2z4u: Difference between revisions
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==Crystal structure of wild type PD-L4 from Phytolacca dioica leaves== | ==Crystal structure of wild type PD-L4 from Phytolacca dioica leaves== | ||
<StructureSection load='2z4u' size='340' side='right' caption='[[2z4u]], [[Resolution|resolution]] 1.10Å' scene=''> | <StructureSection load='2z4u' size='340' side='right'caption='[[2z4u]], [[Resolution|resolution]] 1.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2z4u]] is a 1 chain structure with 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=2Z4U OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[2z4u]] is a 1 chain structure with 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=2Z4U OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2Z4U FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> | </td></tr><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qcg|1qcg]], [[2z53|2z53]], [[2qes|2qes]], [[2qet|2qet]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qcg|1qcg]], [[2z53|2z53]], [[2qes|2qes]], [[2qet|2qet]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2z4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z4u OCA], [http://pdbe.org/2z4u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z4u RCSB], [http://www.ebi.ac.uk/pdbsum/2z4u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z4u ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Phytolacca dioica]] | [[Category: Phytolacca dioica]] | ||
[[Category: RRNA N-glycosylase]] | [[Category: RRNA N-glycosylase]] | ||
Revision as of 14:57, 29 July 2020
Crystal structure of wild type PD-L4 from Phytolacca dioica leavesCrystal structure of wild type PD-L4 from Phytolacca dioica leaves
Structural highlights
Function[RIPL2_PHYDI] Inhibits protein synthesis. Does not cleave supercoiled pBR322 dsDNA.[1] [2] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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