7kh2: Difference between revisions
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==Structure of N-citrylornithine decarboxylase bound with PLP== | ==Structure of N-citrylornithine decarboxylase bound with PLP== | ||
<StructureSection load='7kh2' size='340' side='right'caption='[[7kh2]]' scene=''> | <StructureSection load='7kh2' size='340' side='right'caption='[[7kh2]], [[Resolution|resolution]] 2.05Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KH2 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[7kh2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"francisella_tularensis_subsp._novicida"_(larson_et_al._1955)_sjostedt_2005 "francisella tularensis subsp. novicida" (larson et al. 1955) sjostedt 2005]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KH2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KH2 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </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=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">figC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264 "Francisella tularensis subsp. novicida" (Larson et al. 1955) Sjostedt 2005])</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=7kh2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kh2 OCA], [https://pdbe.org/7kh2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kh2 RCSB], [https://www.ebi.ac.uk/pdbsum/7kh2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kh2 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The siderophore rhizoferrin (N (1),N (4)-dicitrylputrescine) is produced in fungi and bacteria to scavenge iron. Putrescine-producing bacterium Ralstonia pickettii synthesizes rhizoferrin and encodes a single nonribosomal peptide synthetase-independent siderophore (NIS) synthetase. From biosynthetic logic, we hypothesized that this single enzyme is sufficient for rhizoferrin biosynthesis. We confirmed this by expression of R. pickettii NIS synthetase in E. coli, resulting in rhizoferrin production. This was further confirmed in vitro using the recombinant NIS synthetase, synthesizing rhizoferrin from putrescine and citrate. Heterologous expression of homologous lbtA from Legionella pneumophila, required for rhizoferrin biosynthesis in that species, produced siderophore activity in E. coli Rhizoferrin is also synthesized by Francisella tularensis and F. novicida, but unlike R. pickettii or L. pneumophila, Francisella species lack putrescine biosynthetic pathways due to genomic decay. Francisella encodes a NIS synthetase FslA/FigA and an ornithine decarboxylase (ODC) homologue FslC/FigC, required for rhizoferrin biosynthesis. ODC produces putrescine from ornithine but we show here in vitro that FigA synthesizes N-citrylornithine, and FigC is an N-citrylornithine decarboxylase that together synthesize rhizoferrin without using putrescine. We co-expressed F. novicida figA and figC in E. coli, and produced rhizoferrin. A 2.1A X-ray crystal structure of the FigC N-citrylornithine decarboxylase reveals how the larger substrate is accommodated and how active site residues have changed to recognize N-citrylornithine. FigC belongs to a new subfamily of alanine racemase-fold PLP-dependent decarboxylases that are not involved in polyamine biosynthesis. These data reveal a natural product biosynthetic workaround that evolved to bypass a missing precursor and re-establish it in the final structure. | |||
Alternative pathways utilize or circumvent putrescine for biosynthesis of putrescine-containing rhizoferrin.,Li B, Deng X, Kim SH, Buhrow L, Tomchick DR, Phillips MA, Michael AJ J Biol Chem. 2020 Dec 4. pii: S0021-9258(20)00139-8. doi:, 10.1074/jbc.RA120.016738. PMID:33277357<ref>PMID:33277357</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7kh2" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Deng X]] | [[Category: Deng, X]] | ||
[[Category: Michael A]] | [[Category: Michael, A]] | ||
[[Category: Phillips M]] | [[Category: Phillips, M]] | ||
[[Category: Tomchick D]] | [[Category: Tomchick, D]] | ||
[[Category: Biosynthetic protein]] | |||
[[Category: Citrate]] | |||
[[Category: Decarboxylase]] | |||
[[Category: Francisella]] | |||
[[Category: Iron]] | |||
[[Category: Legionella]] | |||
[[Category: Lyase]] | |||
[[Category: Ornithine]] | |||
[[Category: Polyamine]] | |||
[[Category: Putrescine]] | |||
[[Category: Ralstonia]] | |||
[[Category: Rhizoferrin]] | |||
[[Category: Siderophore]] | |||
[[Category: Spermidine]] | |||
Latest revision as of 06:49, 2 July 2021
Structure of N-citrylornithine decarboxylase bound with PLPStructure of N-citrylornithine decarboxylase bound with PLP
Structural highlights
Publication Abstract from PubMedThe siderophore rhizoferrin (N (1),N (4)-dicitrylputrescine) is produced in fungi and bacteria to scavenge iron. Putrescine-producing bacterium Ralstonia pickettii synthesizes rhizoferrin and encodes a single nonribosomal peptide synthetase-independent siderophore (NIS) synthetase. From biosynthetic logic, we hypothesized that this single enzyme is sufficient for rhizoferrin biosynthesis. We confirmed this by expression of R. pickettii NIS synthetase in E. coli, resulting in rhizoferrin production. This was further confirmed in vitro using the recombinant NIS synthetase, synthesizing rhizoferrin from putrescine and citrate. Heterologous expression of homologous lbtA from Legionella pneumophila, required for rhizoferrin biosynthesis in that species, produced siderophore activity in E. coli Rhizoferrin is also synthesized by Francisella tularensis and F. novicida, but unlike R. pickettii or L. pneumophila, Francisella species lack putrescine biosynthetic pathways due to genomic decay. Francisella encodes a NIS synthetase FslA/FigA and an ornithine decarboxylase (ODC) homologue FslC/FigC, required for rhizoferrin biosynthesis. ODC produces putrescine from ornithine but we show here in vitro that FigA synthesizes N-citrylornithine, and FigC is an N-citrylornithine decarboxylase that together synthesize rhizoferrin without using putrescine. We co-expressed F. novicida figA and figC in E. coli, and produced rhizoferrin. A 2.1A X-ray crystal structure of the FigC N-citrylornithine decarboxylase reveals how the larger substrate is accommodated and how active site residues have changed to recognize N-citrylornithine. FigC belongs to a new subfamily of alanine racemase-fold PLP-dependent decarboxylases that are not involved in polyamine biosynthesis. These data reveal a natural product biosynthetic workaround that evolved to bypass a missing precursor and re-establish it in the final structure. Alternative pathways utilize or circumvent putrescine for biosynthesis of putrescine-containing rhizoferrin.,Li B, Deng X, Kim SH, Buhrow L, Tomchick DR, Phillips MA, Michael AJ J Biol Chem. 2020 Dec 4. pii: S0021-9258(20)00139-8. doi:, 10.1074/jbc.RA120.016738. PMID:33277357[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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