2k5z | pdb_00002k5z

Solution structure and dynamics of the apical stem-loop of Duck hepatitis B virus

spinqualitylabelsall models 2k5z, 10 NMR models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2k5z is a 1 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Related: 2oj7, 2oj8, 2k5y Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed Hepatitis B virus (HBV) replication starts with binding of reverse transcriptase (RT) to the apical stem-loop region of epsilon, a conserved element of the RNA pregenome. For duck HBV, an in vitro replication system has provided molecular details of this interaction. Further insights can be obtained from the structure and dynamics of the duck and human apical stem-loops. Previously, we reported these for the human apical stem-loop. Here, we present the same for the duck counterpart. Unlike its human counterpart, the duck apical stem is unstable in its middle/upper part and contains noncanonical base pairs. This dynamics study is the first of an unstable RNA-DNA stem. Similar to the human stem, the duck apical stem comprises two helical segments with a bend angle of ca. 10 degrees , separated by a nonpaired mobile U residue. It is capped by a well-structured conserved UGUU loop with two residues mobile on the pico- to nanosecond time scale, one of which is involved in RT binding. Remarkably, the unstable middle/upper part of the stem does not show enhanced pico- to nanosecond time scale dynamics. Instead, adenine dispersion relaxation studies indicate enhanced millisecond time scale dynamics involving base pair opening. It can then be concluded that base pair opening is essential for epsilon-RT binding, because stabilization of the stem abolishes binding. We hypothesize that binding occurs by conformational capture of bases in the base pair open state. The unstable secondary structure of the apical stem-loop makes duck epsilon-RT binding unusual in light of recent classifications of RNA target interactions that assume stable secondary structures. The unstable part of the apical stem of duck hepatitis B virus epsilon shows enhanced base pair opening but not pico- to nanosecond dynamics and is essential for reverse transcriptase binding.,Ampt KA, van der Werf RM, Nelissen FH, Tessari M, Wijmenga SS Biochemistry. 2009 Nov 10;48(44):10499-508. PMID:19817488 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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