1d1u: Difference between revisions

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[[Image:1d1u.gif|left|200px]]
{{Seed}}
[[Image:1d1u.png|left|200px]]


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{{STRUCTURE_1d1u|  PDB=1d1u  |  SCENE=  }}  
{{STRUCTURE_1d1u|  PDB=1d1u  |  SCENE=  }}  


'''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'''
===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===




==Overview==
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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.
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{{ABSTRACT_PUBMED_10957631}}


==About this Structure==
==About this Structure==
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[[Category: Single-strand overhang]]
[[Category: Single-strand overhang]]
[[Category: Syn-adenine]]
[[Category: Syn-adenine]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:07:19 2008''

Revision as of 19:07, 30 June 2008

File:1d1u.png

Template:STRUCTURE 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

Template:ABSTRACT PUBMED 10957631

About this Structure

1D1U is a Single protein structure of sequence from Moloney murine leukemia virus. Full crystallographic information is available from OCA.

Reference

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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