Crystal structure of the DNA mimic protein DMP19

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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Neisseria conserved protein DMP19 is a DNA mimic protein that prevents DNA binding to a hypothetical nitrogen-response transcription factor

Wang, H.-C.Ko, T.-P.Wu, M.-L.Ku, S.-C.Wu, H.-J.Wang, A.H.-J.

(2012) Nucleic Acids Res 

  • DOI: https://doi.org/10.1093/nar/gks177
  • Primary Citation of Related Structures:  
    3VJZ, 3VK0

  • 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.

  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein
A, B
166Neisseria meningitidis MC58Mutation(s): 0 
Gene Names: NMB0541
Find proteins for Q9K0P4 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9K0P4 
Go to UniProtKB:  Q9K0P4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K0P4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.878α = 90
b = 65.309β = 99.7
c = 59.094γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references