7pga

From Proteopedia

(Difference between revisions)

Revision as of 07:32, 22 March 2023

Chimeric carminomycin-4-O-methyltransferase (DnrK) with regions from 10-hydroxylase RdmB and 10-decarboxylase TamK

Structural highlights

7pga is a 4 chain structure with sequence from Streptomyces peucetius, Streptomyces purpurascens and Streptomyces tsukubensis NRRL18488. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RDMB_STREF Involved in the biosynthesis of the anthracycline aclacinomycin which is an aromatic polyketide antibiotic that exhibits high cytotoxicity and is widely applied in the chemotherapy of a variety of cancers. In vivo and in vitro, RdmB catalyzes the removal of the carboxylic group from the C-10 position of 15-demethoxyaclacinomycin T coupled to hydroxylation at the same C-10 position. It could also catalyze the removal of the carboxylic group at the C-10 position of 15-demethoxy-epsilon-rhodomycin coupled to hydroxylation at the same C-10 position to yield rhodomycin B. The reaction catalyzes by RdmB is intriguing, since the enzyme does not use any of the cofactors usually associated with hydroxylases such as flavins and/or metal ions to activate molecular oxygen.^[1] ^[2] I2N5E8_STRT9 DNRK_STRPE Involved in the biosynthesis of the anthracyclines carminomycin and daunorubicin (daunomycin) which are aromatic polyketide antibiotics that exhibit high cytotoxicity and are widely applied in the chemotherapy of a variety of cancers. In vivo, catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to the 4-O-position of carminomycin to form daunorubicin. In vitro, it also methylates the anthracyclines rhodomycin D (10-carbomethoxy-13-deoxycarminomycin) and 13-deoxy-carminomycin at the 4-hydroxyl position. It is quite specific with respect to the length of the carbohydrate chain at the C7 position, but it can accept substrates with bulky substituent at C10 position.^[3]

Publication Abstract from PubMed

Streptomyces soil bacteria produce hundreds of anthracycline anticancer agents with a relatively conserved set of genes. This diversity depends on the rapid evolution of biosynthetic enzymes to acquire novel functionalities. Previous work has identified S-adenosyl-l-methionine-dependent methyltransferase-like proteins that catalyze 4-O-methylation, 10-decarboxylation, or 10-hydroxylation, with additional differences in substrate specificities. Here we focused on four protein regions to generate chimeric enzymes using sequences from four distinct subfamilies to elucidate their influence in catalysis. Combined with structural studies we managed to depict factors that influence gain-of-hydroxylation, loss-of-methylation, and substrate selection. The engineering expanded the catalytic repertoire to include novel 9,10-elimination activity, and 4-O-methylation and 10-decarboxylation of unnatural substrates. The work provides an instructive account on how the rise of diversity of microbial natural products may occur through subtle changes in biosynthetic enzymes.

Evolution-inspired engineering of anthracycline methyltransferases.,Dinis P, Tirkkonen H, Wandi BN, Siitonen V, Niemi J, Grocholski T, Metsa-Ketela M PNAS Nexus. 2023 Feb 28;2(2):pgad009. doi: 10.1093/pnasnexus/pgad009. eCollection , 2023 Feb. PMID:36874276^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang Y, Niemi J, Airas K, Ylihonko K, Hakala J, Mantsala P. Modifications of aclacinomycin T by aclacinomycin methyl esterase (RdmC) and aclacinomycin-10-hydroxylase (RdmB) from Streptomyces purpurascens. Biochim Biophys Acta. 2000 Jul 14;1480(1-2):191-200. PMID:11004563
↑ Jansson A, Koskiniemi H, Erola A, Wang J, Mantsala P, Schneider G, Niemi J. Aclacinomycin 10-hydroxylase is a novel substrate-assisted hydroxylase requiring S-adenosyl-L-methionine as cofactor. J Biol Chem. 2005 Feb 4;280(5):3636-44. Epub 2004 Nov 17. PMID:15548527 doi:10.1074/jbc.M412095200
↑ Jansson A, Koskiniemi H, Mantsala P, Niemi J, Schneider G. Crystal structure of a ternary complex of DnrK, a methyltransferase in daunorubicin biosynthesis, with bound products. J Biol Chem. 2004 Sep 24;279(39):41149-56. Epub 2004 Jul 24. PMID:15273252 doi:10.1074/jbc.M407081200
↑ Dinis P, Tirkkonen H, Wandi BN, Siitonen V, Niemi J, Grocholski T, Metsä-Ketelä M. Evolution-inspired engineering of anthracycline methyltransferases. PNAS Nexus. 2023 Feb 28;2(2):pgad009. PMID:36874276 doi:10.1093/pnasnexus/pgad009

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7pga"

