146d: Difference between revisions
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|PDB= 146d |SIZE=350|CAPTION= <scene name='initialview01'>146d</scene> | |PDB= 146d |SIZE=350|CAPTION= <scene name='initialview01'>146d</scene> | ||
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= <scene name='pdbligand=CRH:1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE'>CRH</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DDA:2,6-DIDEOXY-BETA-D-GLUCOSE'>DDA</scene>, <scene name='pdbligand=DDL:2,6-DIDEOXY-BETA-D-GALACTOSE'>DDL</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MDA:2,6-DIDEOXY-3+C-METHYL-D-RIBOPYRANOSIDE'>MDA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=146d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=146d OCA], [http://www.ebi.ac.uk/pdbsum/146d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=146d RCSB]</span> | |||
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[[Category: Patel, D J.]] | [[Category: Patel, D J.]] | ||
[[Category: Sastry, M.]] | [[Category: Sastry, M.]] | ||
[[Category: dna]] | [[Category: dna]] | ||
[[Category: mithramycin dimer]] | [[Category: mithramycin dimer]] | ||
[[Category: nmr]] | [[Category: nmr]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:28:12 2008'' | ||
Revision as of 18:28, 30 March 2008
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| Ligands: | , , , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX
OverviewOverview
We have characterized the NMR parameters for the complexes formed by the Mg(2+)-coordinated mithramycin dimer with self-complementary d(T-G-G-C-C-A) and d(T-C-G-C-G-A) duplexes. The solution structure of the latter complex has been determined using a combined NMR-molecular dynamics study including relaxation matrix refinement. The Mg(2+)-coordinated mithramycin dimer-d(T-C-G-C-G-A) complex exhibits a 2-fold center of symmetry with the divalent cation coordinated aglycons positioned opposite the central (G3-C4).(G3-C4) segment such that the aglycon C8 hydroxyl oxygens form symmetrical sequence-specific hydrogen bonds to guanine amino protons in the complex. The C-D-E trisaccharide segments of each monomer in the mithramycin dimer adopt extended conformations, are positioned inside the minor groove, and are directed toward either end of the duplex. The C-D saccharide component of one monomer and the aglycon of the other monomer in the mithramycin dimer share a widened minor groove with the hydrophobic edges of the C and D sugars interacting with individual strands of the duplex. The E-sugar ring is positioned in the floor of the minor groove, and its hydroxyl-bearing face interacts with both strands of the duplex through hydrogen-bonding and hydrophobic intermolecular interactions. The A-B disaccharide and the hydrophilic side chain form intermolecular contacts with the sugar-phosphate backbone in the complex. The antiparallel alignment of divalent cation coordinated monomers in the mithramycin dimer results in the two outwardly directed C-D-E trisaccharide segments generating a right-handed continuous hexasaccharide domain that spans six base pairs in the minor groove of the duplex. The solution structure of the mithramycin dimer-DNA complex reported in this study and the solution structure of the chromomycin dimer-DNA complex reported previously [Gao, X., Mirau, P., & Patel, D. J. (1992) J. Mol. Biol. 223, 259-279] show global similarities, as well as local differences that are of interest. All four nucleotides in the tetranucleotide segment of the duplex centered about the sequence-specific (G-C).(G-C) step adopt A-DNA sugar puckers and glycosidic torsion angles in the chromomycin dimer-DNA complex, while only the central cytidine adopts an A-DNA sugar pucker and glycosidic torsion angle in the mithramycin dimer-DNA complex.(ABSTRACT TRUNCATED AT 400 WORDS)
About this StructureAbout this Structure
146D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Solution structure of the mithramycin dimer-DNA complex., Sastry M, Patel DJ, Biochemistry. 1993 Jul 6;32(26):6588-604. PMID:8329387
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