1D1U

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

Summary for 1D1U

• Entry DOI: 10.2210/pdb1d1u/pdb
• Descriptor: DNA (5'-D(*CP*TP*CP*GP*TP*G)-3'), DNA (5'-D(*AP*CP*GP*GP*CP*AP*CP*GP*AP*G)-3'), PROTEIN (REVERSE TRANSCRIPTASE), ... (4 entities in total)
• Functional Keywords: g-a mispair, syn-adenine, nucleic acid, protein-dna complex, single-strand overhang, reverse transcriptase, moloney murine leukemia virus, hydrolase-dna complex, hydrolase/dna
• Biological source: Moloney murine leukemia virus; More
• Cellular location: Gag-Pol polyprotein: Host cell membrane; Lipid-anchor (Potential). Matrix protein p15: Virion (Potential). Capsid protein p30: Virion (Potential). Nucleocapsid protein p10: Virion (Potential): P03355
• Total number of polymer chains: 3
• Total formula weight: 33813.52

Authors

Cote, M.L.,Yohannan, S.,Georgiadis, M.M. (deposition date: 1999-09-21, release date: 2000-04-02, Last modification date: 2024-02-07)

Primary citation

Cote, M.L.,Yohannan, S.J.,Georgiadis, M.M.
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.
Acta Crystallogr.,Sect.D, 56:1120-1131, 2000

PubMed Abstract: 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.

PubMed: 10957631
DOI: 10.1107/S0907444900008246

Experimental method

X-RAY DIFFRACTION (2.3 Å)