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1ixn

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[[Image:1ixn.gif|left|200px]]
 
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{{Structure
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==Enzyme-Substrate Complex of Pyridoxine 5'-Phosphate Synthase==
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|PDB= 1ixn |SIZE=350|CAPTION= <scene name='initialview01'>1ixn</scene>, resolution 2.3&Aring;
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<StructureSection load='1ixn' size='340' side='right'caption='[[1ixn]], [[Resolution|resolution]] 2.30&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=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>
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<table><tr><td colspan='2'>[[1ixn]] is a 4 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=1IXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IXN 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]] 2.3&#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=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</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=1ixn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixn OCA], [https://pdbe.org/1ixn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ixn RCSB], [https://www.ebi.ac.uk/pdbsum/1ixn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ixn ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1ho1|1HO1]], [[1ho4|1HO4]], [[1ixo|1IXO]], [[1ixq|1IXQ]], [[1ixp|1IXP]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ixn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixn OCA], [http://www.ebi.ac.uk/pdbsum/1ixn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ixn 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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'''Enzyme-Substrate Complex of Pyridoxine 5'-Phosphate Synthase'''
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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/ix/1ixn_consurf.spt"</scriptWhenChecked>
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Pyridoxine 5'-phosphate (PNP) synthase is the last enzyme in the de novo biosynthesis of vitamin B(6) catalyzing the complicated ring-closure reaction between 1-deoxy-D-xylulose-5-phosphate and 1-amino-acetone-3-phosphate. Here we present the crystal structures of four PNP synthase complexes with substrates and substrate analogs. While the overall fold of the enzyme is conserved in all complexes, characteristic readjustments were observed in the active site. The complementary structural information allowed us to postulate a detailed reaction mechanism. The observed binding mode of substrates indicates how the first reaction intermediate, the Schiff-base conjugate, is formed. The most important mechanistic features are the presence of two phosphate-binding sites with distinct affinities and the existence of a water relay system for the release of reaction water molecules. Furthermore, the complexes provide the basis to rationalize the open-closed transition of a flexible loop located on the C-terminal side of the TIM-barrel. Binding of both substrate molecules to the active site seems to be a prerequisite to trigger this transition. Highly conserved mechanistically important residues in the PNP synthase family imply a similar active site organization and reaction mechanism for all family members. Due to the exclusive presence of PNP synthase in a subset of eubacteria, including several well-known pathogens, and due to its outstanding physiological importance for these organisms, the enzyme appears to be a promising novel target for antibacterial drug design.
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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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1IXN 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=1IXN 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=1ixn ConSurf].
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<div style="clear:both"></div>
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==Reference==
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== References ==
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Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis., Garrido-Franco M, Laber B, Huber R, Clausen T, J Mol Biol. 2002 Aug 23;321(4):601-12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12206776 12206776]
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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: Clausen, T.]]
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[[Category: Clausen T]]
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[[Category: Garrido-Franco, M.]]
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[[Category: Garrido-Franco M]]
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[[Category: Huber, R.]]
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[[Category: Huber R]]
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[[Category: Laber, B.]]
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[[Category: Laber B]]
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[[Category: enzyme-substrate complex]]
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[[Category: open-closed transition]]
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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 21:26:05 2008''
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Current revision

Enzyme-Substrate Complex of Pyridoxine 5'-Phosphate Synthase

PDB ID 1ixn

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