3eip: Difference between revisions
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==CRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO A RIBOSOME-INACTIVATING RNASE== | |||
<StructureSection load='3eip' size='340' side='right'caption='[[3eip]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3eip]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._W3110 Escherichia coli str. K-12 substr. W3110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EIP 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]] 1.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3eip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eip OCA], [https://pdbe.org/3eip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eip RCSB], [https://www.ebi.ac.uk/pdbsum/3eip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eip ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/IMM3_ECOLX IMM3_ECOLX] This protein inhibits the 16S RNA hydrolyzing activity of colicin E3 by binding with high affinity to the C-terminal catalytic domain of E3. This protein is able to protect a cell, which harbors the plasmid ColE3 against colicin E3. | |||
== 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/ei/3eip_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=3eip ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: Colicins are antibiotic-like proteins of Escherichia coli that kill related strains. Colicin E3 acts as an RNase that specifically cleaves 16S rRNA, thereby inactivating the ribosomes in the infected cell. The producing organism is protected against colicin E3 by a specific inhibitor, the immunity protein Im3, which forms a tight 1:1 complex with colicin E3 and renders it inactive. Crystallographic studies on colicin E3 and Im3 have been undertaken to unravel the structural basis for the ribonucleolytic activity and its inhibition. RESULTS: The crystal structure of Im3 has been determined to a resolution of 1.8 A. The structure consists of a four-standard antiparallel beta sheet flanked by three alpha helices on one side of the sheet. Thr7, Phe9, Phe16 and Phe74 form a hydrophobic cluster on the surface of the protein in the vicinity of Cys47. This cluster is part of a putative binding pocket which also includes nine polar residues. CONCLUSIONS: The putative binding pocket of Im3 is the probable site of interaction with colicin E3. The six acidic residues in the pocket may interact with some of the numerous basic residues of colicin E3. The involvement of hydrophobic moieties in the binding is consistent with the observation that the tight complex can only be dissociated by denaturation. The structure of Im3 resembles those of certain nucleic acid binding proteins, in particular domain II of topoisomerase I and RNA-binding proteins that contain the ribonucleoprotein (RNP) sequence motif. This observation suggests that Im3 has a nucleic acid binding function in addition to binding colicin E3. | |||
Crystal structure of colicin E3 immunity protein: an inhibitor of a ribosome-inactivating RNase.,Li C, Zhao D, Djebli A, Shoham M Structure. 1999 Nov 15;7(11):1365-72. PMID:10574790<ref>PMID:10574790</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3eip" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Colicin | *[[Colicin immunity protein 3D structures|Colicin immunity protein 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: Escherichia coli str. | </StructureSection> | ||
[[Category: Djebli | [[Category: Escherichia coli str. K-12 substr. W3110]] | ||
[[Category: Li | [[Category: Large Structures]] | ||
[[Category: Shoham | [[Category: Djebli A]] | ||
[[Category: Zhao | [[Category: Li C]] | ||
[[Category: Shoham M]] | |||
[[Category: Zhao D]] | |||
Latest revision as of 03:23, 28 December 2023
CRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO A RIBOSOME-INACTIVATING RNASECRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO A RIBOSOME-INACTIVATING RNASE
Structural highlights
FunctionIMM3_ECOLX This protein inhibits the 16S RNA hydrolyzing activity of colicin E3 by binding with high affinity to the C-terminal catalytic domain of E3. This protein is able to protect a cell, which harbors the plasmid ColE3 against colicin E3. 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 PubMedBACKGROUND: Colicins are antibiotic-like proteins of Escherichia coli that kill related strains. Colicin E3 acts as an RNase that specifically cleaves 16S rRNA, thereby inactivating the ribosomes in the infected cell. The producing organism is protected against colicin E3 by a specific inhibitor, the immunity protein Im3, which forms a tight 1:1 complex with colicin E3 and renders it inactive. Crystallographic studies on colicin E3 and Im3 have been undertaken to unravel the structural basis for the ribonucleolytic activity and its inhibition. RESULTS: The crystal structure of Im3 has been determined to a resolution of 1.8 A. The structure consists of a four-standard antiparallel beta sheet flanked by three alpha helices on one side of the sheet. Thr7, Phe9, Phe16 and Phe74 form a hydrophobic cluster on the surface of the protein in the vicinity of Cys47. This cluster is part of a putative binding pocket which also includes nine polar residues. CONCLUSIONS: The putative binding pocket of Im3 is the probable site of interaction with colicin E3. The six acidic residues in the pocket may interact with some of the numerous basic residues of colicin E3. The involvement of hydrophobic moieties in the binding is consistent with the observation that the tight complex can only be dissociated by denaturation. The structure of Im3 resembles those of certain nucleic acid binding proteins, in particular domain II of topoisomerase I and RNA-binding proteins that contain the ribonucleoprotein (RNP) sequence motif. This observation suggests that Im3 has a nucleic acid binding function in addition to binding colicin E3. Crystal structure of colicin E3 immunity protein: an inhibitor of a ribosome-inactivating RNase.,Li C, Zhao D, Djebli A, Shoham M Structure. 1999 Nov 15;7(11):1365-72. PMID:10574790[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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