2pwt
From Proteopedia
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|PDB= 2pwt |SIZE=350|CAPTION= <scene name='initialview01'>2pwt</scene>, resolution 1.800Å | |PDB= 2pwt |SIZE=350|CAPTION= <scene name='initialview01'>2pwt</scene>, resolution 1.800Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=LHA:DOUBLY FUNCTIONALIZED PAROMOMYCIN PM-II-162'>LHA</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=LHA:DOUBLY+FUNCTIONALIZED+PAROMOMYCIN+PM-II-162'>LHA</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pwt OCA], [http://www.ebi.ac.uk/pdbsum/2pwt PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pwt RCSB]</span> | ||
}} | }} | ||
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[[Category: Szychowski, J.]] | [[Category: Szychowski, J.]] | ||
[[Category: Westhof, E.]] | [[Category: Westhof, E.]] | ||
| - | [[Category: | + | [[Category: aminoglycoside]] |
| - | [[Category: | + | [[Category: haba group]] |
| + | [[Category: ribosomal decoding site]] | ||
| + | [[Category: rna]] | ||
| + | [[Category: x-ray analysis]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:41:48 2008'' |
Revision as of 01:41, 31 March 2008
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| , resolution 1.800Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group
Overview
The crystal structure of the complex between oligonucleotide containing the bacterial ribosomal decoding site (A site) and the synthetic paromomycin analogue 1, which contains the gamma-amino-alpha-hydroxybutyryl (L-haba) group at position N1 of ring II (2-DOS ring), and an ether chain with an O-phenethylaminoethyl group at position C2 of ring III, is reported. Interestingly, next to the paromomycin analogue 1 specifically bound to the A site, a second molecule of 1 with a different conformation is observed at the crystal packing interface which mimics the A-minor interaction between two bulged-out adenines from the A site and the codon-anticodon stem of the mRNA-tRNA complex. Improved antibacterial activity supports the conclusion that analogue 1 might affect protein synthesis on the ribosome in two different ways: 1) specific binding to the A site forces maintenance of the "on" state with two bulged out adenines, and 2) a new binding mode of 1 to an A-minor motif which stabilizes complex formation between the ribosome and the mRNA-tRNA complex regardless of whether the codon-anticodon stem is of the cognate or near-cognate type.
About this Structure
2PWT is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity., Kondo J, Pachamuthu K, Francois B, Szychowski J, Hanessian S, Westhof E, ChemMedChem. 2007 Nov 12;2(11):1631-1638. PMID:17722211
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