA, Wang CC, Tang Y. Biosynthesis of lovastatin analogs with a broadly specific acyltransferase. Chem Biol. 2006 Nov;13(11):1161-9. PMID:17113998 doi:10.1016/j.chembiol.2006.09.008

[5] Xie X, Pashkov I, Gao X, Guerrero JL, Yeates TO, Tang Y. Rational improvement of simvastatin synthase solubility in Escherichia coli leads to higher whole-cell biocatalytic activity. Biotechnol Bioeng. 2009 Jan 1;102(1):20-8. PMID:18988191 doi:10.1002/bit.22028

[6] Xie X, Meehan MJ, Xu W, Dorrestein PC, Tang Y. Acyltransferase mediated polyketide release from a fungal megasynthase. J Am Chem Soc. 2009 Jun 24;131(24):8388-9. doi: 10.1021/ja903203g. PMID:19530726 doi:https://dx.doi.org/10.1021/ja903203g

[7] Gao X, Xie X, Pashkov I, Sawaya MR, Laidman J, Zhang W, Cacho R, Yeates TO, Tang Y. Directed evolution and structural characterization of a simvastatin synthase. Chem Biol. 2009 Oct 30;16(10):1064-74. PMID:19875080 doi:10.1016/j.chembiol.2009.09.017

[8] Ma SM, Li JW, Choi JW, Zhou H, Lee KK, Moorthie VA, Xie X, Kealey JT, Da Silva NA, Vederas JC, Tang Y. Complete reconstitution of a highly reducing iterative polyketide synthase. Science. 2009 Oct 23;326(5952):589-92. doi: 10.1126/science.1175602. PMID:19900898 doi:https://dx.doi.org/10.1126/science.1175602

[9] Meehan MJ, Xie X, Zhao X, Xu W, Tang Y, Dorrestein PC. FT-ICR-MS characterization of intermediates in the biosynthesis of the alpha-methylbutyrate side chain of lovastatin by the 277 kDa polyketide synthase LovF. Biochemistry. 2011 Jan 18;50(2):287-99. doi: 10.1021/bi1014776. Epub 2010 Dec 22. PMID:21069965 doi:https://dx.doi.org/10.1021/bi1014776

[10] Barriuso J, Nguyen DT, Li JW, Roberts JN, MacNevin G, Chaytor JL, Marcus SL, Vederas JC, Ro DK. Double oxidation of the cyclic nonaketide dihydromonacolin L to monacolin J by a single cytochrome P450 monooxygenase, LovA. J Am Chem Soc. 2011 Jun 1;133(21):8078-81. doi: 10.1021/ja201138v. Epub 2011 Apr , 15. PMID:21495633 doi:https://dx.doi.org/10.1021/ja201138v

[11] Ames BD, Nguyen C, Bruegger J, Smith P, Xu W, Ma S, Wong E, Wong S, Xie X, Li JW, Vederas JC, Tang Y, Tsai SC. Crystal structure and biochemical studies of the trans-acting polyketide enoyl reductase LovC from lovastatin biosynthesis. Proc Natl Acad Sci U S A. 2012 Jun 25. PMID:22733743 doi:10.1073/pnas.1113029109

[12] Xu W, Chooi YH, Choi JW, Li S, Vederas JC, Da Silva NA, Tang Y. LovG: the thioesterase required for dihydromonacolin L release and lovastatin nonaketide synthase turnover in lovastatin biosynthesis. Angew Chem Int Ed Engl. 2013 Jun 17;52(25):6472-5. doi: 10.1002/anie.201302406., Epub 2013 May 7. PMID:23653178 doi:https://dx.doi.org/10.1002/anie.201302406

[13] Jimenez-Oses G, Osuna S, Gao X, Sawaya MR, Gilson L, Collier SJ, Huisman GW, Yeates TO, Tang Y, Houk KN. The role of distant mutations and allosteric regulation on LovD active site dynamics. Nat Chem Biol. 2014 Jun;10(6):431-6. doi: 10.1038/nchembio.1503. Epub 2014 Apr, 13. PMID:24727900 doi:https://dx.doi.org/10.1038/nchembio.1503

