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1yjn

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[[Image:1yjn.gif|left|200px]]<br /><applet load="1yjn" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yjn, resolution 3.00&Aring;" />
 
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'''Crystal Structure Of Clindamycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui'''<br />
 
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==Overview==
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==Crystal Structure Of Clindamycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui==
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Crystal structures of H. marismortui large ribosomal subunits containing the mutation G2099A (A2058 in E. coli) with erythromycin, azithromycin, clindamycin, virginiamycin S, and telithromycin bound explain why eubacterial ribosomes containing the mutation A2058G are resistant to them. Azithromycin binds almost identically to both G2099A and wild-type subunits, but the erythromycin affinity increases by more than 10(4)-fold, implying that desolvation of the N2 of G2099 accounts for the low wild-type affinity for macrolides. All macrolides bind similarly to the H. marismortui subunit, but their binding differs significantly from what has been reported in the D. radioidurans subunit. The synergy in the binding of streptogramins A and B appears to result from a reorientation of the base of A2103 (A2062, E. coli) that stacks between them. The structure of large subunit containing a three residue deletion mutant of L22 shows a change in the L22 structure and exit tunnel shape that illuminates its macrolide resistance phenotype.
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<StructureSection load='1yjn' size='340' side='right'caption='[[1yjn]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1yjn]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YJN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YJN FirstGlance]. <br>
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</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&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLY:CLINDAMYCIN'>CLY</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yjn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yjn OCA], [https://pdbe.org/1yjn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yjn RCSB], [https://www.ebi.ac.uk/pdbsum/1yjn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yjn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yj/1yjn_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1yjn ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1YJN is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui] with <scene name='pdbligand=CLY:'>CLY</scene>, <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=K:'>K</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=CD:'>CD</scene> and <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YJN OCA].
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*[[Ribosome 3D structures|Ribosome 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance., Tu D, Blaha G, Moore PB, Steitz TA, Cell. 2005 Apr 22;121(2):257-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15851032 15851032]
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[[Category: Haloarcula marismortui]]
[[Category: Haloarcula marismortui]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Blaha, G.]]
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[[Category: Blaha G]]
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[[Category: Moore, P B.]]
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[[Category: Moore PB]]
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[[Category: Steitz, T A.]]
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[[Category: Steitz TA]]
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[[Category: Tu, D.]]
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[[Category: Tu D]]
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[[Category: CD]]
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[[Category: CL]]
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[[Category: CLY]]
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[[Category: K]]
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[[Category: MG]]
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[[Category: NA]]
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[[Category: antibiotic complexes]]
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[[Category: clindamycin]]
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[[Category: mutated 50s subunits]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:06:10 2008''
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Current revision

Crystal Structure Of Clindamycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui

PDB ID 1yjn

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