PDBsum entry 1n4l

Transferase/DNA

PDB id: 1n4l

Contents

Protein chain

255 a.a. *

DNA/RNA

Waters ×145

* Residue conservation analysis

PDB id:

1n4l

Name:

Transferase/DNA

Title:

A DNA analogue of the polypurine tract of HIV-1

Structure:

5'-d( Cp Tp Tp Tp Tp Tp Ap Ap Ap Ap Gp Ap Ap Ap Ap G)-3'. Chain: b. Engineered: yes. 5'-d( Cp Tp Tp Tp Tp Cp Tp Tp Tp Tp Ap Ap Ap Ap Ap G)-3'. Chain: d. Engineered: yes. Reverse transcriptase. Chain: a. Synonym: mmlv rt.

Source:

Synthetic: yes. Moloney murine leukemia virus. Organism_taxid: 11801. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Trimer (from PDB file)

Resolution:

2.00Å R-factor: 0.241 R-free: 0.269

Authors:

M.L.Cote,M.Pflomm,M.M.Georgiadis

Key ref:

M.L.Coté et al. (2003). Staying straight with A-tracts: a DNA analog of the HIV-1 polypurine tract. J Mol Biol, 330, 57-74. PubMed id: 12818202 DOI: 10.1016/S0022-2836(03)00554-0

Date:

31-Oct-02 Release date: 24-Jun-03

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-T-T-T-A-A-A-A-G-A-A-A-A-G 16 bases

C-T-T-T-T-C-T-T-T-T-A-A-A-A-A-G 16 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: 10.1016/S0022-2836(03)00554-0

J Mol Biol 330:57-74 (2003)

PubMed id: 12818202

Staying straight with A-tracts: a DNA analog of the HIV-1 polypurine tract.

M.L.Coté, M.Pflomm, M.M.Georgiadis.

ABSTRACT

The polypurine tract (PPT) from the HIV-1 genome is resistant to digestion by reverse transcriptase following (-)-strand synthesis and is used to prime (+)-strand synthesis during retroviral replication. We have determined the crystal structure of the asymmetric DNA/DNA analog16-mer duplex (CTTTTTAAAAGAAAAG/CTTTTCTTTTAAAAAG) comprising most of the "visible" portion of the RNA:DNA hybrid from the polypurine tract of HIV-1, which was previously reported in a complex with HIV-1 reverse transcriptase. Our 16-mer completely encompasses a 10-mer DNA duplex analog of the HIV-1 PPT. We report here a detailed analysis of our B' form 16-mer DNA structure, including three full pure A-tracts, as well as a comparative structural analysis with polypurine tract and other A-tract-containing nucleic acid structures. Our analysis reveals that the polypurine tract structures share structural features despite being different nucleic acid forms (i.e. DNA:DNA versus RNA:DNA). In addition, the previously reported A-tract-containing DNA molecules bound to topoisomerase I are remarkably similar to our polypurine tract 16-mer structure. On the basis of our analysis, we suggest that the specific topology of long pure A-tracts is remarkably comparable across a wide array of biological environments.

Selected figure(s)

Figure 3.
Figure 3. View[41.] of the PPT DNA 16-mer of form IVc with its numbering scheme. The asterisk (*) in the center indicates where the crystallographic 2-fold rotation axis bisects the non-self-complementary DNA. In this view the 2-fold axis is neither identically parallel with nor perpendicular to the viewer, hence the distorted asterisk for emphasis. Each model used in structural refinement is a different color. The DNA is self-complementary in its first five and last five base-pairs, then there is a "type" similarity (pyrimidine/pyrimidine) in step 6 (11), then the A versus T and T versus A differences of the middle four base-pairs.

Figure 8.
Figure 8. Difference electron density maps are shown following refinement of only the protein, illustrating the roadmap-like quality of the DNA density. The 2F[o] -F[c] map is shown in green and contoured at 1.5s; the F[o] -F[c] map is shown in white and contoured at 3.0s. The protein model is shown with narrow stick figures, and the fitted DNA is shown with thick stick figures.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 57-74) copyright 2003.

Figures were selected by an automated process.