PDBsum entry 1ztt

Transferase/DNA

PDB id: 1ztt

Contents

Protein chain

255 a.a. *

DNA/RNA

Ligands

_NT

Waters ×282

* Residue conservation analysis

PDB id:

1ztt

Name:

Transferase/DNA

Title:

Netropsin bound to d(cttaattcgaattaag) in complex with mmlv rt catalytic fragment

Structure:

5'-d( Cp Tp Tp Ap Ap Tp Tp C)-3'. Chain: b. Engineered: yes. 5'-d(p Gp Ap Ap Tp Tp Ap Ap G)-3'. Chain: g. Engineered: yes. Reverse transcriptase. Chain: a. Fragment: rt catalytic fragment.

Source:

Synthetic: yes. Moloney murine leukemia virus. Organism_taxid: 11801. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Trimer (from PDB file)

Resolution:

1.85Å R-factor: 0.220 R-free: 0.246

Authors:

K.D.Goodwin,E.C.Long,M.M.Georgiadis

Key ref:

K.D.Goodwin et al. (2005). A host-guest approach for determining drug-DNA interactions: an example using netropsin. Nucleic Acids Res, 33, 4106-4116. PubMed id: 16049022

Date:

27-May-05 Release date: 30-Aug-05

Protein chain

P03355  (POL_MLVMS) -  Gag-Pol polyprotein from Moloney murine leukemia virus (isolate Shinnick)

Seq: 1738 a.a.

Struc: 255 a.a.

DNA/RNA chains

C-T-T-A-A-T-T-C 8 bases

G-A-A-T-T-A-A-G 8 bases

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.- - ?????
• Enzyme class 3: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 5: E.C.3.1.-.-
• Enzyme class 6: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
• Enzyme class 7: E.C.3.4.23.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Nucleic Acids Res 33:4106-4116 (2005)

PubMed id: 16049022

A host-guest approach for determining drug-DNA interactions: an example using netropsin.

K.D.Goodwin, E.C.Long, M.M.Georgiadis.

ABSTRACT

Netropsin is a well-characterized DNA minor groove binding compound that serves as a model for the study of drug-DNA interactions. Our laboratory has developed a novel host-guest approach to study drug-DNA interactions in which the host, the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) is co-crystallized with a DNA oligonucleotide guest in the presence and absence of drug. We have co-crystallized netropsin with the RT fragment bound to the symmetric 16mer d(CTTAATTCGAATTAAG)2 and determined the structure of the complex at 1.85 A. In contrast to previously reported netropsin-DNA structures, our oligonucleotide contains two AATT sites that bind netropsin with flanking 5' and 3' sequences that are not symmetric. The asymmetric unit of the RT fragment-DNA-netropsin crystals contains one protein molecule and one-half of the 16mer with one netropsin molecule bound. The guanidinium moiety of netropsin binds in a narrow part of the minor groove, while the amidinium is bound in the widest region within the site. We compare this structure to other Class I netropsin-DNA structures and find that the asymmetry of minor groove widths in the AATT site contributes to the orientation of netropsin within the groove while hydrogen bonding patterns vary in the different structures.

Selected figure(s)

Figure 1.
(A) The crystal structure of an RT fragment-DNA-netropsin complex. The asymmetric unit consists of one protein molecule, an 8 bp oligonucleotide duplex and one netropsin molecule representing half of the symmetric complex. The dashed vertical line divides the symmetrically equivalent halves of the 16 bp oligonucleotide. The DNA oligonucleotide is shown in a red sticks model, and netropsin is shown in a purple CPK model. RT is shown as a ribbon rendering with ß-strands in green, coils in yellow and {alpha} -helices in blue except for the {alpha} D helix in magenta. Residues Tyr-64, Asp-114, Leu-115, Arg-116 and Gly-191 that make contacts with the DNA are shown in black ball-and-sticks models. (B) Schematic of the oligonucleotide duplex with the two complementary strands (B and G) and the numbering scheme referred to in the text. Arrows denote netropsin molecules oriented from guanidinium (tail) to amidinium end (head).

Figure 6.
(A) Minor groove widths of DNA base-pair steps (from 3DNA calculations) in the absence (open circle) and presence (black diamond) of netropsin. (B) Stereo diagram of structures of DNA in the absence (red) and presence (blue) of netropsin (r.m.s.d = 0.9 Å). Superimpositioning of C1' of all 16 bp was done using O (19).

Figures were selected by an automated process.