1sm1: Difference between revisions

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-[[Image:1sm1.png|left|200px]]
-{{STRUCTURE_1sm1|  PDB=1sm1  |  SCENE=  }}
+==COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN==
+<StructureSection load='1sm1' size='340' side='right'caption='[[1sm1]], [[Resolution|resolution]] 3.42&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1sm1]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans] and [https://en.wikipedia.org/wiki/Streptomyces_graminofaciens Streptomyces graminofaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SM1 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]] 3.42&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=004:(2S)-AMINO(PHENYL)ETHANOIC+ACID'>004</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DOL:5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE'>DOL</scene>, <scene name='pdbligand=MHT:(3S)-3-(METHYLSULFANYL)-1-AZABICYCLO[2.2.2]OCTANE'>MHT</scene>, <scene name='pdbligand=MHU:4-N,N-(DIMETHYLAMINO)-L-PHENYLALANINE'>MHU</scene>, <scene name='pdbligand=MHV:4-OXO-L-PIPECOLIC+ACID'>MHV</scene>, <scene name='pdbligand=MHW:3-HYDROXYPICOLINIC+ACID'>MHW</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=1sm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sm1 OCA], [https://pdbe.org/1sm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sm1 RCSB], [https://www.ebi.ac.uk/pdbsum/1sm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sm1 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/sm/1sm1_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=1sm1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: The bacterial ribosome is a primary target of several classes of antibiotics. Investigation of the structure of the ribosomal subunits in complex with different antibiotics can reveal the mode of inhibition of ribosomal protein synthesis. Analysis of the interactions between antibiotics and the ribosome permits investigation of the specific effect of modifications leading to antimicrobial resistances.Streptogramins are unique among the ribosome-targeting antibiotics because they consist of two components, streptogramins A and B, which act synergistically. Each compound alone exhibits a weak bacteriostatic activity, whereas the combination can act bactericidal. The streptogramins A display a prolonged activity that even persists after removal of the drug. However, the mode of activity of the streptogramins has not yet been fully elucidated, despite a plethora of biochemical and structural data. RESULTS: The investigation of the crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with the clinically relevant streptogramins quinupristin and dalfopristin reveals their unique inhibitory mechanism. Quinupristin, a streptogramin B compound, binds in the ribosomal exit tunnel in a similar manner and position as the macrolides, suggesting a similar inhibitory mechanism, namely blockage of the ribosomal tunnel. Dalfopristin, the corresponding streptogramin A compound, binds close to quinupristin directly within the peptidyl transferase centre affecting both A- and P-site occupation by tRNA molecules. CONCLUSIONS: The crystal structure indicates that the synergistic effect derives from direct interaction between both compounds and shared contacts with a single nucleotide, A2062. Upon binding of the streptogramins, the peptidyl transferase centre undergoes a significant conformational transition, which leads to a stable, non-productive orientation of the universally conserved U2585. Mutations of this rRNA base are known to yield dominant lethal phenotypes. It seems, therefore, plausible to conclude that the conformational change within the peptidyl transferase centre is mainly responsible for the bactericidal activity of the streptogramins and the post-antibiotic inhibition of protein synthesis.
-===COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN===
+Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin.,Harms JM, Schlunzen F, Fucini P, Bartels H, Yonath A BMC Biol. 2004 Apr 1;2:4. PMID:15059283<ref>PMID:15059283</ref>
-{{ABSTRACT_PUBMED_15059283}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1sm1" style="background-color:#fffaf0;"></div>
-[[1sm1]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SM1 OCA].
 ==See Also==
-*[[Ribosomal protein L11|Ribosomal protein L11]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[Ribosomal protein L13|Ribosomal protein L13]]
+== References ==
-*[[Ribosomal protein L14|Ribosomal protein L14]]
+<references/>
-*[[Ribosomal protein L15|Ribosomal protein L15]]
+__TOC__
-*[[Ribosomal protein L16|Ribosomal protein L16]]
+</StructureSection>
-*[[Ribosomal protein L17|Ribosomal protein L17]]
-*[[Ribosomal protein L18|Ribosomal protein L18]]
-*[[Ribosomal protein L19|Ribosomal protein L19]]
-*[[Ribosomal protein L2|Ribosomal protein L2]]
-*[[Ribosomal protein L20|Ribosomal protein L20]]
-*[[Ribosomal protein L21|Ribosomal protein L21]]
-*[[Ribosomal protein L22|Ribosomal protein L22]]
-*[[Ribosomal protein L23|Ribosomal protein L23]]
-*[[Ribosomal protein L24|Ribosomal protein L24]]
-*[[Ribosomal protein L27|Ribosomal protein L27]]
-*[[Ribosomal protein L29|Ribosomal protein L29]]
-*[[Ribosomal protein L3|Ribosomal protein L3]]
-*[[Ribosomal protein L30|Ribosomal protein L30]]
-*[[Ribosomal protein L31|Ribosomal protein L31]]
-*[[Ribosomal protein L32|Ribosomal protein L32]]
-*[[Ribosomal protein L33|Ribosomal protein L33]]
-*[[Ribosomal protein L34|Ribosomal protein L34]]
-*[[Ribosomal protein L35|Ribosomal protein L35]]
-*[[Ribosomal protein L36|Ribosomal protein L36]]
-*[[Ribosomal protein L4|Ribosomal protein L4]]
-*[[Ribosomal protein L5|Ribosomal protein L5]]
-*[[Ribosomal protein L6|Ribosomal protein L6]]
-*[[Ribosomal protein L9|Ribosomal protein L9]]
-==Reference==
-<ref group="xtra">PMID:015059283</ref><references group="xtra"/>
 [[Category: Deinococcus radiodurans]]
-[[Category: Bartels, H.]]
+[[Category: Large Structures]]
-[[Category: Fucini, P.]]
+[[Category: Streptomyces graminofaciens]]
-[[Category: Harms, J M.]]
+[[Category: Bartels H]]
-[[Category: Schluenzen, F.]]
+[[Category: Fucini P]]
-[[Category: Yonath, A.]]
+[[Category: Harms JM]]
-[[Category: 50s ribosomal subunit]]
+[[Category: Schluenzen F]]
-[[Category: Dalfopristin]]
+[[Category: Yonath A]]
-[[Category: Quinupristin]]
-[[Category: Ribosom-antibiotic complex]]
-[[Category: Ribosome]]
-[[Category: Ribosome-antibiotic complex]]
-[[Category: Streptogramin]]
-[[Category: Synercid]]