View source for 5zwa


==Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium in complex with ADP, PL-linked to Lys233 via Schiff base in protomer A and the product (PLP) in protomer B==
<StructureSection load='5zwa' size='340' side='right'caption='[[5zwa]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5zwa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica Salmonella enterica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZWA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZWA 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]] 2.45&#8491;</td></tr>
<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=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JLP:(2S)-2-azanyl-6-[E-[5-(hydroxymethyl)-2-methyl-3-oxidanyl-pyridin-4-yl]methylideneamino]hexanoic+acid'>JLP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5zwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zwa OCA], [https://pdbe.org/5zwa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zwa RCSB], [https://www.ebi.ac.uk/pdbsum/5zwa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zwa ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0A0F7J8S0_SALTM A0A0F7J8S0_SALTM] B6-vitamer kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxine (PN), pyridoxal (PL), and pyridoxamine (PM), forming their respective 5'-phosphorylated esters, i.e. PNP, PLP and PMP.[HAMAP-Rule:MF_01638]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A large number of enzymes depend on the ubiquitous cofactor pyridoxal 5' phosphate (PLP) for their activity. Pyridoxal kinase (PLK) is the key enzyme involved in the synthesis of PLP from the three forms of vitamin B6 via the salvage pathway. In the present work, we determined the unliganded structure of StPLK in a monoclinic form and its ternary complex with bound pyridoxal (PL), ADP and Mg(2+) in two different tetragonal crystal forms (Form I and Form II). We found that, in the ternary complex structure of StPLK, the active site Lys233 forms a Schiff base linkage with the substrate (PL). Although formation of a Schiff base with the active site Lys229 was demonstrated in the Escherichia coli enzyme based on biochemical studies, the ternary complex of StPLK represents the first crystal structure where the Schiff bond formation has been observed. We also identified an additional site for PLP binding away from the active site in one of the ternary complexes (crystal Form I), suggesting a probable route for the product release. This is the first ternary complex structure where the modeled gamma-phosphate of ATP is close enough to PL for the phosphorylation of the substrate. StPLK prefers PL over pyridoxamine as its substrate and follows a sequential mechanism of catalysis. Surface plasmon resonance studies suggest that StPLK interacts with apo-PLP-dependent enzymes with mum affinity supporting the earlier proposed direct transfer mechanism of PLP from PLK to PLP-dependent enzymes.

Structural and functional studies on Salmonella typhimurium pyridoxal kinase: the first structural evidence for the formation of Schiff base with the substrate.,Deka G, Kalyani JN, Jahangir FB, Sabharwal P, Savithri HS, Murthy MRN FEBS J. 2019 Sep;286(18):3684-3700. doi: 10.1111/febs.14933. Epub 2019 Jun 17. PMID:31116912<ref>PMID:31116912</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5zwa" style="background-color:#fffaf0;"></div>

==See Also==
*[[Pyridoxal kinase|Pyridoxal kinase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Salmonella enterica]]
[[Category: Benazir JF]]
[[Category: Deka G]]
[[Category: Kalyani JN]]
[[Category: Murthy MRN]]
[[Category: Savithri HS]]