5jxq
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==TRNA-GUANINE TRANSGLYCOSYLASE (TGT) IN COMPLEX WITH 6-AMINO-2-{[4-(2-HYDROXYETHYL)PHENETHYL]AMINO}-1,7-DIHYDRO-8H-IMIDAZO[4,5-g]QUINAZOLIN-8-ONE== | ==TRNA-GUANINE TRANSGLYCOSYLASE (TGT) IN COMPLEX WITH 6-AMINO-2-{[4-(2-HYDROXYETHYL)PHENETHYL]AMINO}-1,7-DIHYDRO-8H-IMIDAZO[4,5-g]QUINAZOLIN-8-ONE== | ||
| - | <StructureSection load='5jxq' size='340' side='right' caption='[[5jxq]], [[Resolution|resolution]] 1.20Å' scene=''> | + | <StructureSection load='5jxq' size='340' side='right'caption='[[5jxq]], [[Resolution|resolution]] 1.20Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5jxq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXQ OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[5jxq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis_subsp._mobilis Zymomonas mobilis subsp. mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JXQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OK:6-AMINO-2-({2-[4-(2-HYDROXYETHYL)PHENYL]ETHYL}AMINO)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>6OK</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6OK:6-AMINO-2-({2-[4-(2-HYDROXYETHYL)PHENYL]ETHYL}AMINO)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>6OK</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=5jxq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxq OCA], [https://pdbe.org/5jxq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jxq RCSB], [https://www.ebi.ac.uk/pdbsum/5jxq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxq ProSAT]</span></td></tr> | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
== Function == | == 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] |
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Small-molecule ligands binding with partial disorder or enhanced residual mobility are usually assumed as unfavorable with respect to their binding properties. Considering thermodynamics, disorder or residual mobility is entropically favorable and contributes to the Gibbs energy of binding. In the present study, we analyzed a series of congeneric ligands inhibiting the tRNA-modifying enzyme TGT. Attached to the parent lin-benzoguanine scaffold, substituents in position 2 accommodate in a flat solvent-exposed pocket and exhibit varying degree of residual mobility. This is indicated in the crystal structures by enhanced B-factors, reduced occupancies, or distributions over split conformers. MD simulations of the complexes suggest an even larger scatter over several conformational families. Introduction of a terminal acidic group fixes the substituent by a salt-bridge to an Arg residue. Overall, all substituted derivatives show the same affinity underpinning that neither order nor disorder is a determinant factor for binding affinity. The additional salt bridge remains strongly solvent-exposed and thus does not contribute to affinity. MD suggests temporary fluctuation of this contact. | ||
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| + | Occupying a flat subpocket in a tRNA-modifying enzyme with ordered or disordered side chains: Favorable or unfavorable for binding?,Neeb M, Hohn C, Ehrmann FR, Hartsch A, Heine A, Diederich F, Klebe G Bioorg Med Chem. 2016 Jul 26. pii: S0968-0896(16)30570-3. doi:, 10.1016/j.bmc.2016.07.053. PMID:27501913<ref>PMID:27501913</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5jxq" style="background-color:#fffaf0;"></div> | ||
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| + | ==See Also== | ||
| + | *[[TRNA-guanine transglycosylase 3D structures|TRNA-guanine transglycosylase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Zymomonas mobilis subsp. mobilis]] |
| - | [[Category: | + | [[Category: Heine A]] |
| - | [[Category: | + | [[Category: Klebe G]] |
| - | [[Category: | + | [[Category: Neeb M]] |
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Current revision
TRNA-GUANINE TRANSGLYCOSYLASE (TGT) IN COMPLEX WITH 6-AMINO-2-{[4-(2-HYDROXYETHYL)PHENETHYL]AMINO}-1,7-DIHYDRO-8H-IMIDAZO[4,5-g]QUINAZOLIN-8-ONE
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