6knk: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

The ~~entry 6knk~~ is ~~ON HOLD~~ until ~~Paper Publication~~

==Crystal structure of SbnH in complex with citryl-diaminoethane==

== Structural highlights ==

<table><tr><td colspan='2'>[[6knk]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KNK FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DN9:(2~{S})-2-[2-[2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]ethylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic+acid'>DN9</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=X3J:(2S)-2-{2-[(2-AMINOETHYL)AMINO]-2-OXOETHYL}-2-HYDROXYBUTANEDIOIC+ACID'>X3J</scene></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=6knk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6knk OCA], [http://pdbe.org/6knk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6knk RCSB], [http://www.ebi.ac.uk/pdbsum/6knk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6knk ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Staphyloferrin B is a hydroxycarboxylate siderophore that is crucial for the invasion and virulence of Staphylococcus aureus in mammalian hosts where free iron ions are scarce. The assembly of staphyloferrin B involves four enzymatic steps, in which SbnH, a pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, catalyzes the second step. Here, we report the X-ray crystal structures of S. aureus SbnH (SaSbnH) in complex with PLP, citrate and the decarboxylation product citryl-diaminoethane (citryl-Dae). The overall structure of SaSbnH resembles those of the previously reported PLP-dependent amino acid decarboxylases, but the active site of SaSbnH showed unique structural features. Structural and mutagenesis analysis revealed that the citryl moiety of the substrate citryl-L-2,3-diaminopropionic acid (citryl-L-Dap) inserts into a narrow groove at the dimer interface of SaSbnH and forms hydrogen bonding interactions with both subunits. In the active site, a conserved lysine residue forms an aldimine linkage with the cofactor PLP, and a phenylalanine residue is essential for accommodating the L-configuration Dap of the substrate. Interestingly, the free-standing citrate molecule was found to bind to SaSbnH in a conformation inverse to that of the citryl group of citryl-Dae and efficiently inhibit SaSbnH. As an intermediate in the tricarboxylic acid (TCA) cycle, citrate is highly abundant in bacterial cells until iron depletion; thus, its inhibition of SaSbnH may serve as an iron-dependent regulatory mechanism in staphyloferrin B biosynthesis.

~~Authors~~:

Structural insights into substrate recognition and activity regulation of the key decarboxylase SbnH in staphyloferrin B biosynthesis.,Tang J, Ju Y, Gu Q, Xu J, Zhou H J Mol Biol. 2019 Oct 18. pii: S0022-2836(19)30605-9. doi:, 10.1016/j.jmb.2019.10.009. PMID:31634470<ref>PMID:31634470</ref>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Ju, Y]]

[[Category: Tang, J]]

[[Category: Zhou, H]]

[[Category: Biosynthetic protein]]

[[Category: Plp-dependent decarboxylase]]

[[Category: Staphyloferrin b]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6knk is ON HOLD  until Paper Publication
+==Crystal structure of SbnH in complex with citryl-diaminoethane==
+<StructureSection load='6knk' size='340' side='right'caption='[[6knk]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6knk]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KNK FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DN9:(2~{S})-2-[2-[2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]ethylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic+acid'>DN9</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=X3J:(2S)-2-{2-[(2-AMINOETHYL)AMINO]-2-OXOETHYL}-2-HYDROXYBUTANEDIOIC+ACID'>X3J</scene></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=6knk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6knk OCA], [http://pdbe.org/6knk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6knk RCSB], [http://www.ebi.ac.uk/pdbsum/6knk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6knk ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Staphyloferrin B is a hydroxycarboxylate siderophore that is crucial for the invasion and virulence of Staphylococcus aureus in mammalian hosts where free iron ions are scarce. The assembly of staphyloferrin B involves four enzymatic steps, in which SbnH, a pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, catalyzes the second step. Here, we report the X-ray crystal structures of S. aureus SbnH (SaSbnH) in complex with PLP, citrate and the decarboxylation product citryl-diaminoethane (citryl-Dae). The overall structure of SaSbnH resembles those of the previously reported PLP-dependent amino acid decarboxylases, but the active site of SaSbnH showed unique structural features. Structural and mutagenesis analysis revealed that the citryl moiety of the substrate citryl-L-2,3-diaminopropionic acid (citryl-L-Dap) inserts into a narrow groove at the dimer interface of SaSbnH and forms hydrogen bonding interactions with both subunits. In the active site, a conserved lysine residue forms an aldimine linkage with the cofactor PLP, and a phenylalanine residue is essential for accommodating the L-configuration Dap of the substrate. Interestingly, the free-standing citrate molecule was found to bind to SaSbnH in a conformation inverse to that of the citryl group of citryl-Dae and efficiently inhibit SaSbnH. As an intermediate in the tricarboxylic acid (TCA) cycle, citrate is highly abundant in bacterial cells until iron depletion; thus, its inhibition of SaSbnH may serve as an iron-dependent regulatory mechanism in staphyloferrin B biosynthesis.
-Authors:
+Structural insights into substrate recognition and activity regulation of the key decarboxylase SbnH in staphyloferrin B biosynthesis.,Tang J, Ju Y, Gu Q, Xu J, Zhou H J Mol Biol. 2019 Oct 18. pii: S0022-2836(19)30605-9. doi:, 10.1016/j.jmb.2019.10.009. PMID:31634470<ref>PMID:31634470</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6knk" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Ju, Y]]
+[[Category: Tang, J]]
+[[Category: Zhou, H]]
+[[Category: Biosynthetic protein]]
+[[Category: Plp-dependent decarboxylase]]
+[[Category: Staphyloferrin b]]