1dy3: Difference between revisions

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[[Image:1dy3.gif|left|200px]]<br />
<applet load="1dy3" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1dy3, resolution 2.0&Aring;" />
'''TERNARY COMPLEX OF 7,8-DIHYDRO-6-HYDROXYMETHYLPTERINPYROPHOSPHOKINASE FROM ESCHERICHIA COLI WITH ATP AND A SUBSTRATE ANALOGUE.'''<br />


==Overview==
==Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue.==
The X-ray crystal structure of, 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase (PPPK) in a ternary, complex with ATP and a pterin analogue has been solved to 2.0 A, resolution, giving, for the first time, detailed information of the, PPPK/ATP intermolecular interactions and the accompanying conformational, change. The first 100 residues of the 158 residue peptide contain a, betaalpha betabeta alphabeta motif present in several other proteins, including nucleoside diphosphate kinase. Comparative sequence examination, of a wide range of prokaryotic and lower eukaryotic species confirms the, conservation of the PPPK active site, indicating the value of this de novo, folate biosynthesis pathway enzyme as a potential target for the, development of novel broad-spectrum anti-infective agents.
<StructureSection load='1dy3' size='340' side='right'caption='[[1dy3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1dy3]] is a 1 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=1DY3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DY3 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=87Y:7,8-DIHYDRO-6-HYDROXYMETHYL-7-METHYL-7-[2-PHENYLETHYL]-PTERIN'>87Y</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1dy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dy3 OCA], [https://pdbe.org/1dy3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dy3 RCSB], [https://www.ebi.ac.uk/pdbsum/1dy3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dy3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HPPK_ECOLI HPPK_ECOLI]
== 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/dy/1dy3_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=1dy3 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The X-ray crystal structure of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase (PPPK) in a ternary complex with ATP and a pterin analogue has been solved to 2.0 A resolution, giving, for the first time, detailed information of the PPPK/ATP intermolecular interactions and the accompanying conformational change. The first 100 residues of the 158 residue peptide contain a betaalpha betabeta alphabeta motif present in several other proteins including nucleoside diphosphate kinase. Comparative sequence examination of a wide range of prokaryotic and lower eukaryotic species confirms the conservation of the PPPK active site, indicating the value of this de novo folate biosynthesis pathway enzyme as a potential target for the development of novel broad-spectrum anti-infective agents.


==About this Structure==
2.0 A X-ray structure of the ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue.,Stammers DK, Achari A, Somers DO, Bryant PK, Rosemond J, Scott DL, Champness JN FEBS Lett. 1999 Jul 30;456(1):49-53. PMID:10452528<ref>PMID:10452528</ref>
1DY3 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 MG, ATP and 87Y as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/Transferase Transferase]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3]]. Structure known Active Sites: AC1, AC2, AC3 and AC4. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DY3 OCA]].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2.0 A X-ray structure of the ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue., Stammers DK, Achari A, Somers DO, Bryant PK, Rosemond J, Scott DL, Champness JN, FEBS Lett. 1999 Jul 30;456(1):49-53. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10452528 10452528]
</div>
<div class="pdbe-citations 1dy3" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[HPPK 3D structures|HPPK 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Achari, A.]]
[[Category: Achari A]]
[[Category: Bryant, P.K.]]
[[Category: Bryant PK]]
[[Category: Champness, J.N.]]
[[Category: Champness JN]]
[[Category: Rosemond, J.]]
[[Category: Rosemond J]]
[[Category: Scott, D.L.]]
[[Category: Scott DL]]
[[Category: Somers, D.O.]]
[[Category: Somers DO]]
[[Category: Stammers, D.K.]]
[[Category: Stammers DK]]
[[Category: 87Y]]
[[Category: ATP]]
[[Category: MG]]
[[Category: de novo folate biosynthesis]]
[[Category: pyrophosphorylase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 08:34:32 2007''

Latest revision as of 08:44, 9 May 2024

Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue.

1dy3, resolution 2.00Å

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