2z53: Difference between revisions

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[[Image:2z53.jpg|left|200px]]


{{Structure
==Crystal structure of the S211A mutant of the ribosome inactivating protein PDL4 from P. dioica leaves==
|PDB= 2z53 |SIZE=350|CAPTION= <scene name='initialview01'>2z53</scene>, resolution 1.29&Aring;
<StructureSection load='2z53' size='340' side='right'caption='[[2z53]], [[Resolution|resolution]] 1.29&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Edo+Binding+Site+For+Residue+A+501'>AC1</scene> and <scene name='pdbsite=AC2:Edo+Binding+Site+For+Residue+A+502'>AC2</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>
<table><tr><td colspan='2'>[[2z53]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phytolacca_dioica Phytolacca dioica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z53 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z53 FirstGlance]. <br>
|ACTIVITY= [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]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.29&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=2z53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z53 OCA], [https://pdbe.org/2z53 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z53 RCSB], [https://www.ebi.ac.uk/pdbsum/2z53 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z53 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RIPL2_PHYDI RIPL2_PHYDI] Inhibits protein synthesis. Does not cleave supercoiled pBR322 dsDNA.<ref>PMID:10213004</ref> <ref>PMID:15899692</ref>
== 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/z5/2z53_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2z53 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The ribosome inactivating protein PD-L4 from Phytolacca dioica is a N-beta-glycosidase, probably involved in plant defence. The crystal structures of wild type PD-L4 and of the S211A PD-L4 mutant with significantly decreased catalytic activity were determined at atomic resolution. To determine the structural determinants for the reduced activity of S211A PD-L4, both forms have also been co-crystallized with adenine, the major product of PD-L4 catalytic reaction. In the structure of the S211A mutant, the cavity formed by the lack of the Ser hydroxyl group is filled by a water molecule; the insertion of this non-isosteric group leads to small albeit concerted changes in the tightly packed active site of the enzyme. These changes have been correlated to the different activity of the mutant enzyme. This work highlights the importance of atomic resolution studies for the deep understanding of enzymatic properties. Proteins 2008. (c) 2007 Wiley-Liss, Inc.


'''Crystal structure of the S211A mutant of the ribosome inactivating protein PDL4 from P. dioica leaves'''
Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves.,Ruggiero A, Chambery A, Maro AD, Parente A, Berisio R Proteins. 2007 Oct 26;71(1):8-15. PMID:17963235<ref>PMID:17963235</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2z53" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
The ribosome inactivating protein PD-L4 from Phytolacca dioica is a N-beta-glycosidase, probably involved in plant defence. The crystal structures of wild type PD-L4 and of the S211A PD-L4 mutant with significantly decreased catalytic activity were determined at atomic resolution. To determine the structural determinants for the reduced activity of S211A PD-L4, both forms have also been co-crystallized with adenine, the major product of PD-L4 catalytic reaction. In the structure of the S211A mutant, the cavity formed by the lack of the Ser hydroxyl group is filled by a water molecule; the insertion of this non-isosteric group leads to small albeit concerted changes in the tightly packed active site of the enzyme. These changes have been correlated to the different activity of the mutant enzyme. This work highlights the importance of atomic resolution studies for the deep understanding of enzymatic properties. Proteins 2008. (c) 2007 Wiley-Liss, Inc.
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
 
== References ==
==About this Structure==
<references/>
2Z53 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Phytolacca_dioica Phytolacca dioica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z53 OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves., Ruggiero A, Chambery A, Maro AD, Parente A, Berisio R, Proteins. 2007 Oct 26;71(1):8-15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17963235 17963235]
[[Category: Phytolacca dioica]]
[[Category: Phytolacca dioica]]
[[Category: Single protein]]
[[Category: Berisio R]]
[[Category: rRNA N-glycosylase]]
[[Category: Ruggiero A]]
[[Category: Berisio, R.]]
[[Category: Ruggiero, A.]]
[[Category: EDO]]
[[Category: crystal]]
[[Category: hydrolase]]
[[Category: ribosome inactivating protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:52:15 2008''

Latest revision as of 09:39, 6 November 2024

Crystal structure of the S211A mutant of the ribosome inactivating protein PDL4 from P. dioica leaves

2z53, resolution 1.29Å

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