PDBsum entry 2r2t

Transferase/DNA

PDB id: 2r2t

Contents

Protein chain

255 a.a. *

DNA/RNA

Waters ×176

* Residue conservation analysis

PDB id:

2r2t

Name:

Transferase/DNA

Title:

D(atttagttaactaaat) complexed with mmlv rt catalytic fragment

Structure:

DNA (5'-d( Dap Dtp Dtp Dtp Dap Dgp Dtp Dt)-3'). Chain: b. Engineered: yes. DNA (5'-d(p Dap Dap Dcp Dtp Dap Dap Dap Dt)-3'). Chain: g. Engineered: yes. Reverse transcriptase. Chain: a. Fragment: residues 144-398.

Source:

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

Resolution:

2.00Å R-factor: 0.224 R-free: 0.264

Authors:

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

Key ref:

K.D.Goodwin et al. (2008). Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding. Proc Natl Acad Sci U S A, 105, 5052-5056. PubMed id: 18362349 DOI: 10.1073/pnas.0708143105

Date:

27-Aug-07 Release date: 22-Jul-08

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

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

A-A-C-T-A-A-A-T 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

DOI no: 10.1073/pnas.0708143105

Proc Natl Acad Sci U S A 105:5052-5056 (2008)

PubMed id: 18362349

Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding.

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

ABSTRACT

Bleomycins constitute a widely studied class of complex DNA cleaving natural products that are used to treat various cancers. Since their first isolation, the bleomycins have provided a paradigm for the development and discovery of additional DNA-cleaving chemotherapeutic agents. The bleomycins consist of a disaccharide-modified metal-binding domain connected to a bithiazole/C-terminal tail via a methylvalerate-Thr linker and induce DNA damage after oxygen activation through site-selective cleavage of duplex DNA at 5'-GT/C sites. Here, we present crystal structures of two different 5'-GT containing oligonucleotides in both the presence and absence of bound Co(III).bleomycin B(2). Several findings from our studies impact the current view of bleomycin binding to DNA. First, we report that the bithiazole intercalates in two distinct modes and can do so independently of well ordered minor groove binding of the metal binding/disaccharide domains. Second, the Co(III)-coordinating equatorial ligands in our structure include the imidazole, histidine amide, pyrimidine N1, and the secondary amine of the beta aminoalanine, whereas the primary amine acts as an axial ligand. Third, minor groove binding of Co(III).bleomycin involves direct hydrogen bonding interactions of the metal binding domain and disaccharide with the DNA. Finally, modeling of a hydroperoxide ligand coordinated to Co(III) suggests that it is ideally positioned for initiation of C4'-H abstraction.

Selected figure(s)

Figure 4.
Interactions of the bithiazole/C-terminal tail and linker with the DNA. (A) Stereodiagram of 1 with DNA (gray) and intercalated bithiazole/C-terminal tail (blue) and linker (red) as a ball-and-stick model with waters (magenta) that contribute to bithiazole/C-terminal tail positioning. Hydrogen bonds represented as black dashed lines. Oxygen atoms in red (DNA) or pink (BLM) and nitrogen atoms in blue (DNA) or cyan (Co·BLM) are involved in H-bonding. Sulfur atoms are yellow. (B) Superimposed 1 (gray) and 2 (black) 5′-GTT sites with intercalated bithiazole/C-terminal tails (1, blue; 2, orange) and relevant water from 1 (magenta) (rmsd of 5′-GT base pairs = 0.54 Å).

Figure 5.
Interactions of the metal-binding domain and disaccharide with the DNA. (A) Stereodiagram of the minor groove of DNA (gray) shown with the metal-binding (yellow with Co in green) and disaccharide (purple) domains and a modeled peroxide ligand (cyan) as a ball-and-stick model. Hydrogen bonds are represented as dashed lines with interacting O atoms in red and N atoms in blue. Intermolecular bonds are black, intramolecular bonds are blue, and magenta bonds represent interactions of the propionamide as modeled (the propioanamide is absent in electron density). The red stick indicates the connection to the linker domain. (B) Schematic showing the hydrogen-bonding interactions of the metal-binding and disaccharide domains in the minor groove with bonds colored as in A.

Figures were selected by an automated process.