1d1u: Difference between revisions

Revision as of 13:12, 21 February 2008

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

Page seeded by OCA on Thu Feb 21 12:12:03 2008

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-[[Image:1d1u.gif|left|200px]]<br /><applet load="1d1u" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1d1u.gif|left|200px]]<br /><applet load="1d1u" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1d1u, resolution 2.30&Aring;" />
 '''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'''<br />
 ==Overview==
-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.
+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 Structure==
-D1U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Moloney_murine_leukemia_virus Moloney murine leukemia virus]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D1U OCA].
+D1U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Moloney_murine_leukemia_virus Moloney murine leukemia virus]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D1U OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Moloney murine leukemia virus]]
 [[Category: Single protein]]
-[[Category: Cote, M.L.]]
+[[Category: Cote, M L.]]
-[[Category: Georgiadis, M.M.]]
+[[Category: Georgiadis, M M.]]
 [[Category: Yohannan, S.]]
 [[Category: crystal structure]]
@@ Line 26: / Line 26: @@
 [[Category: syn-adenine]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:56:28 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:12:03 2008''