1mwl: Difference between revisions

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Revision as of 01:48, 3 May 2008

File:1mwl.gif

1mwl, resolution 2.40Å ()

Ligands:

Related:

1j7t, 1lc4

Resources:

FirstGlance, OCA, RCSB, PDBsum

Coordinates:

save as pdb, mmCIF, xml

Crystal structure of geneticin bound to the eubacterial 16S rRNA A site

OverviewOverview

Aminoglycosides are antibacterial molecules that decrease translation accuracy by binding to the decoding aminoacyl-tRNA site (A site) on 16S ribosomal RNA. We have solved the crystal structure of an RNA fragment containing the A site bound to geneticin at 2.40A resolution. Geneticin, also known as G418, is a gentamicin-related aminoglycoside: it contains three rings that are functionalized by hydroxyl, ammonium and methyl groups. The detailed comparison of the distinctive behaviour of geneticin (binding to pro- and eukaryotic A sites) with the crystallographic, biochemical and microbiological results obtained so far for aminoglycoside-A site complexes offers new insights on the system. The two sugar rings constituting the neamine part common to most of the aminoglycosides bind to the A site, as already observed in the crystal structures solved previously with paromomycin and tobramycin. The essential hydrogen bonds involving ring I (to A1408) and ring II (to the phosphate oxygen atoms of the bulged adenine bases 1492 and 1493 and to G1494) are conserved and additional contacts are observed from ring III (to phosphate oxygen atoms of G1405 and U1406). The present work illustrates a molecular basis of the range in sensitiveness exhibited by geneticin towards common point A site mutations associated to resistance phenotypes. In addition, analysis and comparisons of the structures cast light on the role played by the conserved U1406.U1495 pair in the recognition of the A site by aminoglycosides.

About this StructureAbout this Structure

Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide., Vicens Q, Westhof E, J Mol Biol. 2003 Feb 28;326(4):1175-88. PMID:12589761 Page seeded by OCA on Sat May 3 01:48:25 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:1mwl.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1mwl |SIZE=350|CAPTION= <scene name='initialview01'>1mwl</scene>, resolution 2.40&Aring;
+The line below this paragraph, containing "STRUCTURE_1mwl", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=GET:GENETICIN'>GET</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY=
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1mwl|  PDB=1mwl  |  SCENE=  }}
-|RELATEDENTRY=[[1j7t|1J7T]], [[1lc4|1LC4]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mwl OCA], [http://www.ebi.ac.uk/pdbsum/1mwl PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1mwl RCSB]</span>
-}}
 '''Crystal structure of geneticin bound to the eubacterial 16S rRNA A site'''
@@ Line 19: / Line 16: @@
 ==About this Structure==
-MWL is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MWL OCA].
+Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MWL OCA].
 ==Reference==
 Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide., Vicens Q, Westhof E, J Mol Biol. 2003 Feb 28;326(4):1175-88. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12589761 12589761]
-[[Category: Protein complex]]
 [[Category: Vicens, Q.]]
 [[Category: Westhof, E.]]
 [[Category: 16s ribosomal rna]]
-[[Category: aminoglycoside antibiotic]]
+[[Category: Aminoglycoside antibiotic]]
-[[Category: bulged adenine]]
+[[Category: Bulged adenine]]
-[[Category: geneticin-a-site complex]]
+[[Category: Geneticin-a-site complex]]
-[[Category: uou pair]]
+[[Category: Uou pair]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 01:48:25 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:22:08 2008''