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 3hlc is ON HOLD  until Paper Publication
+==Simvastatin Synthase (LovD) from Aspergillus terreus, S5 mutant, unliganded==
+<StructureSection load='3hlc' size='340' side='right'caption='[[3hlc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3hlc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_terreus Aspergillus terreus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HLC FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hlc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hlc OCA], [https://pdbe.org/3hlc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hlc RCSB], [https://www.ebi.ac.uk/pdbsum/3hlc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hlc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LOVD_ASPTE LOVD_ASPTE] Monacolin J acid methylbutanoyltransferase; part of the gene cluster that mediates the biosynthesis of lovastatin (also known as mevinolin, mevacor or monacolin K), a hypolipidemic inhibitor of (3S)-hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR) (PubMed:10334994, PubMed:12929390, PubMed:21495633). The first step in the biosynthesis of lovastatin is the production of dihydromonacolin L acid by the lovastatin nonaketide synthase lovB and the trans-acting enoyl reductase lovC via condensation of one acetyl-CoA unit and 8 malonyl-CoA units (PubMed:10334994, PubMed:10381407, PubMed:19900898, PubMed:22733743). Dihydromonacolin L acid is released from lovB by the thioesterase lovG (PubMed:23653178). Next, dihydromonacolin L acid is oxidized by the dihydromonacolin L monooxygenase lovA twice to form monacolin J acid (PubMed:12929390, PubMed:21495633). The 2-methylbutyrate moiety of lovastatin is synthesized by the lovastatin diketide synthase lovF via condensation of one acetyl-CoA unit and one malonyl-CoA unit (PubMed:19530726, PubMed:21069965). Finally, the covalent attachment of this moiety to monacolin J acid is catalyzed by the transesterase lovD to yield lovastatin (PubMed:10334994, PubMed:17113998, PubMed:18988191, PubMed:19875080, PubMed:24727900). LovD has broad substrate specificity and can also convert monacolin J to simvastatin using alpha-dimethylbutanoyl-S-methyl-3-mercaptopropionate (DMB-S-MMP) as the thioester acyl donor, and can also catalyze the reverse reaction and function as hydrolase in vitro (PubMed:19875080). LovD has much higher activity with LovF-bound 2-methylbutanoate than with free diketide substrates (PubMed:21069965).<ref>PMID:10334994</ref> <ref>PMID:10381407</ref> <ref>PMID:12929390</ref> <ref>PMID:17113998</ref> <ref>PMID:18988191</ref> <ref>PMID:19530726</ref> <ref>PMID:19875080</ref> <ref>PMID:19900898</ref> <ref>PMID:21069965</ref> <ref>PMID:21495633</ref> <ref>PMID:22733743</ref> <ref>PMID:23653178</ref> <ref>PMID:24727900</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hl/3hlc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3hlc ConSurf].
+<div style="clear:both"></div>
-Authors: Sawaya, M.R., Yeates, T.O., Laidman, J., Pashkov, I., Gao, X., Tang, Y.
+==See Also==
+*[[Simvastatin Synthase|Simvastatin Synthase]]
-Description: Simvastatin Synthase (LovD) from Aspergillus terreus, S5 mutant, unliganded
+== References ==
+<references/>
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  1 08:56:02 2009''
+__TOC__
+</StructureSection>
+[[Category: Aspergillus terreus]]
+[[Category: Large Structures]]
+[[Category: Gao X]]
+[[Category: Laidman J]]
+[[Category: Pashkov I]]
+[[Category: Sawaya MR]]
+[[Category: Tang Y]]
+[[Category: Yeates TO]]

3hlc: Difference between revisions

Latest revision as of 10:00, 21 February 2024

Simvastatin Synthase (LovD) from Aspergillus terreus, S5 mutant, unliganded

Structural highlights

Function

Evolutionary Conservation

See Also

References

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