2i5b: Difference between revisions

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==The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution==
==The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution==
<StructureSection load='2i5b' size='340' side='right' caption='[[2i5b]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='2i5b' size='340' side='right'caption='[[2i5b]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2i5b]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I5B FirstGlance]. <br>
<table><tr><td colspan='2'>[[2i5b]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I5B FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">thiD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphomethylpyrimidine_kinase Phosphomethylpyrimidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.7 2.7.4.7] </span></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=2i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i5b OCA], [https://pdbe.org/2i5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i5b RCSB], [https://www.ebi.ac.uk/pdbsum/2i5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i5b ProSAT]</span></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=2i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i5b OCA], [http://pdbe.org/2i5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i5b RCSB], [http://www.ebi.ac.uk/pdbsum/2i5b PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/THID_BACSU THID_BACSU]] Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and of HMP to HMP-P. Shows no activity with pyridoxal, pyridoxamine or pyridoxine.  
[https://www.uniprot.org/uniprot/PDXK_BACSU PDXK_BACSU] Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates. Can also use hydroxymethylpyrimidine (HMP) as substrate.<ref>PMID:14973012</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i5/2i5b_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i5/2i5b_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus globigii migula 1900]]
[[Category: Bacillus subtilis]]
[[Category: Phosphomethylpyrimidine kinase]]
[[Category: Large Structures]]
[[Category: Das, S K]]
[[Category: Das SK]]
[[Category: Newman, J A]]
[[Category: Newman JA]]
[[Category: Rice, D W]]
[[Category: Rice DW]]
[[Category: Sedelnikova, S E]]
[[Category: Sedelnikova SE]]
[[Category: Adp complex]]
[[Category: Pdxk]]
[[Category: Ribokinase superfamily]]
[[Category: Thid]]
[[Category: Transferase]]
Retrieved from "https://proteopedia.org/2i5b"