6ON0

STRUCTURE OF N15 CRO COMPLEXED WITH CONSENSUS OPERATOR DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the lambda Cro complex.

Hall, B.M.Roberts, S.A.Cordes, M.H.J.

(2019) Nucleic Acids Res 47: 7118-7129

  • DOI: 10.1093/nar/gkz507
  • Primary Citation of Related Structures:  
    6ON0

  • PubMed Abstract: 
  • The gene cro promotes lytic growth of phages through binding of Cro protein dimers to regulatory DNA sites. Most Cro proteins are one-to-one orthologs, yet their sequence, structure and binding site sequences are quite divergent across lambdoid phages. We report the cocrystal structure of bacteriophage N15 Cro with a symmetric consensus site ...

    The gene cro promotes lytic growth of phages through binding of Cro protein dimers to regulatory DNA sites. Most Cro proteins are one-to-one orthologs, yet their sequence, structure and binding site sequences are quite divergent across lambdoid phages. We report the cocrystal structure of bacteriophage N15 Cro with a symmetric consensus site. We contrast this complex with an orthologous structure from phage λ, which has a dissimilar binding site sequence and a Cro protein that is highly divergent in sequence, dimerization interface and protein fold. The N15 Cro complex has less DNA bending and smaller DNA-induced changes in protein structure. N15 Cro makes fewer direct contacts and hydrogen bonds to bases, relying mostly on water-mediated and Van der Waals contacts to recognize the sequence. The recognition helices of N15 Cro and λ Cro make mostly nonhomologous and nonanalogous contacts. Interface alignment scores show that half-site binding geometries of N15 Cro and λ Cro are less similar to each other than to distantly related CI repressors. Despite this divergence, the Cro family shows several code-like protein-DNA sequence covariations. In some cases, orthologous genes can achieve a similar biological function using very different specific molecular interactions.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gp39A, B71Escherichia virus N15Mutation(s): 0 
Gene Names: crogene 39
UniProt
Find proteins for Q37964 (Escherichia phage N15)
Explore Q37964 
Go to UniProtKB:  Q37964
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*TP*TP*AP*TP*AP*GP*CP*TP*AP*GP*CP*TP*AP*TP*AP*A)-3')C, D [auth N]17Escherichia virus N15
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.60 Å
    • R-Value Free: 0.217 
    • R-Value Work: 0.206 
    • R-Value Observed: 0.206 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 56.64α = 90
    b = 56.64β = 90
    c = 195.93γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    iMOSFLMdata reduction
    Aimlessdata scaling
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Science Foundation (NSF, United States)United StatesMCB-0643790

    Revision History  (Full details and data files)

    • Version 1.0: 2019-05-15
      Type: Initial release
    • Version 1.1: 2019-06-26
      Changes: Data collection, Database references
    • Version 1.2: 2019-07-31
      Changes: Data collection, Database references
    • Version 1.3: 2019-11-27
      Changes: Author supporting evidence