2z53: Difference between revisions

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

Structural highlights

2z53 is a 1 chain structure with sequence from Phytolacca dioica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.29Å
Ligands:	EDO
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 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.

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

↑ Di Maro A, Valbonesi P, Bolognesi A, Stirpe F, De Luca P, Siniscalco Gigliano G, Gaudio L, Delli Bovi P, Ferranti P, Malorni A, Parente A. Isolation and characterization of four type-1 ribosome-inactivating proteins, with polynucleotide:adenosine glycosidase activity, from leaves of Phytolacca dioica L. Planta. 1999 Mar;208(1):125-31. PMID:10213004
↑ Aceto S, Di Maro A, Conforto B, Siniscalco GG, Parente A, Delli Bovi P, Gaudio L. Nicking activity on pBR322 DNA of ribosome inactivating proteins from Phytolacca dioica L. leaves. Biol Chem. 2005 Apr;386(4):307-17. PMID:15899692 doi:10.1515/BC.2005.037
↑ Ruggiero A, Chambery A, Maro AD, Parente A, Berisio R. Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves. Proteins. 2007 Oct 26;71(1):8-15. PMID:17963235 doi:https://dx.doi.org/10.1002/prot.21712

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Di Maro A, Valbonesi P, Bolognesi A, Stirpe F, De Luca P, Siniscalco Gigliano G, Gaudio L, Delli Bovi P, Ferranti P, Malorni A, Parente A. Isolation and characterization of four type-1 ribosome-inactivating proteins, with polynucleotide:adenosine glycosidase activity, from leaves of Phytolacca dioica L. Planta. 1999 Mar;208(1):125-31. PMID:10213004

[2] Aceto S, Di Maro A, Conforto B, Siniscalco GG, Parente A, Delli Bovi P, Gaudio L. Nicking activity on pBR322 DNA of ribosome inactivating proteins from Phytolacca dioica L. leaves. Biol Chem. 2005 Apr;386(4):307-17. PMID:15899692 doi:10.1515/BC.2005.037

[3] Ruggiero A, Chambery A, Maro AD, Parente A, Berisio R. Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves. Proteins. 2007 Oct 26;71(1):8-15. PMID:17963235 doi:https://dx.doi.org/10.1002/prot.21712

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Crystal structure of the S211A mutant of the ribosome inactivating protein PDL4 from P. dioica leaves==
-<StructureSection load='2z53' size='340' side='right' caption='[[2z53]], [[Resolution|resolution]] 1.29&Aring;' scene=''>
+<StructureSection load='2z53' size='340' side='right'caption='[[2z53]], [[Resolution|resolution]] 1.29&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2z53]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bella_sombra_tree Bella sombra tree]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z53 FirstGlance]. <br>
+<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>
-</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='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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2z4u|2z4u]], [[2qes|2qes]], [[2qet|2qet]]</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='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'>[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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z53 OCA], [http://pdbe.org/2z53 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z53 RCSB], [http://www.ebi.ac.uk/pdbsum/2z53 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
+     <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/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 2z53" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bella sombra tree]]
+[[Category: Large Structures]]
-[[Category: RRNA N-glycosylase]]
+[[Category: Phytolacca dioica]]
-[[Category: Berisio, R]]
+[[Category: Berisio R]]
-[[Category: Ruggiero, A]]
+[[Category: Ruggiero A]]
-[[Category: Crystal]]
-[[Category: Hydrolase]]
-[[Category: Ribosome inactivating protein]]

2z53: Difference between revisions

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools