2b7u: Difference between revisions

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<StructureSection load='2b7u' size='340' side='right'caption='[[2b7u]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='2b7u' size='340' side='right'caption='[[2b7u]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2b7u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Charybdis_maritima Charybdis maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B7U FirstGlance]. <br>
<table><tr><td colspan='2'>[[2b7u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Squilla_maritima Squilla maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B7U FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 1.6&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1abr|1abr]], [[1nio|1nio]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [https://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=2b7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b7u OCA], [https://pdbe.org/2b7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b7u RCSB], [https://www.ebi.ac.uk/pdbsum/2b7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b7u ProSAT]</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=2b7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b7u OCA], [https://pdbe.org/2b7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b7u RCSB], [https://www.ebi.ac.uk/pdbsum/2b7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b7u ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RIP_DRIMA RIP_DRIMA]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2b7u ConSurf].
</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=2b7u ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A novel, type 1 ribosome-inactivating protein designated charybdin was isolated from bulbs of Charybdis maritima agg. The protein, consisting of a single polypeptide chain with a molecular mass of 29 kDa, inhibited translation in rabbit reticulocytes with an IC50 of 27.2 nm. Plant genomic DNA extracted from the bulb was amplified by PCR between primers based on the N-terminal and C-terminal sequence of the protein from dissolved crystals. The complete mature protein sequence was derived by partial DNA sequencing and terminal protein sequencing, and was confirmed by high-resolution crystal structure analysis. The protein contains Val at position 79 instead of the conserved Tyr residue of the ribosome-inactivating proteins known to date. To our knowledge, this is the first observation of a natural substitution of a catalytic residue at the active site of a natural ribosome-inactivating protein. This substitution in the active site may be responsible for the relatively low in vitro translation inhibitory effect compared with other ribosome-inactivating proteins. Single crystals were grown in the cold room from PEG6000 solutions. Diffraction data collected to 1.6 A resolution were used to determine the protein structure by the molecular replacement method. The fold of the protein comprises two structural domains: an alpha + beta N-terminal domain (residues 4-190) and a mainly alpha-helical C-terminal domain (residues 191-257). The active site is located in the interface between the two domains and comprises residues Val79, Tyr117, Glu167 and Arg170.


Isolation, characterization, sequencing and crystal structure of charybdin, a type 1 ribosome-inactivating protein from Charybdis maritima agg.,Touloupakis E, Gessmann R, Kavelaki K, Christofakis E, Petratos K, Ghanotakis DF FEBS J. 2006 Jun;273(12):2684-92. PMID:16817896<ref>PMID:16817896</ref>
==See Also==
 
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2b7u" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Charybdis maritima]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: RRNA N-glycosylase]]
[[Category: Squilla maritima]]
[[Category: Gessmann, R]]
[[Category: Gessmann R]]
[[Category: Petratos, K]]
[[Category: Petratos K]]
[[Category: Hydrolase]]
[[Category: Ribosome inactivating protein]]

Revision as of 09:24, 3 April 2024

Ribosome inactivating protein type 1 from Charybdis maritima AGGRibosome inactivating protein type 1 from Charybdis maritima AGG

Structural highlights

2b7u is a 1 chain structure with sequence from Squilla maritima. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIP_DRIMA

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2b7u, resolution 1.60Å

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