3VH0

Crystal structure of E. coli YncE complexed with DNA

Summary for 3VH0

• Entry DOI: 10.2210/pdb3vh0/pdb
• Descriptor: Uncharacterized protein YncE, DNA (5'-D(*CP*GP*GP*GP*TP*AP*CP*TP*CP*AP*G)-3') (3 entities in total)
• Functional Keywords: beta-propeller, protein binding-dna complex, protein binding/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 6
• Total formula weight: 161407.95

Authors

Kagawa, W.,Sagawa, T.,Niki, H.,Kurumizaka, H. (deposition date: 2011-08-23, release date: 2011-11-16, Last modification date: 2023-11-08)

Primary citation

Kagawa, W.,Sagawa, T.,Niki, H.,Kurumizaka, H.
Structural basis for the DNA-binding activity of the bacterial beta-propeller protein YncE
Acta Crystallogr.,Sect.D, 67:1045-1053, 2011

PubMed Abstract: β-Propellers are widely utilized in nature as recognition modules. The well conserved β-propeller fold exhibits a high degree of functional diversity, which is probably accomplished through variations in the surface properties of the proteins. Little is known about the interactions between β-propeller proteins and nucleic acids. In the present study, it has been found that the bacterial β-propeller protein YncE binds to DNA. Crystal structures of YncE in the free form and complexed with DNA revealed that the surface region of YncE corresponding to the `canonical' substrate-binding site forms essential contacts with DNA. A single DNA base within a single-stranded DNA region is trapped in the hydrophobic pocket located within the central channel of the β-propeller protein. These data provide physical evidence for the DNA-binding ability of the previously uncharacterized YncE and also suggest that the `canonical' substrate-binding site may be commonly adapted to facilitate nucleic acid binding in a subset of β-propeller proteins.

PubMed: 22120742
DOI: 10.1107/S0907444911045033

Experimental method

X-RAY DIFFRACTION (2.9 Å)