2da8

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[[Image:2da8.gif|left|200px]]
[[Image:2da8.gif|left|200px]]
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{{Structure
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|PDB= 2da8 |SIZE=350|CAPTION= <scene name='initialview01'>2da8</scene>
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The line below this paragraph, containing "STRUCTURE_2da8", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=CH3:METHYL+GROUP'>CH3</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=QUI:2-CARBOXYQUINOXALINE'>QUI</scene>
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{{STRUCTURE_2da8| PDB=2da8 | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2da8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2da8 OCA], [http://www.ebi.ac.uk/pdbsum/2da8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2da8 RCSB]</span>
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'''SOLUTION STRUCTURE OF A COMPLEX BETWEEN (N-MECYS3,N-MECYS7)TANDEM AND (D(GATATC))2'''
'''SOLUTION STRUCTURE OF A COMPLEX BETWEEN (N-MECYS3,N-MECYS7)TANDEM AND (D(GATATC))2'''
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==About this Structure==
==About this Structure==
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2DA8 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DA8 OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DA8 OCA].
==Reference==
==Reference==
Solution structure of a complex between [N-MeCys3,N-MeCys7]TANDEM and [d(GATATC)]2., Addess KJ, Sinsheimer JS, Feigon J, Biochemistry. 1993 Mar 16;32(10):2498-508. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8448108 8448108]
Solution structure of a complex between [N-MeCys3,N-MeCys7]TANDEM and [d(GATATC)]2., Addess KJ, Sinsheimer JS, Feigon J, Biochemistry. 1993 Mar 16;32(10):2498-508. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8448108 8448108]
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[[Category: Protein complex]]
 
[[Category: Addess, K J.]]
[[Category: Addess, K J.]]
[[Category: Feigon, J.]]
[[Category: Feigon, J.]]
[[Category: Sinsheimer, J S.]]
[[Category: Sinsheimer, J S.]]
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[[Category: dna]]
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[[Category: Dna]]
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[[Category: dna/protein complex]]
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[[Category: Dna/protein complex]]
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[[Category: double helix]]
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[[Category: Double helix]]
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[[Category: nmr]]
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[[Category: Nmr]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 00:00:14 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:32:00 2008''
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Revision as of 21:00, 3 May 2008

Image:2da8.gif

Template:STRUCTURE 2da8

SOLUTION STRUCTURE OF A COMPLEX BETWEEN (N-MECYS3,N-MECYS7)TANDEM AND (D(GATATC))2


Overview

[N-MeCys3,N-MeCys7]TANDEM (CysMeTANDEM) is an octadepsipeptide quinoxaline antibiotic that binds specifically by bisintercalation to double-stranded DNA at NTAN sites [Addess, K. J., Gilbert, D. E., Olsen, R. K., & Feigon, J. (1992) Biochemistry 31, 339-350; Addess, K. J., Gilbert, D. E., & Feigon, J. (1992) in Structure and Function Volume 1: Nucleic Acids (Sarma, R. H., & Sarma, M. H., Eds.) pp 147-164, Adenine Press, Schenectady, NY]. We have determined the three-dimensional structure of a complex of CysMeTANDEM and the DNA hexamer [d(GATATC)]2 using two-dimensional 1H NMR derived NOE and dihedral bond angle constraints. This is the first structure of a TpA-specific quinoxaline antibiotic in complex with DNA. Initial structures of the complex were generated by metric matrix distance geometry followed by simulated annealing. Eight of these structures, refined by restrained molecular dynamics, energy minimization, and NOE-based relaxation matrix refinement, have an average pairwise RMSD of 1.11 A for all structures, calculated using all heavy atoms of the drug and the DNA except the terminal base pairs. CysMeTANDEM binds to and affects the structure of the DNA in a manner similar to that observed in complexes of the CpG-specific quinoxaline antibiotics triostin A and echinomycin with DNA [Ughetto, G., Wang, A. H.-J., Quigley, G. J., van der Marel, G. A., van Boom, J. H., & Rich, A. (1985) Nucleic Acids Res. 13, 2305-2323; Wang, A. H.-J., Ughetto G., Quigley, G. J., Hakoshima, T., van der Marel, G. A., van Boom, J. H., & Rich, A. (1984) Science 225, 1115-1121; Wang, A. H.-J., Ughetto, G., Quigley, G. J., & Rich, A. (1986) J. Biomol. Struct. Dyn. 4, 319-342]. The two quinoxaline rings bisintercalate on either side of the two central T.A base pairs and the peptide ring lies in the minor groove. The central A.T base pairs of the complex are underwound (average helical twist angle of approximately -10 degrees) and buckle inward by approximately 20 degrees. There are intermolecular hydrogen bonds between each of the Ala NH and the AN3 protons of the TpA binding site, analogous to those observed between Ala NH and GN3 in the crystal structures of the CpG-specific complexes of echinomycin and triostin A with DNA. However, the structure of the peptide ring of CysMeTANDEM in the complex differs from that of echinomycin and triostin A.(ABSTRACT TRUNCATED AT 400 WORDS)

About this Structure

Full crystallographic information is available from OCA.

Reference

Solution structure of a complex between [N-MeCys3,N-MeCys7]TANDEM and [d(GATATC)]2., Addess KJ, Sinsheimer JS, Feigon J, Biochemistry. 1993 Mar 16;32(10):2498-508. PMID:8448108 Page seeded by OCA on Sun May 4 00:00:14 2008

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