1yit

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "1yit" [edit=sysop:move=sysop])
Current revision (07:31, 9 October 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1yit.png|left|200px]]
 
-
<!--
+
==Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of Haloarcula Marismortui==
-
The line below this paragraph, containing "STRUCTURE_1yit", creates the "Structure Box" on the page.
+
<StructureSection load='1yit' size='340' side='right'caption='[[1yit]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1yit]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui] and [https://en.wikipedia.org/wiki/Streptomyces_virginiae Streptomyces virginiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YIT FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#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=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=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MEA:N-METHYLPHENYLALANINE'>MEA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MHV:4-OXO-L-PIPECOLIC+ACID'>MHV</scene>, <scene name='pdbligand=MHW:3-HYDROXYPICOLINIC+ACID'>MHW</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>, <scene name='pdbligand=VIR:VIRGINIAMYCIN+M1'>VIR</scene></td></tr>
-
{{STRUCTURE_1yit| PDB=1yit | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yit OCA], [https://pdbe.org/1yit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yit RCSB], [https://www.ebi.ac.uk/pdbsum/1yit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yit ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476]
 +
== 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/yi/1yit_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1yit ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
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.
-
===Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of Haloarcula Marismortui===
+
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:15851032<ref>PMID:15851032</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_15851032}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1yit" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 15851032 is the PubMed ID number.
+
-
-->
+
-
{{ABSTRACT_PUBMED_15851032}}
+
-
 
+
-
==About this Structure==
+
-
[[1yit]] is a 30 chain structure of [[Ribosomal protein L10]], [[Ribosomal protein L2]], [[Ribosomal protein L3]], [[Ribosomal protein L5]], [[Ribosomal protein L6]], [[Ribosomal protein L7]] and [[Ribosome]] with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YIT OCA].
+
==See Also==
==See Also==
-
*[[Ribosomal protein L10]]
+
*[[Ribosome 3D structures|Ribosome 3D structures]]
-
*[[Ribosomal protein L2]]
+
== References ==
-
*[[Ribosomal protein L3]]
+
<references/>
-
*[[Ribosomal protein L5]]
+
__TOC__
-
*[[Ribosomal protein L6]]
+
</StructureSection>
-
*[[Ribosomal protein L7]]
+
-
*[[Ribosome]]
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:15851032</ref><references group="xtra"/>
+
[[Category: Haloarcula marismortui]]
[[Category: Haloarcula marismortui]]
-
[[Category: Blaha, G.]]
+
[[Category: Large Structures]]
-
[[Category: Moore, P B.]]
+
[[Category: Streptomyces virginiae]]
-
[[Category: Steitz, T A.]]
+
[[Category: Blaha G]]
-
[[Category: Tu, D.]]
+
[[Category: Moore PB]]
-
[[Category: 50s subunit]]
+
[[Category: Steitz TA]]
-
[[Category: Antibiotic complex]]
+
[[Category: Tu D]]
-
[[Category: Ribosome]]
+
-
[[Category: Virginiamycin m]]
+
-
[[Category: Virginiamycin s]]
+

Current revision

Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of Haloarcula Marismortui

PDB ID 1yit

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yit"
Personal tools