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New page: left|200px<br /><applet load="2yxu" size="350" color="white" frame="true" align="right" spinBox="true" caption="2yxu, resolution 2.2Å" /> '''Human Pyridoxal Kinas...
 
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[[Image:2yxu.jpg|left|200px]]<br /><applet load="2yxu" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2yxu, resolution 2.2&Aring;" />
'''Human Pyridoxal Kinase'''<br />


==Overview==
==Human Pyridoxal Kinase==
<StructureSection load='2yxu' size='340' side='right'caption='[[2yxu]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2yxu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YXU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YXU 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]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2yxu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yxu OCA], [https://pdbe.org/2yxu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yxu RCSB], [https://www.ebi.ac.uk/pdbsum/2yxu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yxu ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PDXK_HUMAN PDXK_HUMAN] Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yx/2yxu_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2yxu ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Pyridoxal kinase catalyzes the transfer of a phosphate group from ATP to the 5' alcohol of pyridoxine, pyridoxamine, and pyridoxal. In this work, kinetic studies were conducted to examine monovalent cation dependence of human pyridoxal kinase kinetic parameters. The results show that hPLK affinity for ATP and PL is increased manyfold in the presence of K(+) when compared to Na(+); however, the maximal activity of the Na(+) form of the enzyme is more than double the activity in the presence of K(+). Other monovalent cations, Li(+), Cs(+), and Rb(+) do not show significant activity. We have determined the crystal structure of hPLK in the unliganded form, and in complex with MgATP to 2.0 and 2.2 A resolution, respectively. Overall, the two structures show similar open conformation, and likely represent the catalytically idle state. The crystal structure of the MgATP complex also reveals Mg(2+) and Na(+) acting in tandem to anchor the ATP at the active site. Interestingly, the active site of hPLK acts as a sink to bind several molecules of MPD. The features of monovalent and divalent metal cation binding, active site structure, and vitamin B6 specificity are discussed in terms of the kinetic and structural studies, and are compared with those of the sheep and Escherichia coli enzymes.
Pyridoxal kinase catalyzes the transfer of a phosphate group from ATP to the 5' alcohol of pyridoxine, pyridoxamine, and pyridoxal. In this work, kinetic studies were conducted to examine monovalent cation dependence of human pyridoxal kinase kinetic parameters. The results show that hPLK affinity for ATP and PL is increased manyfold in the presence of K(+) when compared to Na(+); however, the maximal activity of the Na(+) form of the enzyme is more than double the activity in the presence of K(+). Other monovalent cations, Li(+), Cs(+), and Rb(+) do not show significant activity. We have determined the crystal structure of hPLK in the unliganded form, and in complex with MgATP to 2.0 and 2.2 A resolution, respectively. Overall, the two structures show similar open conformation, and likely represent the catalytically idle state. The crystal structure of the MgATP complex also reveals Mg(2+) and Na(+) acting in tandem to anchor the ATP at the active site. Interestingly, the active site of hPLK acts as a sink to bind several molecules of MPD. The features of monovalent and divalent metal cation binding, active site structure, and vitamin B6 specificity are discussed in terms of the kinetic and structural studies, and are compared with those of the sheep and Escherichia coli enzymes.


==About this Structure==
Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.,Musayev FN, di Salvo ML, Ko TP, Gandhi AK, Goswami A, Schirch V, Safo MK Protein Sci. 2007 Oct;16(10):2184-94. Epub 2007 Aug 31. PMID:17766369<ref>PMID:17766369</ref>
2YXU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=ATP:'>ATP</scene> and <scene name='pdbligand=MPD:'>MPD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] Known structural/functional Sites: <scene name='pdbsite=AC1:Mg+Binding+Site+For+Residue+A+1404'>AC1</scene>, <scene name='pdbsite=AC2:Na+Binding+Site+For+Residue+A+1406'>AC2</scene>, <scene name='pdbsite=AC3:Mg+Binding+Site+For+Residue+B+2404'>AC3</scene>, <scene name='pdbsite=AC4:Na+Binding+Site+For+Residue+B+2406'>AC4</scene>, <scene name='pdbsite=AC5:Po4+Binding+Site+For+Residue+A+1501'>AC5</scene>, <scene name='pdbsite=AC6:Po4+Binding+Site+For+Residue+B+1517'>AC6</scene>, <scene name='pdbsite=AC7:Po4+Binding+Site+For+Residue+B+1527'>AC7</scene>, <scene name='pdbsite=AC8:Atp+Binding+Site+For+Residue+A+1410'>AC8</scene>, <scene name='pdbsite=AC9:Atp+Binding+Site+For+Residue+B+2410'>AC9</scene>, <scene name='pdbsite=BC1:Mpd+Binding+Site+For+Residue+A+1011'>BC1</scene>, <scene name='pdbsite=BC2:Mpd+Binding+Site+For+Residue+A+1013'>BC2</scene>, <scene name='pdbsite=BC3:Mpd+Binding+Site+For+Residue+B+1015'>BC3</scene>, <scene name='pdbsite=BC4:Mpd+Binding+Site+For+Residue+B+1019'>BC4</scene>, <scene name='pdbsite=BC5:Mpd+Binding+Site+For+Residue+B+1021'>BC5</scene>, <scene name='pdbsite=BC6:Mpd+Binding+Site+For+Residue+B+1023'>BC6</scene>, <scene name='pdbsite=BC7:Mpd+Binding+Site+For+Residue+B+1025'>BC7</scene>, <scene name='pdbsite=BC8:Mpd+Binding+Site+For+Residue+B+1029'>BC8</scene>, <scene name='pdbsite=BC9:Mpd+Binding+Site+For+Residue+B+1031'>BC9</scene>, <scene name='pdbsite=CC1:Mpd+Binding+Site+For+Residue+A+1037'>CC1</scene>, <scene name='pdbsite=CC2:Mpd+Binding+Site+For+Residue+B+1039'>CC2</scene> and <scene name='pdbsite=CC3:Mpd+Binding+Site+For+Residue+B+1041'>CC3</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YXU OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation., Musayev FN, di Salvo ML, Ko TP, Gandhi AK, Goswami A, Schirch V, Safo MK, Protein Sci. 2007 Oct;16(10):2184-94. Epub 2007 Aug 31. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17766369 17766369]
</div>
<div class="pdbe-citations 2yxu" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Pyridoxal kinase|Pyridoxal kinase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Pyridoxal kinase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Ko TP]]
[[Category: Ko, T P.]]
[[Category: Musayev FN]]
[[Category: Musayev, F N.]]
[[Category: Safo MK]]
[[Category: Safo, M K.]]
[[Category: Schirch V]]
[[Category: Schirch, V.]]
[[Category: ATP]]
[[Category: MG]]
[[Category: MPD]]
[[Category: NA]]
[[Category: PO4]]
[[Category: atp complex]]
[[Category: beta sheet with alpha helix]]
[[Category: metal ion]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Mar 14 09:37:05 2008''
Retrieved from "https://proteopedia.org/2yxu"