1m5w

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(New page: 200px<br /><applet load="1m5w" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m5w, resolution 1.96&Aring;" /> '''1.96 A Crystal Struc...)
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[[Image:1m5w.gif|left|200px]]<br /><applet load="1m5w" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1m5w, resolution 1.96&Aring;" />
 
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'''1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate'''<br />
 
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==Overview==
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==1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate==
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We report the 1.96 A crystal structure of pyridoxine 5'-phosphate synthase, (PdxJ) in complex with 1-deoxy-D-xylulose phosphate (dXP). The octameric, enzyme possesses eight distinct binding sites, and three different binding, states are observed. The observation of these three states supports a, mechanism in which precise conformational changes of a peptide loop and, groups of active site residues modulate binding and specificity. The, differences in protein conformation when one or two substrates are bound, can be correlated with a condensation mechanism that leads productively to, the formation of pyridoxine 5'-phosphate (PNP). "Snapshots" of the, progression from the apo form to a singly occupied "transitional binding", state and, subsequently, to a fully occupied, reactive state are revealed, and indicate how the enzyme structure can be related to a plausible, catalytic mechanism and, moreover, to favorable energetics of reaction.
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<StructureSection load='1m5w' size='340' side='right'caption='[[1m5w]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1m5w]] is a 8 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=1M5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M5W FirstGlance]. <br>
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1M5W is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with DXP and PO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M5W OCA].
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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]] 1.96&#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=DXP:1-DEOXY-D-XYLULOSE-5-PHOSPHATE'>DXP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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==Reference==
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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=1m5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5w OCA], [https://pdbe.org/1m5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m5w RCSB], [https://www.ebi.ac.uk/pdbsum/1m5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5w ProSAT]</span></td></tr>
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Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate., Yeh JI, Du S, Pohl E, Cane DE, Biochemistry. 2002 Oct 1;41(39):11649-57. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12269807 12269807]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PDXJ_ECOLI PDXJ_ECOLI] Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate.<ref>PMID:10225425</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/m5/1m5w_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1m5w ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Cane, D.E.]]
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[[Category: Cane DE]]
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[[Category: Du, S.]]
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[[Category: Du S]]
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[[Category: Pohl, E.]]
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[[Category: Pohl E]]
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[[Category: Yeh, J.I.]]
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[[Category: Yeh JI]]
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[[Category: DXP]]
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[[Category: PO4]]
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[[Category: multi-binding states]]
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[[Category: protein-substrate complex]]
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[[Category: tim barrel]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:10:12 2007''
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Current revision

1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate

PDB ID 1m5w

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