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New page: left|200px<br /><applet load="1k9s" size="450" color="white" frame="true" align="right" spinBox="true" caption="1k9s, resolution 2.00Å" /> '''PURINE NUCLEOSIDE PH...
 
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[[Image:1k9s.jpg|left|200px]]<br /><applet load="1k9s" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1k9s, resolution 2.00&Aring;" />
'''PURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORMYCIN A DERIVATIVE AND PHOSPHATE'''<br />


==Overview==
==PURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORMYCIN A DERIVATIVE AND PHOSPHATE==
The crystal structure of the ternary complex of hexameric purine, nucleoside phosphorylase (PNP) from Escherichia coli with formycin A, derivatives and phosphate or sulphate ions is determined at 2.0 A, resolution. The hexamer is found as a trimer of unsymmetric dimers, which, are formed by pairs of monomers with active sites in different, conformations. The conformational difference stems from a flexible helix, (H8: 214-236), which is continuous in one conformer, and segmented in the, other. With the continuous helix, the entry into the active site pocket is, wide open, and the ligands are bound only loosely ("open" or "loose, binding" conformation). By segmentation of the helix (H8: 214-219 and H8':, 223-236, separated by a gamma-turn), the entry into the active site is, partially closed, the pocket is narrowed and the ligands are bound much, more tightly ("closed" or "tight binding" conformation). Furthermore, the, side-chain of Arg217 is carried by the moving helix into the active site., This residue, conserved in all homologous PNPs, plays an important role in, the proposed catalytic mechanism. In this mechanism, substrate binding, takes place in the open, and and the catalytic action occurs in the closed, conformation. Catalytic action involves protonation of the purine base at, position N7 by the side-chain of Asp204, which is initially in the acid, form. The proton transfer is triggered by the Arg217 side-chain which is, moved by the conformation change into hydrogen bond distance to Asp204., The mechanism explains the broad specificity of E. coli PNP, which allows, 6-amino as well as 6-oxo-nucleosides as substrates. The observation of two, kinds of binding sites is fully in line with solution experiments which, independently observe strong and weak binding sites for phosphate as well, as for the nucleoside inhibitor.
<StructureSection load='1k9s' size='340' side='right'caption='[[1k9s]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1k9s]] is a 6 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=1K9S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K9S FirstGlance]. <br>
</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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FM1:2-HYDROXYMETHYL-5-(7-METHYLAMINO-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-TETRAHYDRO-FURAN-3,4-DIOL'>FM1</scene>, <scene name='pdbligand=FM2:2-(7-AMINO-6-METHYL-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL'>FM2</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k9s OCA], [https://pdbe.org/1k9s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k9s RCSB], [https://www.ebi.ac.uk/pdbsum/1k9s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k9s ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DEOD_ECOLI DEOD_ECOLI] Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules.[HAMAP-Rule:MF_01627]
== 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/k9/1k9s_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=1k9s ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1K9S 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, FM2 and FM1 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1K9S OCA].
*[[Purine nucleoside phosphorylase 3D structures|Purine nucleoside phosphorylase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Open and closed conformation of the E. coli purine nucleoside phosphorylase active center and implications for the catalytic mechanism., Koellner G, Bzowska A, Wielgus-Kutrowska B, Luic M, Steiner T, Saenger W, Stepinski J, J Mol Biol. 2002 Jan 18;315(3):351-71. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11786017 11786017]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Purine-nucleoside phosphorylase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Bzowska A]]
[[Category: Bzowska, A.]]
[[Category: Koellner G]]
[[Category: Koellner, G.]]
[[Category: Luic M]]
[[Category: Luic, M.]]
[[Category: Saenger W]]
[[Category: Saenger, W.]]
[[Category: Steiner T]]
[[Category: Steiner, T.]]
[[Category: Stepinski J]]
[[Category: Stepinski, J.]]
[[Category: Wielgus-Kutrowska B]]
[[Category: Wielgus-Kutrowska, B.]]
[[Category: FM1]]
[[Category: FM2]]
[[Category: PO4]]
[[Category: e. coli]]
[[Category: glycosyltransferase]]
[[Category: purine nucleoside phosphorylase]]
[[Category: transferase]]
 
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