PDBsum entry 1bf4

DNA-binding protein/DNA

PDB id: 1bf4

Contents

Protein chain

63 a.a.

DNA/RNA

Waters ×114

PDB id:

1bf4

Name:

DNA-binding protein/DNA

Title:

Chromosomal DNA-binding protein sso7d/d(gcgaacgc) complex

Structure:

DNA (5'-d( Gp Cp Gp Tp 5Iup Cp Gp C)-3'). Chain: b. Engineered: yes. DNA (5'-d( Gp Cp Gp Ap Ap Cp Gp C)-3'). Chain: c. Engineered: yes. Protein (chromosomal protein sso7d). Chain: a. Synonym: DNA-binding protein 7d, 7 kd DNA-binding protein d, sso7d.

Source:

Synthetic: yes. Sulfolobus acidocaldarius. Organism_taxid: 2285. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Trimer (from PQS)

Resolution:

1.60Å R-factor: 0.211 R-free: 0.288

Authors:

S.Su,Y.-G.Gao,H.Robinson,S.Padmanabhan,L.Lim,J.W.Shriver,A.H.-J.Wang

Key ref:

Y.G.Gao et al. (1998). The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA. Nat Struct Biol, 5, 782-786. PubMed id: 9731772 DOI: 10.1038/1822

Date:

27-May-98 Release date: 10-Nov-99

Protein chain

P13123  (DN7D_SULAC) -  DNA-binding protein 7d from Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)

Seq: 66 a.a.

Struc: 63 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

DNA/RNA chains

G-C-G-T-5IU-C-G-C 8 bases

G-C-G-A-A-C-G-C 8 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/1822

Nat Struct Biol 5:782-786 (1998)

PubMed id: 9731772

The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.

Y.G.Gao, S.Y.Su, H.Robinson, S.Padmanabhan, L.Lim, B.S.McCrary, S.P.Edmondson, J.W.Shriver, A.H.Wang.

ABSTRACT

Sso7d and Sac7d are two small (approximately 7,000 Mr), but abundant, chromosomal proteins from the hyperthermophilic archaeabacteria Sulfolobus solfataricus and S. acidocaldarius respectively. These proteins have high thermal, acid and chemical stability. They bind DNA without marked sequence preference and increase the Tm of DNA by approximately 40 degrees C. Sso7d in complex with GTAATTAC and GCGT(iU)CGC + GCGAACGC was crystallized in different crystal lattices and the crystal structures were solved at high resolution. Sso7d binds in the minor groove of DNA and causes a single-step sharp kink in DNA (approximately 60 degrees) by the intercalation of the hydrophobic side chains of Val 26 and Met 29. The intercalation sites are different in the two complexes. Observations of this novel DNA binding mode in three independent crystal lattices indicate that it is not a function of crystal packing.

Selected figure(s)

Figure 3.
Figure 3. a, Detailed local structures at the protein−DNA interface of the Sso7d− GCGT(^iU)CGC + GCGAACGC complex. Selected side chains of Sso7d are shown. b, Schematic diagram summarizing all the important Sso7d−DNA contacts. The filled, open and dashed arrows represent direct hydrogen bonds/salt bridges, van der Waals close contacts, and potential hydrogen bonds/salt bridges respectively.

Figure 4.
Figure 4. Stereoscopic view of the intercalation sites. The local structures of the two Sso−DNA complexes are superimposed. The DNA octamer is kinked 61° at the C2pG3 step in the Sso7d−GCGT(^ iU)CGC + GCGAACGC complex and 62° at the A3−A4 step in the Sso7d−GTAATTAC complex. The sharp kink is due to the intercalation of Val 26 and Met 29 amino acid side chains into DNA base pairs from the minor groove direction, widening the minor groove at this step. The insertions of 4-Met 29 and 3-Val 26 amino acid side chains are ~1.5 Å deep. The side chain of Met 29 lies close to the base pair with the S-CH[ 3] moiety wedged between the C14 and G15 bases. Similarly the side chain of Val 26 is wedged between the C2 and G3 bases, with each of the CH[ 3] groups pointing toward a base.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1998, 5, 782-786) copyright 1998.

Figures were selected by an automated process.