PDBsum entry 2b1b

DNA

PDB id: 2b1b

Contents

DNA/RNA

Metals

_MG

Waters ×29

PDB id:

2b1b

Name:

DNA

Title:

5'-d( Gp Cp Gp Tp Gp Gp Gp Cp Ap C)-3' zif268 binding site

Structure:

5'-d( Gp Cp Gp Tp Gp Gp Gp Cp Ap C)-3'. Chain: a. Engineered: yes. 5'-d( Gp Tp Gp Cp Cp Cp Ap Cp Gp C)-3'. Chain: b. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.212 R-free: 0.255

Authors:

H.M.Berman,A.A.Napoli

Key ref:

J.W.Locasale et al. (2009). Signatures of protein-DNA recognition in free DNA binding sites. J Mol Biol, 386, 1054-1065. PubMed id: 19244617 DOI: 10.1016/j.jmb.2009.01.007

Date:

15-Sep-05 Release date: 27-Sep-05

DNA/RNA chains

G-C-G-T-G-G-G-C-A-C 10 bases

G-T-G-C-C-C-A-C-G-C 10 bases

DOI no: 10.1016/j.jmb.2009.01.007

J Mol Biol 386:1054-1065 (2009)

PubMed id: 19244617

Signatures of protein-DNA recognition in free DNA binding sites.

J.W.Locasale, A.A.Napoli, S.Chen, H.M.Berman, C.L.Lawson.

ABSTRACT

One obstacle to achieving complete understanding of the principles underlying sequence-dependent recognition of DNA is the paucity of structural data for DNA recognition sequences in their free (unbound) state. Here, we carried out crystallization screening of 50 DNA duplexes containing cognate protein binding sites and obtained new crystal structures of free DNA binding sites for three distinct modes of DNA recognition: anti-parallel beta strands (MetR), helix-turn-helix motif + hinge helices (PurR), and zinc fingers (Zif268). Structural changes between free and protein-bound DNA are manifested differently in each case. The new DNA structures reveal that distinctive sequence-dependent DNA geometry dominates recognition by MetR, protein-induced bending of DNA dictates recognition by PurR, and deformability of DNA along the A-B continuum is important in recognition by Zif268. Together, our findings show that crystal structures of free DNA binding sites provide new information about the nature of protein-DNA interactions and thus lend insights towards a structural code for DNA recognition.

Selected figure(s)

Figure 4.
Fig. 4. Purine repressor DNA binding site in free and protein-bound crystal structures. (a) The PurR dodecamer (5′-GCAAACGTTTGC-3′)[2] adopts a straight B-DNA structure. (b) The protein-bound binding site^23 is bent vert, similar 50° towards the major groove at the central CG base pair (top right, PDB ID 1qpz). The DNA binding region of the purine repressor is shown as a semi-transparent surface. The color scheme is as described for Fig. 1.

Figure 8.
Fig. 8. Comparison of free and bound intermediate A/B DNA structures. Average roll (°) versus average slide (Å) are plotted per duplex for free (red triangles) and bound (red diamonds) Zif268 binding sites, and free (cyan triangles) and bound (cyan diamond) binding sites for Runt. Two clusters formed by the Zif268 and runt binding site structures are indicated with ovals. For reference, average roll versus average slide are plotted for the TGGG-containing A/B intermediate (green triangle, PDB ID 1dc0),^38 and A/B intermediate structures of d-(GGCGCC) derivatives^34 (gray dots, PDB ids 1ih2, 1ih3, 1ih4, 1ih5, 1ih6).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 386, 1054-1065) copyright 2009.

Figures were selected by an automated process.