PDBsum entry 199d

DNA

PDB id: 199d

Contents

DNA/RNA

Ligands

MOC

PDB id:

199d

Name:

DNA

Title:

Solution structure of the monoalkylated mitomycin c-DNA complex

Structure:

DNA (5'-d( (Di)p Cp Ap Cp Gp Tp Cp (Di)p T)-3'). Chain: a. Engineered: yes. DNA (5'-d( Ap Cp Gp Ap Cp Gp Tp Gp C)-3'). Chain: b. Engineered: yes

Source:

Synthetic: yes. Other_details: chemically synthesized. Other_details: chemically synthesized

NMR struc:

3 models

Authors:

M.Sastry,R.Fiala,R.Lipman,M.Tomasz,D.J.Patel

Key ref:

M.Sastry et al. (1995). Solution structure of the monoalkylated mitomycin C-DNA complex. J Mol Biol, 247, 338-359. PubMed id: 7707379 DOI: 10.1006/jmbi.1994.0143

Date:

01-Dec-94 Release date: 07-Feb-95

DNA/RNA chains

I-C-A-C-G-T-C-I-T 9 bases

A-C-G-A-C-G-T-G-C 9 bases

DOI no: 10.1006/jmbi.1994.0143

J Mol Biol 247:338-359 (1995)

PubMed id: 7707379

Solution structure of the monoalkylated mitomycin C-DNA complex.

M.Sastry, R.Fiala, R.Lipman, M.Tomasz, D.J.Patel.

ABSTRACT

Mitomycin C (MC) is a potent antitumor antibiotic which alkylates DNA through covalent linkage of its C-1" position with the exocyclic N2 amino group of guanine to yield the [MC]dG adduct at the duplex level. We report on the solution structure of the monoalkylated MC-DNA 9-mer complex where the [MC]dG5 adduct is positioned opposite dC14 in the d(A3-C4-[MC]G5-T6).d(A13-C14-G15-T16) sequence context. The solution structure was solved based on a combined NMR-molecular dynamics study including NOE intensity based refinement. The formation of the [MC]dG adduct occurs with retention of the Watson-Crick alignment at the [MC]dG5.dC14 base-pair and flanking pairs in the complex. The MC ring is positioned in the minor groove with its indoloquinone aromatic ring system at a approximately 45 degrees angle relative to the helix axis and directed towards the 3'-direction on the unmodified strand. The MC indoloquinone chromophore is asymmetrically positioned in a slightly widened minor groove so that its plane is parallel to and stacked over the d(C14-G15-T16) segment on the unmodified strand with its other face exposed to solvent. The MC five-membered ring adopts an envelope pucker with its C-2" atom displaced from the mean plane and directed away from the unmodified strand. We observe conformational perturbations in the DNA 9-mer duplex on formation of the monoalkylated MC complex. Specifically, the base-pairs are displaced by approximately -3.0 A towards the major groove on positioning the MC in the minor groove. This perturbation is accompanied by base stacking patterns similar to those observed in A-DNA while the majority of the sugars adopt puckers characteristic of B-DNA. Conformational perturbations as monitored by helix twist, sugar pucker pseudorotation and glycosidic torsion angles are also observed for the d(T6-C7-I8).d(C11-G12-A13) segment that is adjacent to but does not overlap the MC binding on the 9-mer duplex. We note that the O-10" atom on the carbamate side-chain of MC forms an intermolecular hydrogen bond with the exocyclic amino group of dG15 in two of the three refined structures of the complex. The solution structure of the complex containing this intramolecular hydrogen bond readily explains both the previously observed d(C-G).d(C-G) sequence requirement for cross-linking and the observed, somewhat less stringent, requirement of the same sequence for the initial monoalkylation step.(ABSTRACT TRUNCATED AT 400 WORDS)

Selected figure(s)

Figure 8.
Figure 8. Stereoviews of base stacking and intermolecular hydrogen bonding pattern in a representative relaxation matrix refined structure (RM-B1) of the MC-DNA 9-mer complex. A, The d(C4-[MC]G5) · d(C14-G15) step with the mitomycin shown in cyan. An intermolecular hydrogen bond is shown between the exposed amino proton of dG15 and the ester oxygen attached to C-10" on the mitomycin. We observe cross strand stacking between the base planes of [MC]dG5 and dG15 at this step. B, The d([MC]G5-T6) · d(A13-C14) step with the mitomycin shown in cyan. We observe stacking between the base planes of [MC]dG5 and dT6 and the base planes of dA13 and dC14 within individual strands.

Figure 9.
Figure 9. Corey-Pauling-Koltum views of the d(A3-C4-[MC]G5-T6) · d(A13-C14-G15-T16) segment of the representative relaxation matrix refined structure (RM-B1 ) of the MC-DNA 9-mer complex. The mitomycin is shown in cyan, the DNA is shown in white except for the phosphates which are shown in red. A, View looking into minor groove and normal to the helix axis. B, An alternate view normal to the helix axis emphasizing the approximately parallel alignment of the MC ring and the sugar-phosphate backbone of the unmodified strand. C, View looking down the minor groove showing the MC ring directed towards the unmodified strand.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 247, 338-359) copyright 1995.

Figures were selected by an automated process.