2lps | pdb_00002lps

Molecular dynamics re-refinement of domain 5 of the yeast ai5(gamma) group II intron

spinqualitylabelsall models 2lps, 5 NMR models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2lps is a 1 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Related: 1r2p, 1kxk, 2lpt Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum Publication Abstract from PubMed Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site. Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.,Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM Nat Struct Mol Biol. 2004 Feb;11(2):187-92. Epub 2004 Jan 25. PMID:14745440 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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