PDBsum entry 1nnd

Transferase

PDB id: 1nnd

Contents

Protein chain

251 a.a. *

Waters ×135

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural and energetic characterization of nucleic acid-Binding to the fingers domain of moloney murine leukemia virus reverse transcriptase.

Authors

R.L.Crowther, D.P.Remeta, C.A.Minetti, D.Das, S.P.Montano, M.M.Georgiadis.

Ref.

Proteins, 2004, 57, 15-26. [DOI no: 10.1002/prot.20224]

PubMed id

15326591

Abstract

Reverse transcriptase is an essential retroviral enzyme that replicates the single-stranded RNA genome of the retrovirus producing a double-stranded DNA copy, which is subsequently integrated into the host's genome. We have previously reported that processive DNA synthesis of Moloney murine leukemia virus reverse transcriptase (MMLV RT) is severely compromised by substitution of an Ala for the fingers domain residue Arg 116. In order to further investigate the role of Arg 116 in interactions of MMLV RT with nucleic acids, we have determined the crystal structure of the R116A N-terminal fragment and characterized the binding of two self-complementary DNA duplexes [d(CATGCATG)2 to both the wild-type and R116A fragments by isothermal titration calorimetry. The resultant thermodynamic profiles extrapolated to 25 degrees C reveal that binding of the wild-type N-terminal fragment to both DNA duplexes is enthalpy-driven and characterized by an unfavorable entropy. Although the temperature dependence of the respective protein-DNA binding enthalpies is markedly different reflecting distinct heat capacity changes, the binding free energies are nearly identical and relatively invariant to temperature (DeltaG approximately -6.0 kcal x mol(-1)). In contrast to the wild-type fragment, the R116A fragment exhibits no measurable affinity for either DNA duplex, yet its crystal structure reveals no significant changes when compared to the wild-type structures. We suggest that hydrogen-bonding interactions involving the fingers domain residue Arg 116 are critical for DNA binding as well as processive DNA synthesis by MMLV RT.

Figure 3.
Figure 3. Comparison of the d(CATGCATG)[2] and d(CGCGCGCG)[2] structures depicted as block renderings. In contrast to the structure of d(CATGCATG)[2] in Panel A, the d(CGCGCGCG)[2] structure in Panel B exhibits significant deviations from ideal B-form DNA.

Figure 5.
Figure 5. The electron density map for the R116A fragment as a semi-transparent rendering is superimposed on an overlay of the side chains of the R116A (blue) and wild-type (red) fragment structures at residue 116. The positions of the atoms for residue 116 are remarkably similar including the C position in the R116A fragment versus the wild-type structure. Substitution of Arg for Ala at residue 116 in the N-terminal fragment does not result in any conformational changes in the fingers domain binding site nor anywhere else in the protein as noted in Figure 4.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 57, 15-26) copyright 2004.