@@ Line 1: / Line 1: @@
 ==Chimeric carminomycin-4-O-methyltransferase (DnrK) with regions from 10-hydroxylase RdmB and 10-decarboxylase TamK==
-<StructureSection load='7pga' size='340' side='right'caption='[[7pga]]' scene=''>
+<StructureSection load='7pga' size='340' side='right'caption='[[7pga]], [[Resolution|resolution]] 2.77&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PGA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7pga]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_peucetius Streptomyces peucetius], [https://en.wikipedia.org/wiki/Streptomyces_purpurascens Streptomyces purpurascens] and [https://en.wikipedia.org/wiki/Streptomyces_tsukubensis_NRRL18488 Streptomyces tsukubensis NRRL18488]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PGA FirstGlance]. <br>
-</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=7pga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pga OCA], [https://pdbe.org/7pga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pga RCSB], [https://www.ebi.ac.uk/pdbsum/7pga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pga ProSAT]</span></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=VAK:METHYL+(1R,2R,4S)-2-ETHYL-2,4,5,7-TETRAHYDROXY-6,11-DIOXO-1,2,3,4,6,11-HEXAHYDROTETRACENE-1-CARBOXYLATE'>VAK</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=7pga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pga OCA], [https://pdbe.org/7pga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pga RCSB], [https://www.ebi.ac.uk/pdbsum/7pga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pga ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/RDMB_STREF RDMB_STREF] Involved in the biosynthesis of the anthracycline aclacinomycin which is an aromatic polyketide antibiotic that exhibits high cytotoxicity and is widely applied in the chemotherapy of a variety of cancers. In vivo and in vitro, RdmB catalyzes the removal of the carboxylic group from the C-10 position of 15-demethoxyaclacinomycin T coupled to hydroxylation at the same C-10 position. It could also catalyze the removal of the carboxylic group at the C-10 position of 15-demethoxy-epsilon-rhodomycin coupled to hydroxylation at the same C-10 position to yield rhodomycin B. The reaction catalyzes by RdmB is intriguing, since the enzyme does not use any of the cofactors usually associated with hydroxylases such as flavins and/or metal ions to activate molecular oxygen.<ref>PMID:11004563</ref> <ref>PMID:15548527</ref> [https://www.uniprot.org/uniprot/I2N5E8_STRT9 I2N5E8_STRT9] [https://www.uniprot.org/uniprot/DNRK_STRPE DNRK_STRPE] Involved in the biosynthesis of the anthracyclines carminomycin and daunorubicin (daunomycin) which are aromatic polyketide antibiotics that exhibit high cytotoxicity and are widely applied in the chemotherapy of a variety of cancers. In vivo, catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to the 4-O-position of carminomycin to form daunorubicin. In vitro, it also methylates the anthracyclines rhodomycin D (10-carbomethoxy-13-deoxycarminomycin) and 13-deoxy-carminomycin at the 4-hydroxyl position. It is quite specific with respect to the length of the carbohydrate chain at the C7 position, but it can accept substrates with bulky substituent at C10 position.<ref>PMID:15273252</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Streptomyces soil bacteria produce hundreds of anthracycline anticancer agents with a relatively conserved set of genes. This diversity depends on the rapid evolution of biosynthetic enzymes to acquire novel functionalities. Previous work has identified S-adenosyl-l-methionine-dependent methyltransferase-like proteins that catalyze 4-O-methylation, 10-decarboxylation, or 10-hydroxylation, with additional differences in substrate specificities. Here we focused on four protein regions to generate chimeric enzymes using sequences from four distinct subfamilies to elucidate their influence in catalysis. Combined with structural studies we managed to depict factors that influence gain-of-hydroxylation, loss-of-methylation, and substrate selection. The engineering expanded the catalytic repertoire to include novel 9,10-elimination activity, and 4-O-methylation and 10-decarboxylation of unnatural substrates. The work provides an instructive account on how the rise of diversity of microbial natural products may occur through subtle changes in biosynthetic enzymes.
+Evolution-inspired engineering of anthracycline methyltransferases.,Dinis P, Tirkkonen H, Wandi BN, Siitonen V, Niemi J, Grocholski T, Metsa-Ketela M PNAS Nexus. 2023 Feb 28;2(2):pgad009. doi: 10.1093/pnasnexus/pgad009. eCollection , 2023 Feb. PMID:36874276<ref>PMID:36874276</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 7pga" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
+[[Category: Streptomyces peucetius]]
+[[Category: Streptomyces purpurascens]]
+[[Category: Streptomyces tsukubensis NRRL18488]]
 [[Category: Dinis P]]
 [[Category: MetsaKetela M]]

7pga

From Proteopedia

Revision as of 07:32, 22 March 2023

Chimeric carminomycin-4-O-methyltransferase (DnrK) with regions from 10-hydroxylase RdmB and 10-decarboxylase TamK

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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