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1m5w

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[[Image:1m5w.gif|left|200px]]
 
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{{Structure
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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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|PDB= 1m5w |SIZE=350|CAPTION= <scene name='initialview01'>1m5w</scene>, resolution 1.96&Aring;
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<StructureSection load='1m5w' size='340' side='right'caption='[[1m5w]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DXP:1-DEOXY-D-XYLULOSE-5-PHOSPHATE'>DXP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>
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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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|ACTIVITY=
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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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|GENE= PDXJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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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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|DOMAIN=
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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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|RELATEDENTRY=[[1ho1|1HO1]], [[1ho4|1HO4]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5w OCA], [http://www.ebi.ac.uk/pdbsum/1m5w PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1m5w RCSB]</span>
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== Function ==
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}}
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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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'''1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate'''
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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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==Overview==
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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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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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<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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==About this Structure==
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</jmolCheckbox>
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1M5W 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=1M5W OCA].
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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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==Reference==
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== References ==
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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://www.ncbi.nlm.nih.gov/pubmed/12269807 12269807]
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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: multi-binding state]]
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[[Category: protein-substrate complex]]
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[[Category: tim barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:11:47 2008''
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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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