5d87: Difference between revisions

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'''Unreleased structure'''


The entry 5d87 is ON HOLD  until Paper Publication
==Staphyloferrin B precursor biosynthetic enzyme SbnA Y152F/S185G variant==
<StructureSection load='5d87' size='340' side='right'caption='[[5d87]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5d87]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_str._Newman Staphylococcus aureus subsp. aureus str. Newman]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D87 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]] 1.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=5d87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d87 OCA], [https://pdbe.org/5d87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d87 RCSB], [https://www.ebi.ac.uk/pdbsum/5d87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d87 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SBNA_STAAE SBNA_STAAE] Probable pyridoxal phosphate-dependent enzyme involved in siderophore biosynthesis.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Staphylococcus aureus assembles the siderophore, staphyloferrin B, from L-2,3-diaminopropionic acid (L-Dap), alpha-ketoglutarate and citrate. Recently, SbnA and SbnB were shown to produce L-Dap and alpha-ketoglutarate from O-phospho-L-serine (OPS) and L-glutamate. SbnA is a pyridoxal 5'-phosphate-dependent enzyme with homology to O-acetyl-L-serine sulfhydrylases; however, SbnA utilizes OPS instead of O-acetyl-L-serine (OAS) and L-glutamate serves as a nitrogen donor instead of a sulfide. In this work, we examined how SbnA dictates substrate specificity for OPS and L-glutamate using a combination of X-ray crystallography, enzyme kinetics and site-directed mutagenesis. Analysis of SbnA crystals incubated with OPS revealed the structure of the PLP-alpha-aminoacrylate intermediate. Intermediate formation induced closure of the active site pocket by trapping a bound citrate molecule adjacent to the PLP-alpha-aminoacrylate. The citrate is likely replaced by the substrate L-glutamate during catalysis. Three active site residues were identified: Arg132, Tyr152, Ser185 that were essential for OPS recognition and turnover. The Y152F/S185G SbnA double mutant was completely inactive and its crystal structure revealed that the mutations induced a closed form of the enzyme in the absence of the alpha-aminoacrylate intermediate. Lastly, L-cysteine was shown to be a competitive inhibitor of SbnA by forming a non-productive external aldimine with the PLP cofactor. These results suggest a regulatory link between siderophore and L-cysteine biosynthesis, revealing a potential mechanism to reduce iron uptake under oxidative stress.


Authors: Kobylarz, M.J., Grigg, J.C., Liu, Y., Lee, M.S.F., Heinrichs, D.E., Murphy, M.E.P.
Deciphering the Substrate Specificity of SbnA, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis.,Kobylarz MJ, Grigg JC, Liu Y, Lee MS, Heinrichs DE, Murphy ME Biochemistry. 2016 Jan 21. PMID:26794841<ref>PMID:26794841</ref>


Description: Staphyloferrin B precursor biosynthetic enzyme SbnA Y152F/S185G variant
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Grigg, J.C]]
<div class="pdbe-citations 5d87" style="background-color:#fffaf0;"></div>
[[Category: Murphy, M.E.P]]
== References ==
[[Category: Liu, Y]]
<references/>
[[Category: Heinrichs, D.E]]
__TOC__
[[Category: Kobylarz, M.J]]
</StructureSection>
[[Category: Lee, M.S.F]]
[[Category: Large Structures]]
[[Category: Staphylococcus aureus subsp. aureus str. Newman]]
[[Category: Grigg JC]]
[[Category: Heinrichs DE]]
[[Category: Kobylarz MJ]]
[[Category: Lee MSF]]
[[Category: Liu Y]]
[[Category: Murphy MEP]]
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