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
Identifieur interne : 003673 ( Main/Exploration ); précédent : 003672; suivant : 003674Use 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
Auteurs : Marie L. Coté [États-Unis] ; Sarah J. Yohannan [États-Unis] ; Millie M. Georgiadis [États-Unis]Source :
- Acta Crystallographica Section D [ 1399-0047 ] ; 2000-09.
English descriptors
- Teeft :
- Acta, Acta cryst, Adenine, Anking, Anking pair, Asymmetric unit, Atom superpositioning, Available parameters, Average width, Backbone torsion angles, Base atoms, Base pair, Base pairs, Binding site, Biochemistry, Biol, Biosym technologies, Canonical structure, Canonical value, Chuprina poltev, Complexation, Conformation, Cote, Cote georgiadis, Cryst, Crystal lattices, Crystal structure, Crystal structures, Crystallographic analysis, Data collection, Dodecamer, Duplex, Electron density, Endo, Exact mapping, Fragment, Georgiadis, Helical, Helpful discussions, Hydrogen bonds, Intact duplex, Lattice, Lavery sklenar, Local helical parameters, Merritt bacon, Methods enzymol, Minor groove, Mispair, Mispair conformation, Mispair models, Mispaired, Mispaired adenine, Mispairs, Mmlv, Molecular replacement, Molecule, Moloney murine leukemia virus, Najmudin, Natl acad, Ngers, Ngers domain, Nucleic, Nucleic acid, Nucleic acid structures, Nucleic acids, Nucleotide, Other crystal forms, Overhang, Phosphate group, Phosphate groups, Phosphodiester, Phosphodiester backbone, Poltev, Poltev shulyupina, Propeller twist, Protein molecule, Protein molecules, Research papers, Research papers table, Resolution range, Rfree, Rfree values, Rich region, Rwork, Sheared, Sheared conformation, Sheared mispair conformation, Sheared mispairs, Sheared model, Short strand, Singlestranded overhangs, Standard model, Structure determination, Sugar moiety, Sugar ring, Symmetry element, Terminal adenine, Third lattice, Unpublished results.
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 Å 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.
Url:
DOI: 10.1107/S0907444900008246
Affiliations:
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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.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>New Jersey</li></region><settlement><li>New Brunswick (New Jersey)</li></settlement><orgName><li>Université Rutgers</li></orgName></list><tree><country name="États-Unis"><region name="New Jersey"><name sortKey="Cote, Marie L" sort="Cote, Marie L" uniqKey="Cote M" first="Marie L." last="Coté">Marie L. Coté</name></region><name sortKey="Georgiadis, Millie M" sort="Georgiadis, Millie M" uniqKey="Georgiadis M" first="Millie M." last="Georgiadis">Millie M. Georgiadis</name><name sortKey="Yohannan, Sarah J" sort="Yohannan, Sarah J" uniqKey="Yohannan S" first="Sarah J." last="Yohannan">Sarah J. Yohannan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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