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New page: left|200px<br /><applet load="1rl0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rl0, resolution 1.40Å" /> '''Crystal structure of... |
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== | ==Crystal structure of a new ribosome-inactivating protein (RIP): dianthin 30== | ||
Ribosome inactivating proteins (RIPs) are plant proteins with enzymatic | <StructureSection load='1rl0' size='340' side='right'caption='[[1rl0]], [[Resolution|resolution]] 1.40Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1rl0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dianthus_caryophyllus Dianthus caryophyllus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RL0 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]] 1.4Å</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=1rl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rl0 OCA], [https://pdbe.org/1rl0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rl0 RCSB], [https://www.ebi.ac.uk/pdbsum/1rl0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rl0 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RIP0_DIACA RIP0_DIACA] Single-chain ribosome-inactivating protein. | |||
== 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/rl/1rl0_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=1rl0 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Ribosome inactivating proteins (RIPs) are plant proteins with enzymatic activity identified as rRNA N-glycosidase (EC 3.2.2.22), which cleaves the N-glycosidic bond of a specific adenine on the ricin/sarcin region of rRNA, thus causing inhibition of protein synthesis. They also depurinate extensively DNA and other polynucleotides. The three-dimensional structure of dianthin 30, a type 1 (single-chain) RIP of Dianthus caryophyllus (leaves), is now described at 1.4 angstroms, a resolution never achieved before for any RIP. The fold typical of RIPs is conserved, despite some differences in the loop regions. The general structure comparison by superimposed alpha-carbon (249 atoms) and the sequence alignment by structure for dianthin 30 and saporin-S6 give a root mean square deviation of 0.625 angstroms. Despite the differences reported for the biological activities of the two RIPs, their structures fit quite well and both show a protein segment containing strands beta7, beta8, and beta9 shorter than other RIPs. However, the surface electrostatic potential in the active site region neatly distinguishes dianthin 30 from saporin-S6. The possible relationship between the charge distribution and the behavior of the proteins toward different substrates is discussed. | |||
The 1.4 anstroms structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins.,Fermani S, Falini G, Ripamonti A, Polito L, Stirpe F, Bolognesi A J Struct Biol. 2005 Feb;149(2):204-12. PMID:15681236<ref>PMID:15681236</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1rl0" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Dianthus caryophyllus]] | [[Category: Dianthus caryophyllus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Bolognesi A]] | |||
[[Category: Bolognesi | [[Category: Falini G]] | ||
[[Category: Falini | [[Category: Fermani S]] | ||
[[Category: Fermani | [[Category: Polito L]] | ||
[[Category: Polito | [[Category: Ripamonti A]] | ||
[[Category: Ripamonti | [[Category: Stirpe F]] | ||
[[Category: Stirpe | |||
Latest revision as of 09:05, 23 August 2023
Crystal structure of a new ribosome-inactivating protein (RIP): dianthin 30Crystal structure of a new ribosome-inactivating protein (RIP): dianthin 30
Structural highlights
FunctionRIP0_DIACA Single-chain ribosome-inactivating protein. 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 PubMedRibosome inactivating proteins (RIPs) are plant proteins with enzymatic activity identified as rRNA N-glycosidase (EC 3.2.2.22), which cleaves the N-glycosidic bond of a specific adenine on the ricin/sarcin region of rRNA, thus causing inhibition of protein synthesis. They also depurinate extensively DNA and other polynucleotides. The three-dimensional structure of dianthin 30, a type 1 (single-chain) RIP of Dianthus caryophyllus (leaves), is now described at 1.4 angstroms, a resolution never achieved before for any RIP. The fold typical of RIPs is conserved, despite some differences in the loop regions. The general structure comparison by superimposed alpha-carbon (249 atoms) and the sequence alignment by structure for dianthin 30 and saporin-S6 give a root mean square deviation of 0.625 angstroms. Despite the differences reported for the biological activities of the two RIPs, their structures fit quite well and both show a protein segment containing strands beta7, beta8, and beta9 shorter than other RIPs. However, the surface electrostatic potential in the active site region neatly distinguishes dianthin 30 from saporin-S6. The possible relationship between the charge distribution and the behavior of the proteins toward different substrates is discussed. The 1.4 anstroms structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins.,Fermani S, Falini G, Ripamonti A, Polito L, Stirpe F, Bolognesi A J Struct Biol. 2005 Feb;149(2):204-12. PMID:15681236[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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