4mp3: Difference between revisions

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~~{{STRUCTURE_4mp3| PDB=4mp3 | SCENE= }}~~

~~===Staphyloferrin B precursor biosynthetic enzyme selenomethionine-labeled SbnB===~~

~~{{ABSTRACT_PUBMED_24485762}}~~

==~~About this Structure~~==

==Staphyloferrin B precursor biosynthetic enzyme selenomethionine-labeled SbnB==

[[4mp3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MP3 OCA].

== Structural highlights ==

<table><tr><td colspan='2'>[[4mp3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_MW2 Staphylococcus aureus subsp. aureus MW2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MP3 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]] 2.11Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4mp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mp3 OCA], [https://pdbe.org/4mp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mp3 RCSB], [https://www.ebi.ac.uk/pdbsum/4mp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mp3 ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

L-2,3-diaminopropionic acid (L-Dap) is an amino acid that is a precursor of antibiotics and staphyloferrin B a siderophore produced by Staphylococcus aureus. SbnA and SbnB are encoded by the staphyloferrin B biosynthetic gene cluster and are implicated in L-Dap biosynthesis. We demonstrate here that SbnA uses PLP and substrates O-phospho-L-serine and L-glutamate to produce a metabolite N-(1-amino-1-carboxyl-2-ethyl)-glutamic acid (ACEGA). SbnB is shown to use NAD(+) to oxidatively hydrolyze ACEGA to yield alpha-ketoglutarate and L-Dap. Also, we describe crystal structures of SbnB in complex with NADH and ACEGA as well as with NAD(+) and alpha-ketoglutarate to reveal the residues required for substrate binding, oxidation, and hydrolysis. SbnA and SbnB contribute to the iron sparing response of S. aureus that enables staphyloferrin B biosynthesis in the absence of an active tricarboxylic acid cycle.

~~==Reference==~~

Synthesis of L-2,3-diaminopropionic Acid, a siderophore and antibiotic precursor.,Kobylarz MJ, Grigg JC, Takayama SJ, Rai DK, Heinrichs DE, Murphy ME Chem Biol. 2014 Mar 20;21(3):379-88. doi: 10.1016/j.chembiol.2013.12.011. Epub, 2014 Jan 30. PMID:24485762<ref>PMID:24485762</ref>

~~[[Category: Grigg, J C.]]~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

~~[[Category: Kobylarz, M J.]]~~

</div>

[[Category: ~~Murphy, M E.P.~~]]

[[Category: ~~Rai, D K~~.]]

== References ==

[[Category: ~~Acega dehydrogenase~~]]

[[Category: ~~L-dap synthesis~~]]

__TOC__

[[Category: ~~Oxidoreductase~~]]

</StructureSection>

[[Category: ~~Siderophore~~]]

[[Category: Large Structures]]

[[Category: Staphylococcus aureus subsp. aureus MW2]]

[[Category: Grigg JC]]

[[Category: Kobylarz MJ]]

[[Category: Murphy MEP]]

[[Category: Rai DK]]

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@@ Line 1: / Line 1: @@
-{{STRUCTURE_4mp3|  PDB=4mp3  |  SCENE=  }}
-===Staphyloferrin B precursor biosynthetic enzyme selenomethionine-labeled SbnB===
-{{ABSTRACT_PUBMED_24485762}}
-==About this Structure==
+==Staphyloferrin B precursor biosynthetic enzyme selenomethionine-labeled SbnB==
-[[4mp3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MP3 OCA].
+<StructureSection load='4mp3' size='340' side='right'caption='[[4mp3]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4mp3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_MW2 Staphylococcus aureus subsp. aureus MW2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MP3 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]] 2.11&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4mp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mp3 OCA], [https://pdbe.org/4mp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mp3 RCSB], [https://www.ebi.ac.uk/pdbsum/4mp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mp3 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+L-2,3-diaminopropionic acid (L-Dap) is an amino acid that is a precursor of antibiotics and staphyloferrin B a siderophore produced by Staphylococcus aureus. SbnA and SbnB are encoded by the staphyloferrin B biosynthetic gene cluster and are implicated in L-Dap biosynthesis. We demonstrate here that SbnA uses PLP and substrates O-phospho-L-serine and L-glutamate to produce a metabolite N-(1-amino-1-carboxyl-2-ethyl)-glutamic acid (ACEGA). SbnB is shown to use NAD(+) to oxidatively hydrolyze ACEGA to yield alpha-ketoglutarate and L-Dap. Also, we describe crystal structures of SbnB in complex with NADH and ACEGA as well as with NAD(+) and alpha-ketoglutarate to reveal the residues required for substrate binding, oxidation, and hydrolysis. SbnA and SbnB contribute to the iron sparing response of S. aureus that enables staphyloferrin B biosynthesis in the absence of an active tricarboxylic acid cycle.
-==Reference==
+Synthesis of L-2,3-diaminopropionic Acid, a siderophore and antibiotic precursor.,Kobylarz MJ, Grigg JC, Takayama SJ, Rai DK, Heinrichs DE, Murphy ME Chem Biol. 2014 Mar 20;21(3):379-88. doi: 10.1016/j.chembiol.2013.12.011. Epub, 2014 Jan 30. PMID:24485762<ref>PMID:24485762</ref>
-<ref group="xtra">PMID:024485762</ref><references group="xtra"/><references/>
-[[Category: Grigg, J C.]]
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Kobylarz, M J.]]
+</div>
-[[Category: Murphy, M E.P.]]
+<div class="pdbe-citations 4mp3" style="background-color:#fffaf0;"></div>
-[[Category: Rai, D K.]]
+== References ==
-[[Category: Acega dehydrogenase]]
+<references/>
-[[Category: L-dap synthesis]]
+__TOC__
-[[Category: Oxidoreductase]]
+</StructureSection>
-[[Category: Siderophore]]
+[[Category: Large Structures]]
+[[Category: Staphylococcus aureus subsp. aureus MW2]]
+[[Category: Grigg JC]]
+[[Category: Kobylarz MJ]]
+[[Category: Murphy MEP]]
+[[Category: Rai DK]]