5d85: Difference between revisions

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<StructureSection load='5d85' size='340' side='right'caption='[[5d85]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
<StructureSection load='5d85' size='340' side='right'caption='[[5d85]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5d85]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staae Staae]. 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 [http://oca.weizmann.ac.il/oca-docs/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"><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]] 1.92&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5d84|5d84]], [[5d86|5d86]], [[5d87|5d87]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sbnA, NWMN_0060 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=426430 STAAE])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5d85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d85 OCA], [http://pdbe.org/5d85 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d85 RCSB], [http://www.ebi.ac.uk/pdbsum/5d85 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d85 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, 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>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Staae]]
[[Category: Staphylococcus aureus subsp. aureus str. Newman]]
[[Category: Grigg, J C]]
[[Category: Grigg JC]]
[[Category: Heinrichs, D E]]
[[Category: Heinrichs DE]]
[[Category: Kobylarz, M J]]
[[Category: Kobylarz MJ]]
[[Category: Lee, M S.F]]
[[Category: Lee MSF]]
[[Category: Liu, Y]]
[[Category: Liu Y]]
[[Category: Murphy, M E.P]]
[[Category: Murphy MEP]]
[[Category: Biosynthetic protein]]
[[Category: Iron]]
[[Category: Plp]]
[[Category: Siderophore]]
Retrieved from "https://proteopedia.org/5d85"