1fyp
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1fyp |SIZE=350|CAPTION= <scene name='initialview01'>1fyp</scene> | |PDB= 1fyp |SIZE=350|CAPTION= <scene name='initialview01'>1fyp</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1fyo|1FYO]], [[1pbr|1PBR]], [[1a3m|1A3M]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fyp OCA], [http://www.ebi.ac.uk/pdbsum/1fyp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1fyp RCSB]</span> | ||
}} | }} | ||
| Line 23: | Line 26: | ||
[[Category: Lynch, S R.]] | [[Category: Lynch, S R.]] | ||
[[Category: Puglisi, J D.]] | [[Category: Puglisi, J D.]] | ||
| - | [[Category: PAR]] | ||
[[Category: aminoglycoside]] | [[Category: aminoglycoside]] | ||
[[Category: g-a base pair]] | [[Category: g-a base pair]] | ||
| Line 30: | Line 32: | ||
[[Category: stem-internal loop-stem-tetraloop]] | [[Category: stem-internal loop-stem-tetraloop]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:32:52 2008'' |
Revision as of 17:32, 30 March 2008
| |||||||
| Ligands: | , , , , | ||||||
| Related: | 1FYO, 1PBR, 1A3M
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
EUKARYOTIC DECODING REGION A-SITE RNA-PAROMOMYCIN COMPLEX
Overview
Aminoglycoside antibiotics, including paromomycin, neomycin and gentamicin, target a region of highly conserved nucleotides in the decoding region aminoacyl-tRNA site (A site) of 16 S rRNA on the 30 S subunit. Change of a single nucleotide, A1408 to G, reduces the affinity of many aminoglycosides for the ribosome; G1408 distinguishes between prokaryotic and eukaryotic ribosomes. The structures of a prokaryotic decoding region A-site oligonucleotide free in solution and bound to the aminoglycosides paromomycin and gentamicin C1a were determined previously. Here, the structure of a eukaryotic decoding region A-site oligonucleotide bound to paromomycin has been determined using NMR spectroscopy and compared to the prokaryotic A-site-paromomycin structure. A conformational change in three adenosine residues of an internal loop, critical for high-affinity antibiotic binding, was observed in the prokaryotic RNA-paromomycin complex in comparison to its free form. This conformational change is not observed in the eukaryotic RNA-paromomycin complex, disrupting the binding pocket for ring I of the antibiotic. The lack of the conformational change supports footprinting and titration calorimetry data that demonstrate approximately 25-50-fold weaker binding of paromomycin to the eukaryotic decoding-site oligonucleotide. Neomycin, which is much less active against Escherichia coli ribosomes with an A1408G mutation, binds non-specifically to the oligonucleotide. These results suggest that eukaryotic ribosomal RNA has a shallow binding pocket for aminoglycosides, which accommodates only certain antibiotics.
About this Structure
1FYP is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structural origins of aminoglycoside specificity for prokaryotic ribosomes., Lynch SR, Puglisi JD, J Mol Biol. 2001 Mar 9;306(5):1037-58. PMID:11237617
Page seeded by OCA on Sun Mar 30 20:32:52 2008
