6yo9: Difference between revisions
New page: '''Unreleased structure''' The entry 6yo9 is ON HOLD Authors: Mais, N.C., Altegoer, F., Bange, G. Description: Product bound structure of the Ectoine utilization protein EutD (DoeA) fr... |
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The | ==Product bound structure of the Ectoine utilization protein EutD (DoeA) from Halomonas elongata== | ||
<StructureSection load='6yo9' size='340' side='right'caption='[[6yo9]], [[Resolution|resolution]] 2.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6yo9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Halomonas_elongata Halomonas elongata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YO9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YO9 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]] 2.4Å</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=P4B:(2~{R})-4-azanyl-2-[[(1~{S})-1-oxidanylethyl]amino]butanoic+acid'>P4B</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=6yo9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yo9 OCA], [https://pdbe.org/6yo9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yo9 RCSB], [https://www.ebi.ac.uk/pdbsum/6yo9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yo9 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DOEA_HALED DOEA_HALED] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
When faced with increased osmolarity in the environment, many bacterial cells accumulate the compatible solute ectoine and its derivative 5-hydroxyectoine. Both compounds are not only potent osmostress protectants, but also serve as effective chemical chaperones stabilizing protein functionality. Ectoines are energy-rich nitrogen and carbon sources that have an ecological impact that shapes microbial communities. Although the biochemistry of ectoine and 5-hydroxyectoine biosynthesis is well understood, our understanding of their catabolism is only rudimentary. Here, we combined biochemical and structural approaches to unravel the core of ectoine and 5-hydroxyectoine catabolisms. We show that a conserved enzyme bimodule consisting of the EutD ectoine/5-hydroxyectoine hydrolase and the EutE deacetylase degrades both ectoines. We determined the high-resolution crystal structures of both enzymes, derived from the salt-tolerant bacteria Ruegeria pomeroyi and Halomonas elongata. These structures, either in their apo-forms or in forms capturing substrates or intermediates, provided detailed insights into the catalytic cores of the EutD and EutE enzymes. The combined biochemical and structural results indicate that the EutD homodimer opens the pyrimidine ring of ectoine through an unusual covalent intermediate, N-alpha-2 acetyl-L-2,4-diaminobutyrate (alpha-ADABA). We found that alpha-ADABA is then deacetylated by the zinc-dependent EutE monomer into diaminobutyric acid (DABA), which is further catabolized to L-aspartate. We observed that the EutD-EutE bimodule synthesizes exclusively the alpha-, but not the gamma-isomers of ADABA or hydroxy-ADABA. Of note, alpha-ADABA is known to induce the MocR/GabR-type repressor EnuR, which controls the expression of many ectoine catabolic genes clusters. We conclude that hydroxy-alpha-ADABA might serve a similar function. | |||
Degradation of the microbial stress protectants and chemical chaperones ectoine and hydroxyectoine by a bacterial hydrolase-deacetylase complex.,Mais CN, Hermann L, Altegoer F, Seubert A, Richter AA, Wernersbach I, Czech L, Bremer E, Bange G J Biol Chem. 2020 May 13. pii: RA120.012722. doi: 10.1074/jbc.RA120.012722. PMID:32404365<ref>PMID:32404365</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6yo9" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Mais | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Halomonas elongata]] | |||
[[Category: Large Structures]] | |||
[[Category: Altegoer F]] | |||
[[Category: Bange G]] | |||
[[Category: Mais C-N]] | |||
Latest revision as of 16:31, 24 January 2024
Product bound structure of the Ectoine utilization protein EutD (DoeA) from Halomonas elongataProduct bound structure of the Ectoine utilization protein EutD (DoeA) from Halomonas elongata
Structural highlights
FunctionPublication Abstract from PubMedWhen faced with increased osmolarity in the environment, many bacterial cells accumulate the compatible solute ectoine and its derivative 5-hydroxyectoine. Both compounds are not only potent osmostress protectants, but also serve as effective chemical chaperones stabilizing protein functionality. Ectoines are energy-rich nitrogen and carbon sources that have an ecological impact that shapes microbial communities. Although the biochemistry of ectoine and 5-hydroxyectoine biosynthesis is well understood, our understanding of their catabolism is only rudimentary. Here, we combined biochemical and structural approaches to unravel the core of ectoine and 5-hydroxyectoine catabolisms. We show that a conserved enzyme bimodule consisting of the EutD ectoine/5-hydroxyectoine hydrolase and the EutE deacetylase degrades both ectoines. We determined the high-resolution crystal structures of both enzymes, derived from the salt-tolerant bacteria Ruegeria pomeroyi and Halomonas elongata. These structures, either in their apo-forms or in forms capturing substrates or intermediates, provided detailed insights into the catalytic cores of the EutD and EutE enzymes. The combined biochemical and structural results indicate that the EutD homodimer opens the pyrimidine ring of ectoine through an unusual covalent intermediate, N-alpha-2 acetyl-L-2,4-diaminobutyrate (alpha-ADABA). We found that alpha-ADABA is then deacetylated by the zinc-dependent EutE monomer into diaminobutyric acid (DABA), which is further catabolized to L-aspartate. We observed that the EutD-EutE bimodule synthesizes exclusively the alpha-, but not the gamma-isomers of ADABA or hydroxy-ADABA. Of note, alpha-ADABA is known to induce the MocR/GabR-type repressor EnuR, which controls the expression of many ectoine catabolic genes clusters. We conclude that hydroxy-alpha-ADABA might serve a similar function. Degradation of the microbial stress protectants and chemical chaperones ectoine and hydroxyectoine by a bacterial hydrolase-deacetylase complex.,Mais CN, Hermann L, Altegoer F, Seubert A, Richter AA, Wernersbach I, Czech L, Bremer E, Bange G J Biol Chem. 2020 May 13. pii: RA120.012722. doi: 10.1074/jbc.RA120.012722. PMID:32404365[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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