1ixn

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(New page: 200px<br /><applet load="1ixn" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ixn, resolution 2.3&Aring;" /> '''Enzyme-Substrate Comp...)
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[[Image:1ixn.gif|left|200px]]<br /><applet load="1ixn" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ixn, resolution 2.3&Aring;" />
 
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'''Enzyme-Substrate Complex of Pyridoxine 5'-Phosphate Synthase'''<br />
 
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==Overview==
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==Enzyme-Substrate Complex of Pyridoxine 5'-Phosphate Synthase==
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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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<StructureSection load='1ixn' size='340' side='right'caption='[[1ixn]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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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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1IXN 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 G3P as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IXN 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]] 2.3&#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=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</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=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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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12206776 12206776]
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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/ix/1ixn_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=1ixn 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: 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: DXP]]
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[[Category: G3P]]
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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://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:45:13 2007''
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Current revision

Enzyme-Substrate Complex of Pyridoxine 5'-Phosphate Synthase

PDB ID 1ixn

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