|
|
| Line 3: |
Line 3: |
| | <StructureSection load='7apl' size='340' side='right'caption='[[7apl]], [[Resolution|resolution]] 1.99Å' scene=''> | | <StructureSection load='7apl' size='340' side='right'caption='[[7apl]], [[Resolution|resolution]] 1.99Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7apl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymmo Zymmo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7APL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7APL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7apl]] 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=7APL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7APL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.99Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tgt, ZMO0363 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264203 ZYMMO])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/tRNA-guanine(34)_transglycosylase tRNA-guanine(34) transglycosylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </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=7apl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apl OCA], [https://pdbe.org/7apl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7apl RCSB], [https://www.ebi.ac.uk/pdbsum/7apl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7apl 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=7apl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apl OCA], [https://pdbe.org/7apl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7apl RCSB], [https://www.ebi.ac.uk/pdbsum/7apl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7apl ProSAT]</span></td></tr> |
| | </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]
| + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 23: |
Line 21: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[TRNA-guanine transglycosylase|TRNA-guanine transglycosylase]] | + | *[[TRNA-guanine transglycosylase 3D structures|TRNA-guanine transglycosylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| Line 29: |
Line 27: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Zymmo]] | + | [[Category: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821]] |
| - | [[Category: Heine, A]] | + | [[Category: Heine A]] |
| - | [[Category: Klebe, G]] | + | [[Category: Klebe G]] |
| - | [[Category: Nguyen, D]] | + | [[Category: Nguyen D]] |
| - | [[Category: Enzyme]]
| + | |
| - | [[Category: Spin label]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
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]
Publication Abstract from PubMed
Mechanistic insights into protein-ligand interactions can yield chemical tools for modulating protein function and enable their use for therapeutic purposes. For the homodimeric enzyme tRNA-guanine transglycosylase (TGT), a putative virulence target of shigellosis, ligand binding has been shown by crystallography to transform the functional dimer geometry into an incompetent twisted one. However, crystallographic observation of both end states does neither verify the ligand-induced transformation of one dimer into the other in solution nor does it shed light on the underlying transformation mechanism. We addressed these questions in an approach that combines site-directed spin labeling (SDSL) with distance measurements based on pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy. We observed an equilibrium between the functional and twisted dimer that depends on the type of ligand, with a pyranose-substituted ligand being the most potent one in shifting the equilibrium toward the twisted dimer. Our experiments suggest a dissociation-association mechanism for the formation of the twisted dimer upon ligand binding.
Unraveling a Ligand-Induced Twist of a Homodimeric Enzyme by Pulsed Electron-Electron Double Resonance.,Nguyen D, Abdullin D, Heubach CA, Pfaffeneder T, Nguyen A, Heine A, Reuter K, Diederich F, Schiemann O, Klebe G Angew Chem Int Ed Engl. 2021 Aug 12. doi: 10.1002/anie.202108179. PMID:34387025[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Nguyen D, Abdullin D, Heubach CA, Pfaffeneder T, Nguyen A, Heine A, Reuter K, Diederich F, Schiemann O, Klebe G. Unraveling a Ligand-Induced Twist of a Homodimeric Enzyme by Pulsed Electron-Electron Double Resonance. Angew Chem Int Ed Engl. 2021 Aug 12. doi: 10.1002/anie.202108179. PMID:34387025 doi:http://dx.doi.org/10.1002/anie.202108179
|
