4c5k: Difference between revisions
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==Structure of the pyridoxal kinase from Staphylococcus aureus in complex with ADP== | ==Structure of the pyridoxal kinase from Staphylococcus aureus in complex with ADP== | ||
<StructureSection load='4c5k' size='340' side='right' caption='[[4c5k]], [[Resolution|resolution]] 1.40Å' scene=''> | <StructureSection load='4c5k' size='340' side='right'caption='[[4c5k]], [[Resolution|resolution]] 1.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4c5k]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4c5k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4C5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4C5K FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=4c5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4c5k OCA], [https://pdbe.org/4c5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4c5k RCSB], [https://www.ebi.ac.uk/pdbsum/4c5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4c5k ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0H3JTP0_STAAM A0A0H3JTP0_STAAM] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4c5k" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Staphylococcus aureus subsp. aureus Mu50]] | ||
[[Category: Alte | [[Category: Alte F]] | ||
[[Category: Nodwell | [[Category: Nodwell M]] | ||
[[Category: Schneider | [[Category: Schneider S]] | ||
[[Category: Sieber | [[Category: Sieber SA]] | ||
Latest revision as of 15:04, 20 December 2023
Structure of the pyridoxal kinase from Staphylococcus aureus in complex with ADPStructure of the pyridoxal kinase from Staphylococcus aureus in complex with ADP
Structural highlights
FunctionPublication Abstract from PubMedPyridoxal 5'-phosphate (PLP) is the active vitamer of vitamin B6 and acts as an essential cofactor in many aspects of amino acid and sugar metabolism. The virulence and survival of pathogenic bacteria such as Mycobacterium tuberculosis depend on PLP and deficiencies in humans have also been associated with neurological disorders and inflammation. While PLP can be synthesized by a de novo pathway in bacteria and plants, most higher organisms rely on a salvage pathway that phosphorylates either pyridoxal (PL) or its related vitamers, pyridoxine (PN) and pyridoxamine (PM). PL kinases (PLKs) are essential for this phosphorylation step and are thus of major importance for cellular viability. We recently identified a pyridoxal kinase (SaPLK) as a target of the natural product antibiotic rugulactone (Ru) in Staphylococcus aureus. Surprisingly, Ru selectively modified SaPLK not at the active site cysteine, but on a remote cysteine residue. Based on structural and biochemical studies, we now provide insight into an unprecedented dual Cys charge relay network that is mandatory for PL phosphorylation. The key component is the reactive Cys 110 residue in the lid region that forms a hemithioactetal intermediate with the 4 -aldehyde of PL. This hemithioacetal, in concert with the catalytic Cys 214, increases the nucleophilicity of the PL 5 -OH group for the inline displacement reaction with the g-phosphate of ATP. A closer inspection of related enzymes reveals that Cys 110 is conserved and thus serves as a characteristic mechanistic feature for a dual-function ribokinase subfamily herein termed CC-PLKs. A sub-family of bacterial ribokinases utilizes a hemithioacetal for pyridoxal phosphate salvage.,Nodwell MB, Koch MF, Alte F, Schneider S, Sieber SA J Am Chem Soc. 2014 Mar 6. PMID:24601602[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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