2i5b

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{{Seed}}
 
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[[Image:2i5b.png|left|200px]]
 
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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==
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The line below this paragraph, containing "STRUCTURE_2i5b", creates the "Structure Box" on the page.
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<StructureSection load='2i5b' size='340' side='right'caption='[[2i5b]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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<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>
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{{STRUCTURE_2i5b| PDB=2i5b | SCENE= }}
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<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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i5/2i5b_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2i5b ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Pyridoxal kinase catalyses the phosphorylation of pyridoxal, pyridoxine and pyridoxamine to their 5' phosphates and plays an important role in the pyridoxal 5' phosphate salvage pathway. The crystal structure of a dimeric pyridoxal kinase from Bacillus subtilis has been solved in complex with ADP to 2.8 A resolution. Analysis of the structure suggests that binding of the nucleotide induces the ordering of two loops, which operate independently to close a flap on the active site. Comparisons with other ribokinase superfamily members reveal that B. subtilis pyridoxal kinase is more closely related in both sequence and structure to the family of HMPP kinases than to other pyridoxal kinases, suggesting that this structure represents the first for a novel family of "HMPP kinase-like" pyridoxal kinases. Moreover this further suggests that this enzyme activity has evolved independently on multiple occasions from within the ribokinase superfamily.
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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===
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The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution.,Newman JA, Das SK, Sedelnikova SE, Rice DW J Mol Biol. 2006 Oct 20;363(2):520-30. Epub 2006 Aug 12. PMID:16978644<ref>PMID:16978644</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2i5b" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16978644}}, adds the Publication Abstract to the page
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*[[Pyridoxal kinase|Pyridoxal kinase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16978644 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16978644}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2I5B is a 5 chains structure of sequences from [http://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].
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==Reference==
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<ref group="xtra">PMID:16978644</ref><references group="xtra"/>
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[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Phosphomethylpyrimidine kinase]]
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[[Category: Large Structures]]
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[[Category: Das, S K.]]
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[[Category: Das SK]]
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[[Category: Newman, J A.]]
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[[Category: Newman JA]]
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[[Category: Rice, D W.]]
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[[Category: Rice DW]]
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[[Category: Sedelnikova, S E.]]
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[[Category: Sedelnikova SE]]
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[[Category: Adp complex]]
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[[Category: Pdxk]]
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[[Category: Ribokinase superfamily]]
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[[Category: Thid]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:42:47 2009''
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Current revision

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution

PDB ID 2i5b

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