5WVZ

The crystal structure of Cren7 mutant L28F in complex with dsDNA

Summary for 5WVZ

• Entry DOI: 10.2210/pdb5wvz/pdb
• Related: 5WVW 5WVY 5WWC
• Descriptor: Chromatin protein Cren7, DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3') (3 entities in total)
• Functional Keywords: beta-sheet, dna binding, dna binding protein-dna complex, crenarchaeal chromatin protein, dna binding protein/dna
• Biological source: Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2); More
• Cellular location: Cytoplasm : Q97ZE3
• Total number of polymer chains: 6
• Total formula weight: 23134.28

Authors

Zhang, Z.F.,Zhao, M.H.,Wang, L.,Chen, Y.Y.,Dong, Y.H.,Gong, Y.,Huang, L. (deposition date: 2016-12-30, release date: 2017-04-26, Last modification date: 2023-11-22)

Primary citation

Zhang, Z.,Zhao, M.,Wang, L.,Chen, Y.,Dong, Y.,Gong, Y.,Huang, L.
Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA
Biochem. J., 474:1727-1739, 2017

PubMed Abstract: Crenarchaeal chromatin protein Cren7 binds double-stranded DNA in the minor groove, introducing a sharp single-step DNA kink. The side chain of Leu28, a residue conserved among all Cren7 homologs, intercalates into the kinked DNA step. In the present study, we replaced Leu28 with a residue containing a hydrophobic side chain of different sizes (i.e. L28A, L28V, L28I, L28M and L28F). Both the stability of the Cren7-DNA complex and the ability of Cren7 to constrain DNA supercoils correlated well with the size of the intercalated side chain. Structural analysis shows that L28A induces a kink (∼43°), nearly as sharp as that produced by wild-type Cren7 (∼48°), in the bound DNA fragment despite the lack of side chain intercalation. In another duplex DNA fragment, L28F inserts a large hydrophobic side chain deep into the DNA step, but introduces a smaller kink (∼39°) than that formed by the wild-type protein (∼50°). Mutation of Leu28 into methionine yields two protein conformers differing in loop β3-β4 orientation, DNA-binding surface and DNA geometry in the protein-DNA structure. Our results indicate that side chain intercalation is not directly responsible for DNA kinking or bending by Cren7, but plays a critical role in the stabilization of the Cren7-DNA complex. In addition, the flexibility of loop β3-β4 in Cren7, as revealed in the crystal structure of L28M-DNA, may serve a role in the modulation of chromosomal organization and function in the cell.

PubMed: 28377493
DOI: 10.1042/BCJ20170036

Experimental method

X-RAY DIFFRACTION (2.3 Å)