View source for 4pum


==tRNA-Guanine Transglycosylase (TGT) Mutant D156N in Complex with 6-Amino-2-(methylamino)-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one==
<StructureSection load='4pum' size='340' side='right'caption='[[4pum]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4pum]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis_subsp._mobilis_ZM4_=_ATCC_31821 Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PUM 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]] 1.93&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2WU:6-AMINO-2-(METHYLAMINO)-3,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>2WU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4pum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pum OCA], [https://pdbe.org/4pum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pum RCSB], [https://www.ebi.ac.uk/pdbsum/4pum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pum ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TGT_ZYMMO TGT_ZYMMO] Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).[HAMAP-Rule:MF_00168]
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== Publication Abstract from PubMed ==
Drug molecules should remain uncharged while traveling through the body and crossing membranes and should only adopt charged state upon protein binding, particularly if charge-assisted interactions can be established in deeply buried binding pockets. Such strategy requires careful pKa design and methods to elucidate whether and where protonation-state changes occur. We investigated the protonation inventory in a series of lin-benzoguanines binding to tRNA-guanine transglycosylase, showing pronounced buffer dependency during ITC measurements. Chemical modifications of the parent scaffold along with ITC measurements, pKa calculations, and site-directed mutagenesis allow elucidating the protonation site. The parent scaffold exhibits two guanidine-type portions, both likely candidates for proton uptake. Even mutually compensating effects resulting from proton release of the protein and simultaneous uptake by the ligand can be excluded. Two adjacent aspartates induce a strong pKa shift at the ligand site, resulting in protonation-state transition. Furthermore, an array of two parallel H-bonds avoiding secondary repulsive effects contributes to the high-affinity binding of the lin-benzoguanines.

Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKa Calculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme.,Neeb M, Czodrowski P, Heine A, Barandun LJ, Hohn C, Diederich F, Klebe G J Med Chem. 2014 Jul 10;57(13):5554-65. doi: 10.1021/jm500401x. Epub 2014 Jun 23. PMID:24955548<ref>PMID:24955548</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 4pum" style="background-color:#fffaf0;"></div>

==See Also==
*[[TRNA-guanine transglycosylase 3D structures|TRNA-guanine transglycosylase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821]]
[[Category: Heine A]]
[[Category: Klebe G]]
[[Category: Neeb M]]