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New page: left|200px<br /><applet load="1ixq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ixq, resolution 2.3Å" /> '''Enzyme-Phosphate2 Com...
 
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'''Enzyme-Phosphate2 Complex of Pyridoxine 5'-Phosphate synthase'''<br />


==Overview==
==Enzyme-Phosphate2 Complex of Pyridoxine 5'-Phosphate synthase==
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.
<StructureSection load='1ixq' size='340' side='right'caption='[[1ixq]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1ixq]] 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=1IXQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IXQ FirstGlance]. <br>
1IXQ 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 PO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IXQ OCA].
</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>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ixq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixq OCA], [https://pdbe.org/1ixq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ixq RCSB], [https://www.ebi.ac.uk/pdbsum/1ixq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ixq ProSAT]</span></td></tr>
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]
</table>
== Function ==
[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>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/1ixq_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1ixq ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Clausen, T.]]
[[Category: Clausen T]]
[[Category: Garrido-Franco, M.]]
[[Category: Garrido-Franco M]]
[[Category: Huber, R.]]
[[Category: Huber R]]
[[Category: Laber, B.]]
[[Category: Laber B]]
[[Category: PO4]]
[[Category: enzyme-ligand complex]]
[[Category: open-closed transition]]
[[Category: tim barrel]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:45:24 2007''

Latest revision as of 09:02, 3 April 2024

Enzyme-Phosphate2 Complex of Pyridoxine 5'-Phosphate synthaseEnzyme-Phosphate2 Complex of Pyridoxine 5'-Phosphate synthase

Structural highlights

1ixq is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Laber B, Maurer W, Scharf S, Stepusin K, Schmidt FS. Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein. FEBS Lett. 1999 Apr 16;449(1):45-8. PMID:10225425

1ixq, resolution 2.30Å

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