ABSTRACT
Proteins containing Dbl homology (DH) domains activate Rho-family GTPases by functioning as specific guanine nucleotide exchange factors. All known DH domains have associated C-terminal pleckstrin homology (PH) domains that are implicated in targeting and regulatory functions. The crystal structure of a fragment of the human Son of sevenless protein containing the DH and PH domains has been determined at 2.3 A resolution. The entirely alpha-helical DH domain is unrelated in architecture to other nucleotide exchange factors. The active site of the DH domain, identified on the basis of sequence conservation and structural features, lies near the interface between the DH and PH domains. The structure suggests that ligation of the PH domain will be coupled structurally to the GTPase binding site.
Subject(s)
Blood Proteins/chemistry , Blood Proteins/genetics , Phosphoproteins , Proteins/chemistry , Proteins/genetics , Binding Sites , Crystallography , Guanine Nucleotide Exchange Factors , Humans , Molecular Sequence Data , Protein Structure, Secondary , Protein Structure, Tertiary , Sequence Homology, Amino AcidABSTRACT
The crystal structure of the sugar-binding and dimerization domain of the Escherichia coli gene regulatory protein, AraC, has been determined in complex with the competitive inhibitor D-fucose at pH 5.5 to a resolution of 1.6 A. An in-depth analysis shows that the structural basis for AraC carbohydrate specificity arises from the precise arrangement of hydrogen bond-forming protein side-chains around the bound sugar molecule. van der Waals interactions also contribute to the epimeric and anomeric selectivity of the protein. The methyl group of D-fucose is accommodated by small side-chain movements in the sugar-binding site that result in a slight distortion in the positioning of the amino-terminal arm. A comparison of this structure with the 1.5 A structure of AraC complexed with L-arabinose at neutral pH surprisingly revealed very small structural changes between the two complexes. Based on solution data, we suspect that the low pH used to crystallize the fucose complex affected the structure, and speculate about the nature of the changes between pH 5.5 and neutral pH and their implications for gene regulation by AraC. A comparison with the structurally unrelated E. coli periplasmic sugar-binding proteins reveals that conserved features of carbohydrate recognition are present, despite a complete lack of structural similarity between the two classes of proteins, suggesting convergent evolution of carbohydrate binding.
Subject(s)
Escherichia coli/chemistry , Fucose/chemistry , Protein Conformation , Repressor Proteins/chemistry , Transcription Factors , Amino Acid Sequence , AraC Transcription Factor , Arabinose/chemistry , Arabinose/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Binding Sites , Carbohydrate Conformation , Crystallization , Crystallography, X-Ray , Dimerization , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins , Fucose/metabolism , Gene Expression Regulation, Bacterial , Hydrogen Bonding , Hydrogen-Ion Concentration , Models, Molecular , Molecular Sequence Data , Protein Structure, Secondary , Repressor Proteins/metabolism , StereoisomerismABSTRACT
The crystal structure of the arabinose-binding and dimerization domain of the Escherchia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The 1.5 angstrom structure of the arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the 2.8 angstrom structure of the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface. The ligand-gated oligomerization as seen in AraC provides the basis of a plausible mechanism for modulating the protein's DNA-looping properties.
Subject(s)
Bacterial Proteins , DNA/metabolism , Protein Conformation , Repressor Proteins/chemistry , Transcription Factors , AraC Transcription Factor , Arabinose/metabolism , Binding Sites , Crystallization , Crystallography, X-Ray , Dimerization , Hydrogen Bonding , Ligands , Models, Molecular , Protein Folding , Protein Structure, Secondary , Repressor Proteins/metabolismABSTRACT
We report that a host nuclear protein of approximately 100 kDa binds to the tandemly reiterated DR2 sequence of herpes simplex virus type 1 (HSV-1). The DR2 sequence is a repeated component in the "a" sequence, which defines the signals for cleavage and encapsidation of viral DNA; the "a" sequence also contains the promoter regulatory signals for the gene encoding the viral neurovirulence factor, ICP34.5. Characterization of the host binding protein by means of gel shifts and DNase I footprinting revealed this protein is the eukaryotic transcription factor, Sp1. Furthermore, as judged from the sequence homology, the DR2 region contains clustered matches to the consensus binding site for Sp1. Comparison of the host factor and purified Sp1 (by means of gel shifts and footprinting) confirmed these findings. Since clustered DNA recognition elements represent unusually high affinity binding sites, these repeated Sp1 motifs proximal to the ICP34.5 gene suggest that this region may be a major Sp1 binding site in the viral genome.
