1n2v

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1n2v" size="450" color="white" frame="true" align="right" spinBox="true" caption="1n2v, resolution 2.1&Aring;" /> '''Crystal Structure of ...)
Current revision (07:51, 14 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1n2v.jpg|left|200px]]<br /><applet load="1n2v" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1n2v, resolution 2.1&Aring;" />
 
-
'''Crystal Structure of TGT in complex with 2-Butyl-5,6-dihydro-1H-imidazo[4,5-d]pyridazine-4,7-dione'''<br />
 
-
==Overview==
+
==Crystal Structure of TGT in complex with 2-Butyl-5,6-dihydro-1H-imidazo[4,5-d]pyridazine-4,7-dione==
-
Eubacterial tRNA-guanine transglycosylase (TGT) is involved in the, hypermodification of cognate tRNAs, leading to the exchange of G34 by, preQ1 at the wobble position in the anticodon loop. Mutation of the tgt, gene in Shigella flexneri results in a significant loss of pathogenicity, of the bacterium due to inefficient translation of a virulence protein, mRNA. Herein, we describe the discovery of a ligand with an unexpected, binding mode. On the basis of this binding mode, three slightly deviating, pharmacophore hypotheses have been derived. Virtual screening based on, this composite pharmacophore model retrieved a set of potential TGT, inhibitors belonging to several compound classes. All nine tested, inhibitors being representatives of these classes showed activity in the, micromolar range, two of them even in the submicromolar range.
+
<StructureSection load='1n2v' size='340' side='right'caption='[[1n2v]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1n2v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N2V 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]] 2.1&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BDI:2-BUTYL-5,6-DIHYDRO-1H-IMIDAZO[4,5-D]PYRIDAZINE-4,7-DIONE'>BDI</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=1n2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2v OCA], [https://pdbe.org/1n2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n2v RCSB], [https://www.ebi.ac.uk/pdbsum/1n2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n2v 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]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n2/1n2v_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1n2v ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1N2V is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis] with ZN and BDI as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Queuine_tRNA-ribosyltransferase Queuine tRNA-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N2V OCA].
+
*[[TRNA-guanine transglycosylase 3D structures|TRNA-guanine transglycosylase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis., Brenk R, Naerum L, Gradler U, Gerber HD, Garcia GA, Reuter K, Stubbs MT, Klebe G, J Med Chem. 2003 Mar 27;46(7):1133-43. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12646024 12646024]
+
[[Category: Large Structures]]
-
[[Category: Queuine tRNA-ribosyltransferase]]
+
-
[[Category: Single protein]]
+
[[Category: Zymomonas mobilis]]
[[Category: Zymomonas mobilis]]
-
[[Category: Brenk, R.]]
+
[[Category: Brenk R]]
-
[[Category: Garcia, G.A.]]
+
[[Category: Garcia GA]]
-
[[Category: Gerber, H.D.]]
+
[[Category: Gerber H-D]]
-
[[Category: Graedler, U.]]
+
[[Category: Graedler U]]
-
[[Category: Klebe, G.]]
+
[[Category: Klebe G]]
-
[[Category: Naerum, L.]]
+
[[Category: Naerum L]]
-
[[Category: Reuter, K.]]
+
[[Category: Reuter K]]
-
[[Category: Stubbs, M.T.]]
+
[[Category: Stubbs MT]]
-
[[Category: BDI]]
+
-
[[Category: ZN]]
+
-
[[Category: protein-ligand complex]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:54:09 2007''
+

Current revision

Crystal Structure of TGT in complex with 2-Butyl-5,6-dihydro-1H-imidazo[4,5-d]pyridazine-4,7-dione

PDB ID 1n2v

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1n2v"
Personal tools