2qes: Difference between revisions

Revision as of 07:00, 3 June 2020

Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine

Structural highlights

2qes 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.
Ligands:	ADE
Related:	2z4u, 2z53, 2qet
Activity:	rRNA N-glycosylase, with EC number 3.2.2.22
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

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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

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[2]

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@@ Line 1: / Line 1: @@
 ==Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine==
-<StructureSection load='2qes' size='340' side='right' caption='[[2qes]], [[Resolution|resolution]] 1.24&Aring;' scene=''>
+<StructureSection load='2qes' size='340' side='right'caption='[[2qes]], [[Resolution|resolution]] 1.24&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qes]] 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=2QES OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QES FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qes]] 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=2QES OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2QES FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2z4u|2z4u]], [[2z53|2z53]], [[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='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=2qes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qes OCA], [http://pdbe.org/2qes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qes RCSB], [http://www.ebi.ac.uk/pdbsum/2qes PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qes ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2qes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qes OCA], [http://pdbe.org/2qes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qes RCSB], [http://www.ebi.ac.uk/pdbsum/2qes PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qes ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 34: / Line 34: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Phytolacca dioica]]
 [[Category: RRNA N-glycosylase]]

2qes: Difference between revisions

Revision as of 07:00, 3 June 2020

Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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