PDBsum entry 2fjw

Transferase/DNA

PDB id: 2fjw

Contents

Protein chain

255 a.a. *

DNA/RNA

Waters ×213

* Residue conservation analysis

PDB id:

2fjw

Name:

Transferase/DNA

Title:

D(cttgaatgcattcaag) in complex with mmlv rt catalytic fragment

Structure:

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

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:

1.95Å R-factor: 0.237 R-free: 0.256

Authors:

K.D.Goodwin,M.M.Georgiadis

Key ref:

K.D.Goodwin et al. (2006). A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: analysis of a "highly twisted" benzimidazole-diamidine. J Am Chem Soc, 128, 7846-7854. PubMed id: 16771498 DOI: 10.1021/ja0600936

Date:

03-Jan-06 Release date: 27-Jun-06

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

C-A-T-T-C-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

DOI no: 10.1021/ja0600936

J Am Chem Soc 128:7846-7854 (2006)

PubMed id: 16771498

A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: analysis of a "highly twisted" benzimidazole-diamidine.

K.D.Goodwin, M.A.Lewis, F.A.Tanious, R.R.Tidwell, W.D.Wilson, M.M.Georgiadis, E.C.Long.

ABSTRACT

A general strategy for the rapid structural analysis of DNA binding ligands is described as it was applied to the study of RT29, a benzimidazole-diamidine compound containing a highly twisted diphenyl ether linkage. By combining the existing high-throughput fluorescent intercalator displacement (HT-FID) assay developed by Boger et al. and a high-resolution (HR) host-guest crystallographic technique, a system was produced that was capable of determining detailed structural information pertaining to RT29-DNA interactions within approximately 3 days. Our application of the HT/HR strategy immediately revealed that RT29 has a preference for 4-base pair (bp), A.T-rich sites (AATT) and a similar tolerance and affinity for three A-T-bp sites (such as ATTC) containing a G.C bp. On the basis of these selectivities, oligonucleotides were designed and the host-guest crystallographic method was used to generate diffraction quality crystals. Analysis of the resulting crystal structures revealed that the diphenyl ether moiety of RT29 undergoes conformational changes that allow it to adopt a crescent shape that now complements the minor groove structure. The presence of a G.C bp in the RT29 binding site of ATTC did not overly perturb its interaction with DNA-the compound adjusted to the nucleobases that were available through water-mediated interactions. Our analyses suggest that the HT/HR strategy may be used to expedite the screening of novel minor groove binding compounds leading to a direct, HR structural determination.