3zzg: Difference between revisions
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==Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase without ligands== | ==Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase without ligands== | ||
<StructureSection load='3zzg' size='340' side='right' caption='[[3zzg]], [[Resolution|resolution]] 2.95Å' scene=''> | <StructureSection load='3zzg' size='340' side='right'caption='[[3zzg]], [[Resolution|resolution]] 2.95Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3zzg]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3zzg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZZG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZZG FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.95Å</td></tr> | ||
<tr | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3zzg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zzg OCA], [https://pdbe.org/3zzg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zzg RCSB], [https://www.ebi.ac.uk/pdbsum/3zzg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zzg ProSAT]</span></td></tr> | ||
</table> | |||
<table> | == Function == | ||
[https://www.uniprot.org/uniprot/ARG56_YEAST ARG56_YEAST] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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Insight on an arginine synthesis metabolon from the tetrameric structure of yeast acetylglutamate kinase.,de Cima S, Gil-Ortiz F, Crabeel M, Fita I, Rubio V PLoS One. 2012;7(4):e34734. Epub 2012 Apr 18. PMID:22529931<ref>PMID:22529931</ref> | Insight on an arginine synthesis metabolon from the tetrameric structure of yeast acetylglutamate kinase.,de Cima S, Gil-Ortiz F, Crabeel M, Fita I, Rubio V PLoS One. 2012;7(4):e34734. Epub 2012 Apr 18. PMID:22529931<ref>PMID:22529931</ref> | ||
From | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3zzg" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Crabeel M]] | |||
[[Category: Crabeel | [[Category: Fita I]] | ||
[[Category: Fita | [[Category: Gil-Ortiz F]] | ||
[[Category: Gil-Ortiz | [[Category: Rubio V]] | ||
[[Category: Rubio | [[Category: De Cima S]] | ||
[[Category: | |||
Latest revision as of 14:16, 20 December 2023
Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase without ligandsCrystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase without ligands
Structural highlights
FunctionPublication Abstract from PubMedN-acetyl-L-glutamate kinase (NAGK) catalyzes the second, generally controlling, step of arginine biosynthesis. In yeasts, NAGK exists either alone or forming a metabolon with N-acetyl-L-glutamate synthase (NAGS), which catalyzes the first step and exists only within the metabolon. Yeast NAGK (yNAGK) has, in addition to the amino acid kinase (AAK) domain found in other NAGKs, a approximately 150-residue C-terminal domain of unclear significance belonging to the DUF619 domain family. We deleted this domain, proving that it stabilizes yNAGK, slows catalysis and modulates feed-back inhibition by arginine. We determined the crystal structures of both the DUF619 domain-lacking yNAGK, ligand-free as well as complexed with acetylglutamate or acetylglutamate and arginine, and of complete mature yNAGK. While all other known arginine-inhibitable NAGKs are doughnut-like hexameric trimers of dimers of AAK domains, yNAGK has as central structure a flat tetramer formed by two dimers of AAK domains. These dimers differ from canonical AAK dimers in the -110 degrees rotation of one subunit with respect to the other. In the hexameric enzymes, an N-terminal extension, found in all arginine-inhibitable NAGKs, forms a protruding helix that interlaces the dimers. In yNAGK, however, it conforms a two-helix platform that mediates interdimeric interactions. Arginine appears to freeze an open inactive AAK domain conformation. In the complete yNAGK structure, two pairs of DUF619 domains flank the AAK domain tetramer, providing a mechanism for the DUF619 domain modulatory functions. The DUF619 domain exhibits the histone acetyltransferase fold, resembling the catalytic domain of bacterial NAGS. However, the putative acetyl CoA site is blocked, explaining the lack of NAGS activity of yNAGK. We conclude that the tetrameric architecture is an adaptation to metabolon formation and propose an organization for this metabolon, suggesting that yNAGK may be a good model also for yeast and human NAGSs. Insight on an arginine synthesis metabolon from the tetrameric structure of yeast acetylglutamate kinase.,de Cima S, Gil-Ortiz F, Crabeel M, Fita I, Rubio V PLoS One. 2012;7(4):e34734. Epub 2012 Apr 18. PMID:22529931[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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