3ude: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Crystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1B== | ==Crystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1B== | ||
<StructureSection load='3ude' size='340' side='right' caption='[[3ude]], [[Resolution|resolution]] 1.88Å' scene=''> | <StructureSection load='3ude' size='340' side='right'caption='[[3ude]], [[Resolution|resolution]] 1.88Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3ude]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3ude]] 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=3UDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UDE FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=J1B:5-S-[1-(2-{[(2-AMINO-7,7-DIMETHYL-4-OXO-3,4,7,8-TETRAHYDROPTERIDIN-6-YL)METHYL]AMINO}ETHYL)PIPERIDIN-4-YL]-5-THIOADENOSINE'>J1B</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=J1B:5-S-[1-(2-{[(2-AMINO-7,7-DIMETHYL-4-OXO-3,4,7,8-TETRAHYDROPTERIDIN-6-YL)METHYL]AMINO}ETHYL)PIPERIDIN-4-YL]-5-THIOADENOSINE'>J1B</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ud5|3ud5]], [[3udv|3udv]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ud5|3ud5]], [[3udv|3udv]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0142, foIK, folK, JW0138 ([ | <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'>[ | <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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ude FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ude OCA], [https://pdbe.org/3ude PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ude RCSB], [https://www.ebi.ac.uk/pdbsum/3ude PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ude ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 21: | Line 21: | ||
==See Also== | ==See Also== | ||
*[[ | *[[HPPK 3D structures|HPPK 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 28: | Line 28: | ||
[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]] | [[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]] | ||
[[Category: Ecoli]] | [[Category: Ecoli]] | ||
[[Category: Large Structures]] | |||
[[Category: Ji, X]] | [[Category: Ji, X]] | ||
[[Category: Shaw, G]] | [[Category: Shaw, G]] | ||
Revision as of 09:08, 13 July 2022
Crystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1BCrystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1B
Structural highlights
Publication Abstract from PubMed6-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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||||||