1d1u
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USE OF AN N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE TO FACILITATE CRYSTALLIZATION AND ANALYSIS OF A PSEUDO-16-MER DNA MOLECULE CONTAINING G-A MISPAIRS
OverviewOverview
Complexation with the N-terminal fragment of Moloney murine leukemia virus, reverse transcriptase offers a novel method of obtaining crystal, structures of nucleic acid duplexes, which can be phased by molecular, replacement. This method is somewhat similar to the method of using a, monoclonal antibody Fab fragment complexed to the molecule of interest in, order to obtain crystals suitable for X-ray crystallographic analysis., Here a novel DNA structure including two G-A mispairs in a, pseudo-hexadecamer determined at 2.3 A resolution in a complex with the, N-terminal fragment is reported. This structure has an asymmetric unit, consisting of the protein molecule bound to the blunt end of a DNA, 6/10-mer, which is composed of a six-base strand (5'-CTCGTG-3') and a, ten-base strand (3'-GAGCACGGCA-5'). The 6/10-mer is thus composed of a, six-base-pair duplex with a four-base single-stranded overhang. In the, crystal structure, the bases of the overhang are reciprocally paired, (symmetry element -x - 1, -y, z), yielding a doubly nicked, pseudo-hexadecamer primarily B-form DNA molecule, which has some, interesting A-like structural features. The pairing between the single, strands results in two standard (G-C) Watson-Crick pairs and two G-A, mispairs. The structural DNA model can accommodate either a standard syn, or a standard anti conformation for the 5'-terminal adenine of the, ten-base strand of the DNA based on analysis of simulated-annealing omit, maps. Although the DNA model here includes nicks in the phosphodiester, backbone, modeling of an intact phosphodiester backbone results in a very, similar DNA model and indicates that the structure is biologically, relevant.
About this StructureAbout this Structure
1D1U is a Single protein structure of sequence from Moloney murine leukemia virus. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.
ReferenceReference
Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs., Cote ML, Yohannan SJ, Georgiadis MM, Acta Crystallogr D Biol Crystallogr. 2000 Sep;56(Pt 9):1120-31. PMID:10957631
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