ISDA

Deposition Date 1999-02-23

Release Date 2000-02-23

Last Version Date 2023-08-09

Entry Detail

PDB ID:

1CA5

Keywords:

STRUCTURAL PROTEIN/DNA

Title:

INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)
Sulfolobus acidocaldarius (Taxon ID: 2285)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Free:

0.27

R-Value Work:

0.19

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CHROMOSOMAL PROTEIN SAC7D
Gene (Uniprot):Saci_0064
Chain IDs:C (auth: A)
Chain Length:66
Number of Molecules:1
Biological Source:Sulfolobus acidocaldarius

UniProt ID:P13123 Pfam ID:PF02294

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3'
Chain IDs:A (auth: B), B (auth: C)
Chain Length:8
Number of Molecules:2
Biological Source:synthetic construct

Primary Citation

Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs

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

J.Mol.Biol. 303 395 403 (2000)

PMID: 11031116 DOI: 10.1006/jmbi.2000.4112

Abstact

Sso7d and Sac7d are two small chromatin proteins from the hyperthermophilic archaeabacterium Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. The crystal structures of Sso7d-GTGATCGC, Sac7d-GTGATCGC and Sac7d-GTGATCAC have been determined and refined at 1.45 A, 2.2 A and 2.2 A, respectively, to investigate the DNA binding property of Sso7d/Sac7d in the presence of a T-G mismatch base-pair. Detailed structural analysis revealed that the intercalation site includes the T-G mismatch base-pair and Sso7d/Sac7d bind to that mismatch base-pair in a manner similar to regular DNA. In the Sso7d-GTGATCGC complex, a new inter-strand hydrogen bond between T2O4 and C14N4 is formed and well-order bridging water molecules are found. The results suggest that the less stable DNA stacking site involving a T-G mismatch may be a preferred site for protein side-chain intercalation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures