5d85
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5d85]] 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=5D85 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D85 FirstGlance]. <br> | <table><tr><td colspan='2'>[[5d85]] 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=5D85 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D85 FirstGlance]. <br> | ||
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P1T:2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC+ACID'>P1T</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.92Å</td></tr> |
+ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P1T:2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC+ACID'>P1T</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=5d85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d85 OCA], [https://pdbe.org/5d85 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d85 RCSB], [https://www.ebi.ac.uk/pdbsum/5d85 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d85 ProSAT]</span></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=5d85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d85 OCA], [https://pdbe.org/5d85 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d85 RCSB], [https://www.ebi.ac.uk/pdbsum/5d85 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d85 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/SBNA_STAAE SBNA_STAAE] Probable pyridoxal phosphate-dependent enzyme involved in siderophore biosynthesis. | [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. | ||
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- | 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> | ||
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- | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
- | </div> | ||
- | <div class="pdbe-citations 5d85" style="background-color:#fffaf0;"></div> | ||
- | == References == | ||
- | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> |
Current revision
Staphyloferrin B precursor biosynthetic enzyme SbnA bound to aminoacrylate intermediate
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