1qd2: Difference between revisions

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New page: left|200px<br /><applet load="1qd2" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qd2, resolution 1.86Å" /> '''CRYSTAL STRUCTURE OF...
 
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[[Image:1qd2.gif|left|200px]]<br /><applet load="1qd2" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1qd2, resolution 1.86&Aring;" />
'''CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG'''<br />


==Overview==
==CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG==
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.
<StructureSection load='1qd2' size='340' side='right'caption='[[1qd2]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== 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>


==About this Structure==
==See Also==
1QD2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Trichosanthes_kirilowii Trichosanthes kirilowii] with ADE as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QD2 OCA].
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10737925 10737925]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Trichosanthes kirilowii]]
[[Category: Trichosanthes kirilowii]]
[[Category: rRNA N-glycosylase]]
[[Category: Gu YJ]]
[[Category: Gu, Y.J.]]
[[Category: Xia ZX]]
[[Category: Xia, Z.X.]]
[[Category: ADE]]
[[Category: enzyme-product complex obtained from enzyme-substrate analog complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:35:19 2007''

Latest revision as of 11:15, 14 February 2024

CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APGCRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG

Structural highlights

1qd2 is a 1 chain structure with sequence from Trichosanthes kirilowii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.86Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIPT_TRIKI Inactivates eukaryotic 60S ribosomal subunits.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1qd2, resolution 1.86Å

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