3cf5: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| (15 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
< | ==Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans== | ||
<StructureSection load='3cf5' size='340' side='right'caption='[[3cf5]], [[Resolution|resolution]] 3.30Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3cf5]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans] and [https://en.wikipedia.org/wiki/Streptomyces_azureus Streptomyces azureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CF5 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]] 3.3Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB9:(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC+ACID'>BB9</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene>, <scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MH6:3-HYDROXY-2-IMINOPROPANOIC+ACID'>MH6</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=QUA:8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC+ACID'>QUA</scene>, <scene name='pdbligand=TS9:(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC+ACID'>TS9</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=3cf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cf5 OCA], [https://pdbe.org/3cf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cf5 RCSB], [https://www.ebi.ac.uk/pdbsum/3cf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cf5 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RL33_DEIRA RL33_DEIRA] Binds the 23S rRNA and the E site tRNA.[HAMAP-Rule:MF_00294] | |||
== 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/cf/3cf5_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=3cf5 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The thiopeptide class of antibiotics targets the GTPase-associated center (GAC) of the ribosome to inhibit translation factor function. Using X-ray crystallography, we have determined the binding sites of thiostrepton (Thio), nosiheptide (Nosi), and micrococcin (Micro), on the Deinococcus radiodurans large ribosomal subunit. The thiopeptides, by binding within a cleft located between the ribosomal protein L11 and helices 43 and 44 of the 23S rRNA, overlap with the position of domain V of EF-G, thus explaining how this class of drugs perturbs translation factor binding to the ribosome. The presence of Micro leads to additional density for the C-terminal domain (CTD) of L7, adjacent to and interacting with L11. The results suggest that L11 acts as a molecular switch to control L7 binding and plays a pivotal role in positioning one L7-CTD monomer on the G' subdomain of EF-G to regulate EF-G turnover during protein synthesis. | |||
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.,Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P Mol Cell. 2008 Apr 11;30(1):26-38. PMID:18406324<ref>PMID:18406324</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3cf5" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribosome 3D structures|Ribosome 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
[[Category: Deinococcus radiodurans]] | [[Category: Deinococcus radiodurans]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Connell | [[Category: Streptomyces azureus]] | ||
[[Category: Fucini | [[Category: Connell SR]] | ||
[[Category: Harms | [[Category: Fucini P]] | ||
[[Category: Schluenzen | [[Category: Harms JM]] | ||
[[Category: Spahn | [[Category: Schluenzen F]] | ||
[[Category: Stachelhaus | [[Category: Spahn CMT]] | ||
[[Category: Wilson | [[Category: Stachelhaus T]] | ||
[[Category: Zaborowska | [[Category: Wilson DN]] | ||
[[Category: Zaborowska Z]] | |||
Latest revision as of 17:57, 1 November 2023
Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radioduransThiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans
Structural highlights
FunctionRL33_DEIRA Binds the 23S rRNA and the E site tRNA.[HAMAP-Rule:MF_00294] 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 PubMedThe thiopeptide class of antibiotics targets the GTPase-associated center (GAC) of the ribosome to inhibit translation factor function. Using X-ray crystallography, we have determined the binding sites of thiostrepton (Thio), nosiheptide (Nosi), and micrococcin (Micro), on the Deinococcus radiodurans large ribosomal subunit. The thiopeptides, by binding within a cleft located between the ribosomal protein L11 and helices 43 and 44 of the 23S rRNA, overlap with the position of domain V of EF-G, thus explaining how this class of drugs perturbs translation factor binding to the ribosome. The presence of Micro leads to additional density for the C-terminal domain (CTD) of L7, adjacent to and interacting with L11. The results suggest that L11 acts as a molecular switch to control L7 binding and plays a pivotal role in positioning one L7-CTD monomer on the G' subdomain of EF-G to regulate EF-G turnover during protein synthesis. Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.,Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P Mol Cell. 2008 Apr 11;30(1):26-38. PMID:18406324[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||