2ddw: Difference between revisions

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-[[Image:2ddw.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2ddw", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_2ddw|  PDB=2ddw  |  SCENE=  }}
-'''Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution'''
+==Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution==
+<StructureSection load='2ddw' size='340' side='right'caption='[[2ddw]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ddw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDW 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]] 3.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</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=2ddw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddw OCA], [https://pdbe.org/2ddw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ddw RCSB], [https://www.ebi.ac.uk/pdbsum/2ddw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddw ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PDXK_ECOLI PDXK_ECOLI] Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates.
+== 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/dd/2ddw_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=2ddw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The pdxK and pdxY genes have been found to code for pyridoxal kinases, enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published, including Escherichia coli pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of the pdxY and pdxK genes, respectively. We now report the crystal structure of E. coli pyridoxal kinase 1 (ePL kinase 1), encoded by a pdxK gene, and an isoform of ePL kinase 2. The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2.1-, 2.6-, and 3.2-A resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4' substituent on the substrate. This is the result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site. Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C-4' of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.
-==Overview==
+Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.,Safo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V J Bacteriol. 2006 Jun;188(12):4542-52. PMID:16740960<ref>PMID:16740960</ref>
-The pdxK and pdxY genes have been found to code for pyridoxal kinases, enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published, including Escherichia coli pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of the pdxY and pdxK genes, respectively. We now report the crystal structure of E. coli pyridoxal kinase 1 (ePL kinase 1), encoded by a pdxK gene, and an isoform of ePL kinase 2. The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2.1-, 2.6-, and 3.2-A resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4' substituent on the substrate. This is the result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site. Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C-4' of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-DDW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDW OCA].
+</div>
+<div class="pdbe-citations 2ddw" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases., Safo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V, J Bacteriol. 2006 Jun;188(12):4542-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16740960 16740960]
+*[[Pyridoxal kinase|Pyridoxal kinase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Pyridoxal kinase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Claude JB]]
-[[Category: Claude, J B.]]
+[[Category: Hunt S]]
-[[Category: Hunt, S.]]
+[[Category: Musayev FN]]
-[[Category: Musayev, F N.]]
+[[Category: Safo MK]]
-[[Category: Safo, M K.]]
+[[Category: Schirch V]]
-[[Category: Salvo, M L.di.]]
+[[Category: Di Salvo ML]]
-[[Category: Schirch, V.]]
-[[Category: Phosphorylation]]
-[[Category: Pyridoxal 5'-phosphate]]
-[[Category: Pyridoxal kinase]]
-[[Category: Ribokinase]]
-[[Category: Vitamin b6]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 00:14:34 2008''