6u7l: Difference between revisions
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<StructureSection load='6u7l' size='340' side='right'caption='[[6u7l]], [[Resolution|resolution]] 2.75Å' scene=''> | <StructureSection load='6u7l' size='340' side='right'caption='[[6u7l]], [[Resolution|resolution]] 2.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6u7l]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U7L OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6u7l]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U7L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U7L FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.75Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PHD:ASPARTYL+PHOSPHATE'>PHD</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=6u7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u7l OCA], [https://pdbe.org/6u7l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u7l RCSB], [https://www.ebi.ac.uk/pdbsum/6u7l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u7l ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/GARD_ECOLI GARD_ECOLI] Catalyzes the dehydration of galactarate to form 5-dehydro-4-deoxy-D-glucarate.[HAMAP-Rule:MF_02031]<ref>PMID:9772162</ref> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Galactarate dehydratase (GarD) is the first enzyme in the galactarate/glucarate pathway and catalyzes the dehydration of galactarate to 3-keto-5-dehydroxygalactarate. This protein is known to increase colonization fitness of intestinal pathogens in antibiotic-treated mice and to promote bacterial survival during stress. The galactarate/glucarate pathway is widespread in bacteria, but not in humans, and thus could be a target to develop new inhibitors for use in combination therapy to combat antibiotic resistance. The structure of almost all the enzymes of the galactarate/glucarate pathway were solved previously, except for GarD, for which only the structure of the N-terminal domain was determined previously. Herein, we report the first crystal structure of full-length GarD solved using a seleno-methoionine derivative revealing a new protein fold. The protein consists of three domains, each presenting a novel twist as compared to their distant homologs. GarD in the crystal structure forms dimers and each monomer consists of three domains. The N-terminal domain is comprised of a beta-clip fold, connected to the second domain by a long unstructured linker. The second domain serves as a dimerization interface between two monomers. The C-terminal domain forms an unusual variant of a Rossmann fold with a crossover and is built around a seven-stranded parallel beta-sheet supported by nine alpha-helices. A metal binding site in the C-terminal domain is occupied by Ca(2+) . The activity of GarD was corroborated by the production of 5-keto-4-deoxy-D-glucarate under reducing conditions and in the presence of iron. Thus, GarD is an unusual enolase with a novel protein fold never previously seen in this class of enzymes. | |||
Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment.,Rosas-Lemus M, Minasov G, Shuvalova L, Wawrzak Z, Kiryukhina O, Mih N, Jaroszewski L, Palsson B, Godzik A, Satchell KJF Protein Sci. 2020 Mar;29(3):711-722. doi: 10.1002/pro.3796. Epub 2019 Dec 17. PMID:31811683<ref>PMID:31811683</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6u7l" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli K-12]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Dubrovska I]] | |||
[[Category: Dubrovska | [[Category: Endres M]] | ||
[[Category: Endres | [[Category: Kiryukhina O]] | ||
[[Category: Kiryukhina | [[Category: Minasov G]] | ||
[[Category: Minasov | [[Category: Satchell KJF]] | ||
[[Category: Satchell | [[Category: Shuvalova L]] | ||
[[Category: Shuvalova | [[Category: Wawrzak Z]] | ||
[[Category: Wawrzak | |||
