3VJZ

Crystal structure of the DNA mimic protein DMP19

Summary for 3VJZ

• Entry DOI: 10.2210/pdb3vjz/pdb
• Related: 3VKQ
• Descriptor: Putative uncharacterized protein (2 entities in total)
• Functional Keywords: helix bundle, dna mimic, gene regulation
• Biological source: Neisseria meningitidis
• Total number of polymer chains: 2
• Total formula weight: 37333.40

Authors

Wang, H.-C.,Ko, T.-P.,Wang, A.H.-J. (deposition date: 2011-11-01, release date: 2012-03-14, Last modification date: 2024-03-20)

Primary citation

Wang, H.-C.,Ko, T.-P.,Wu, M.-L.,Ku, S.-C.,Wu, H.-J.,Wang, A.H.-J.
Neisseria conserved protein DMP19 is a DNA mimic protein that prevents DNA binding to a hypothetical nitrogen-response transcription factor
Nucleic Acids Res., 2012

PubMed Abstract: DNA mimic proteins occupy the DNA binding sites of DNA-binding proteins, and prevent these sites from being accessed by DNA. We show here that the Neisseria conserved hypothetical protein DMP19 acts as a DNA mimic. The crystal structure of DMP19 shows a dsDNA-like negative charge distribution on the surface, suggesting that this protein should be added to the short list of known DNA mimic proteins. The crystal structure of another related protein, NHTF (Neisseria hypothetical transcription factor), provides evidence that it is a member of the xenobiotic-response element (XRE) family of transcriptional factors. NHTF binds to a palindromic DNA sequence containing a 5'-TGTNAN(11)TNACA-3' recognition box that controls the expression of an NHTF-related operon in which the conserved nitrogen-response protein [i.e. (Protein-PII) uridylyltransferase] is encoded. The complementary surface charges between DMP19 and NHTF suggest specific charge-charge interaction. In a DNA-binding assay, we found that DMP19 can prevent NHTF from binding to its DNA-binding sites. Finally, we used an in situ gene regulation assay to provide evidence that NHTF is a repressor of its down-stream genes and that DMP19 can neutralize this effect. We therefore conclude that the interaction of DMP19 and NHTF provides a novel gene regulation mechanism in Neisseria spps.

PubMed: 22373915
DOI: 10.1093/nar/gks177

Experimental method

X-RAY DIFFRACTION (1.8 Å)