1qd2: Difference between revisions

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-[[Image:1qd2.gif|left|200px]]
- {{Structure
+==CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG==
-|PDB= 1qd2 |SIZE=350|CAPTION= <scene name='initialview01'>1qd2</scene>, resolution 1.86&Aring;
+<StructureSection load='1qd2' size='340' side='right'caption='[[1qd2]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ADE:ADENINE'>ADE</scene>
+<table><tr><td colspan='2'>[[1qd2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichosanthes_kirilowii Trichosanthes kirilowii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QD2 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.86&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qd2 OCA], [https://pdbe.org/1qd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qd2 RCSB], [https://www.ebi.ac.uk/pdbsum/1qd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qd2 ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1tcs|1TCS]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qd2 OCA], [http://www.ebi.ac.uk/pdbsum/1qd2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qd2 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/RIPT_TRIKI RIPT_TRIKI] Inactivates eukaryotic 60S ribosomal subunits.
+== 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/qd/1qd2_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=1qd2 ConSurf].
+<div style="clear:both"></div>
-'''CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG'''
+==See Also==
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Four substrate analogs-nicotinamide adenine dinucleotide, adenylyl (3', 5') guanosine, guanylyl (3',5') adenosine, and adenosine 2', 5'-diphosphate-have been used to prepare the complexes with trichosanthin (TCS), a type I ribosome-inactivating protein that possesses the activity of N-glycosidase. The crystal structures of the complexes have been determined and refined at high resolution. The refined structures show that the N-glycosidic bonds of all the four substrate analogues are hydrolyzed and a common structure is shared by the four complexes, in which only adenine, the product of the enzymatic reaction, is bound in the active center. The structure is compared with those of native trichosanthin and a previously reported trichosanthin-NADPH complex in which the N-glycosidic bond is uncleaved. The structural comparison shows that the conformation of Tyr70 obviously differs from those in the latter two structures, i.e., the side chain of Tyr70 is rotated along its Cbeta-Cgamma bond by approximately 70 degrees. The water molecule found to be preassociated with the N-glycosidic bond in the TCS-NADPH complex structure and proposed to be the water candidate responsible for hydrolyzing the N-glycosidic bond disappears in the trichosanthin-product complex structure. Based on the comparison of the three structures representing the different stages of the enzymatic reaction, the catalytic mechanism of RNA N-glycosidase has been further elucidated. Proteins 2000;39:37-46.
+[[Category: Large Structures]]
-==About this Structure==
-QD2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Trichosanthes_kirilowii Trichosanthes kirilowii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QD2 OCA].
-==Reference==
-Crystal structures of the complexes of trichosanthin with four substrate analogs and catalytic mechanism of RNA N-glycosidase., Gu YJ, Xia ZX, Proteins. 2000 Apr 1;39(1):37-46. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10737925 10737925]
-[[Category: Single protein]]
 [[Category: Trichosanthes kirilowii]]
-[[Category: rRNA N-glycosylase]]
+[[Category: Gu YJ]]
-[[Category: Gu, Y J.]]
+[[Category: Xia ZX]]
-[[Category: Xia, Z X.]]
-[[Category: enzyme-product complex obtained from enzyme-substrate analog complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:12:02 2008''