1jzz: Difference between revisions

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New page: left|200px<br /><applet load="1jzz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jzz, resolution 3.8Å" /> '''Structural Basis for ...
 
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[[Image:1jzz.gif|left|200px]]<br /><applet load="1jzz" size="450" color="white" frame="true" align="right" spinBox="true"
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'''Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria'''<br />


==Overview==
==Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria==
Ribosomes, the site of protein synthesis, are a major target for natural, and synthetic antibiotics. Detailed knowledge of antibiotic binding sites, is central to understanding the mechanisms of drug action. Conversely, drugs are excellent tools for studying the ribosome function. To elucidate, the structural basis of ribosome-antibiotic interactions, we determined, the high-resolution X-ray structures of the 50S ribosomal subunit of the, eubacterium Deinococcus radiodurans, complexed with the clinically, relevant antibiotics chloramphenicol, clindamycin and the three macrolides, erythromycin, clarithromycin and roxithromycin. We found that antibiotic, binding sites are composed exclusively of segments of 23S ribosomal RNA at, the peptidyl transferase cavity and do not involve any interaction of the, drugs with ribosomal proteins. Here we report the details of antibiotic, interactions with the components of their binding sites. Our results also, show the importance of putative Mg+2 ions for the binding of some drugs., This structural analysis should facilitate rational drug design.
<StructureSection load='1jzz' size='340' side='right'caption='[[1jzz]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1jzz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JZZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JZZ 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]] 3.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ROX:ROXITHROMYCIN'>ROX</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=1jzz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jzz OCA], [https://pdbe.org/1jzz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jzz RCSB], [https://www.ebi.ac.uk/pdbsum/1jzz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jzz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RL4_DEIRA RL4_DEIRA] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_B]  Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_B]  This protein is located close to the polypeptide exit tunnel, and interacts with the modified macrolide azithromycin, which blocks the tunnel.[HAMAP-Rule:MF_01328_B]
== 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/jz/1jzz_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=1jzz ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1JZZ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans] with ROX and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JZZ OCA].
*[[Ribosomal protein L22|Ribosomal protein L22]]
 
*[[Ribosomal protein L32|Ribosomal protein L32]]
==Reference==
*[[Ribosomal protein L4|Ribosomal protein L4]]
Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria., Schlunzen F, Zarivach R, Harms J, Bashan A, Tocilj A, Albrecht R, Yonath A, Franceschi F, Nature. 2001 Oct 25;413(6858):814-21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11677599 11677599]
__TOC__
</StructureSection>
[[Category: Deinococcus radiodurans]]
[[Category: Deinococcus radiodurans]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Albrecht, R.]]
[[Category: Albrecht R]]
[[Category: Bashan, A.]]
[[Category: Bashan A]]
[[Category: Franceschi, F.]]
[[Category: Franceschi F]]
[[Category: Harms, J.]]
[[Category: Harms J]]
[[Category: Schluenzen, F.]]
[[Category: Schluenzen F]]
[[Category: Tocilj, A.]]
[[Category: Tocilj A]]
[[Category: Yonath, A.]]
[[Category: Yonath A]]
[[Category: Zarivach, R.]]
[[Category: Zarivach R]]
[[Category: MG]]
[[Category: ROX]]
[[Category: 23s]]
[[Category: 50s]]
[[Category: 5s]]
[[Category: antibiotics]]
[[Category: peptidyl transferase center]]
[[Category: ribosome]]
[[Category: roxithromycin]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:44:06 2007''

Latest revision as of 10:43, 7 February 2024

Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in EubacteriaStructural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria

Structural highlights

1jzz is a 4 chain structure with sequence from Deinococcus radiodurans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.8Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL4_DEIRA One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_B] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_B] This protein is located close to the polypeptide exit tunnel, and interacts with the modified macrolide azithromycin, which blocks the tunnel.[HAMAP-Rule:MF_01328_B]

Evolutionary Conservation

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

See Also

1jzz, resolution 3.80Å

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