3ud5: Difference between revisions

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<StructureSection load='3ud5' size='340' side='right'caption='[[3ud5]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3ud5' size='340' side='right'caption='[[3ud5]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ud5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UD5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ud5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UD5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=J1A:5-S-[1-(2-{[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]AMINO}ETHYL)PIPERIDIN-4-YL]-5-THIOADENOSINE'>J1A</scene></td></tr>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ex8|1ex8]], [[3ude|3ude]], [[3udv|3udv]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=J1A:5-S-[1-(2-{[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]AMINO}ETHYL)PIPERIDIN-4-YL]-5-THIOADENOSINE'>J1A</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0142, foIK, folK, JW0138 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></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=3ud5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ud5 OCA], [https://pdbe.org/3ud5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ud5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ud5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ud5 ProSAT]</span></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=3ud5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ud5 OCA], [https://pdbe.org/3ud5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ud5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ud5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ud5 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/HPPK_ECOLI HPPK_ECOLI]
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), a key enzyme in the folate biosynthetic pathway, catalyzes the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin. The enzyme is essential for microorganisms, is absent from humans, and is not the target for any existing antibiotics. Therefore, HPPK is an attractive target for developing novel antimicrobial agents. Previously, we characterized the reaction trajectory of HPPK-catalyzed pyrophosphoryl transfer and synthesized a series of bisubstrate analog inhibitors of the enzyme by linking 6-hydroxymethylpterin to adenosine through 2, 3, or 4 phosphate groups. Here, we report a new generation of bisubstrate analog inhibitors. To improve protein binding and linker properties of such inhibitors, we have replaced the pterin moiety with 7,7-dimethyl-7,8-dihydropterin and the phosphate bridge with a piperidine linked thioether. We have synthesized the new inhibitors, measured their K(d) and IC(50) values, determined their crystal structures in complex with HPPK, and established their structure-activity relationship. 6-Carboxylic acid ethyl ester-7,7-dimethyl-7,8-dihydropterin, a novel intermediate that we developed recently for easy derivatization at position 6 of 7,7-dimethyl-7,8-dihydropterin, offers a much high yield for the synthesis of bisubstrate analogs than that of previously established procedure.
 
Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New design with improved properties.,Shi G, Shaw G, Liang YH, Subburaman P, Li Y, Wu Y, Yan H, Ji X Bioorg Med Chem. 2012 Jan 1;20(1):47-57. Epub 2011 Nov 23. PMID:22169600<ref>PMID:22169600</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ud5" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[HPPK 3D structures|HPPK 3D structures]]
*[[HPPK 3D structures|HPPK 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
[[Category: Escherichia coli K-12]]
[[Category: Ecoli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ji, X]]
[[Category: Ji X]]
[[Category: Shaw, G]]
[[Category: Shaw G]]
[[Category: Shi, G]]
[[Category: Shi G]]
[[Category: Alpha beta]]
[[Category: Atp binding]]
[[Category: Kinase]]
[[Category: Pyrophosphoryl transfer]]
[[Category: Transferase-transferase inhibitor complex]]

Latest revision as of 16:55, 14 March 2024

Crystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1ACrystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1A

Structural highlights

3ud5 is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HPPK_ECOLI

See Also

3ud5, resolution 2.00Å

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