3ORC

CRYSTAL STRUCTURE OF AN ENGINEERED CRO MONOMER BOUND NONSPECIFICALLY TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-type protein.

Albright, R.A.Mossing, M.C.Matthews, B.W.

(1998) Protein Sci 7: 1485-1494

  • DOI: 10.1002/pro.5560070701
  • Primary Citation of Related Structures:  
    3ORC

  • PubMed Abstract: 
  • The structure has been determined at 3.0 A resolution of a complex of engineered monomeric Cro repressor with a seven-base pair DNA fragment. Although the sequence of the DNA corresponds to the consensus half-operator that is recognized by each subunit of the wild-type Cro dimer, the complex that is formed in the crystals by the isolated monomer appears to correspond to a sequence-independent mode of association ...

    The structure has been determined at 3.0 A resolution of a complex of engineered monomeric Cro repressor with a seven-base pair DNA fragment. Although the sequence of the DNA corresponds to the consensus half-operator that is recognized by each subunit of the wild-type Cro dimer, the complex that is formed in the crystals by the isolated monomer appears to correspond to a sequence-independent mode of association. The overall orientation of the protein relative to the DNA is markedly different from that observed for Cro dimer bound to a consensus operator. The recognition helix is rotated 48 degrees further out of the major groove, while the turn region of the helix-turn-helix remains in contact with the DNA backbone. All of the direct base-specific interactions seen in the wild-type Cro-operator complex are lost. Virtually all of the ionic interactions with the DNA backbone, however, are maintained, as is the subset of contacts between the DNA backbone and a channel on the protein surface. Overall, 25% less surface area is buried at the protein DNA interface than for half of the wild-type Cro-operator complex, and the contacts are more ionic in character due to a reduction of hydrogen bonding and van der Waals interactions. Based on this crystal structure, model building was used to develop a possible model for the sequence-nonspecific interaction of the wild-type Cro dimer with DNA. In the sequence-specific complex, the DNA is bent, the protein dimer undergoes a large hinge-bending motion relative to the uncomplexed form, and the complex is twofold symmetric. In contrast, in the proposed nonspecific complex the DNA is straight, the protein retains a conformation similar to the apo form, and the complex lacks twofold symmetry. The model is consistent with thermodynamic, chemical, and mutagenic studies, and suggests that hinge bending of the Cro dimer may be critical in permitting the transition from the binding of protein at generic sites on the DNA to binding at high affinity operator sites.


    Related Citations: 
    • Refined Structure of Cro Repressor Protein from Bacteriophage Lambda Suggests Both Flexibility and Plasticity
      Ohlendorf, D.H., Tronrud, D.E., Matthews, B.W.
      (1998) J Mol Biol 280: 129
    • Crystal Structure of Lambda-Cro Bound to a Consensus Operator at 3.0 A Resolution
      Albright, R.A., Matthews, B.W.
      (1998) J Mol Biol 280: 137
    • High-Resolution Structure of an Engineered Cro Monomer Shows Changes in Conformation Relative to the Native Dimer
      Albright, R.A., Mossing, M.C., Matthews, B.W.
      (1996) Biochemistry 35: 735
    • Stable, Monomeric Variants of Lambda Cro Obtained by Insertion of a Designed Beta-Hairpin Sequence
      Mossing, M.C., Sauer, R.T.
      (1990) Science 250: 1712

    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene 97403, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CRO REPRESSOR)C [auth A]65Escherichia virus LambdaMutation(s): 0 
Gene Names: crolambdap57
Find proteins for P03040 (Escherichia phage lambda)
Explore P03040 
Go to UniProtKB:  P03040
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*AP*TP*CP*GP*AP*TP*A)-3')A [auth R], B [auth S]8N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.00 Å
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 45.72α = 90
    b = 60.66β = 112.7
    c = 45.72γ = 90
    Software Package:
    Software NamePurpose
    EDPDBmodel building
    TNTrefinement
    SDMSdata reduction
    SDMSdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1998-12-02
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2017-11-29
      Changes: Derived calculations