ABSTRACT
Acyl-homoserine-L-lactones (AHLs) are diffusible chemical signals that are required for virulence of many Gram-negative bacteria. AHLs are produced by AHL synthases from two substrates, S-adenosyl-L-methionine and acyl-acyl carrier protein. The AHL synthase EsaI, which is homologous to the AHL synthases from other pathogenic bacterial species, has been crystallized in the primitive tetragonal space group P4(3), with unit-cell parameters a = b = 66.40, c = 47.33 A. The structure was solved by multiple-wavelength anomalous diffraction with a novel use of the rhenium anomalous signal. The rhenium-containing structure has been refined to a resolution of 2.5 A and the perrhenate ion binding sites and liganding residues have been identified.
Subject(s)
Bacterial Proteins/chemistry , Pantoea/enzymology , Rhenium/chemistry , Crystallization , Crystallography, X-Ray , Models, Molecular , Protein ConformationSubject(s)
Anti-Bacterial Agents/chemistry , Nucleic Acid Conformation , RNA, Ribosomal/chemistry , Ribosomal Proteins/chemistry , Base Sequence , Binding Sites , Ligands , Molecular Sequence Data , Molecular Weight , Protein Conformation , RNA, Bacterial/chemistry , RNA, Ribosomal, 16S/chemistry , Thermus thermophilus/geneticsABSTRACT
Chromosomal proteins that form essential architectural components of chromatin bind and bend DNA with an intrinsic low degree of sequence preference. Comparisons made between two recently determined structures of high mobility group (HMG) protein-DNA complexes and other nonsequence-specific protein-DNA complexes reveal the structural basis of this important mode of DNA binding.
Subject(s)
Archaeal Proteins/metabolism , DNA-Binding Proteins/metabolism , DNA/metabolism , High Mobility Group Proteins/metabolism , Archaeal Proteins/chemistry , Binding Sites , DNA/chemistry , DNA-Binding Proteins/chemistry , High Mobility Group Proteins/chemistry , Models, Molecular , Nucleic Acid Conformation , Nucleosomes/metabolism , Protein Conformation , WaterABSTRACT
The high mobility group (HMG) chromosomal proteins, which are common to all eukaryotes, bind DNA in a non-sequence-specific fashion to promote chromatin function and gene regulation. They interact directly with nucleosomes and are believed to be modulators of chromatin structure. They are also important in V(D)J recombination and in activating a number of regulators of gene expression, including p53, Hox transcription factors and steroid hormone receptors, by increasing their affinity for DNA. The X-ray crystal structure, at 2.2 A resolution, of the HMG domain of the Drosophila melanogaster protein, HMG-D, bound to DNA provides the first detailed view of a chromosomal HMG domain interacting with linear DNA and reveals the molecular basis of non-sequence-specific DNA recognition. Ser10 forms water-mediated hydrogen bonds to DNA bases, and Val32 with Thr33 partially intercalates the DNA. These two 'sequence-neutral' mechanisms of DNA binding substitute for base-specific hydrogen bonds made by equivalent residues of the sequence-specific HMG domain protein, lymphoid enhancer factor-1. The use of multiple intercalations and water-mediated DNA contacts may prove to be generally important mechanisms by which chromosomal proteins bind to DNA in the minor groove.
Subject(s)
Chromatin/chemistry , DNA/metabolism , High Mobility Group Proteins/chemistry , Amino Acid Sequence , Animals , Crystallography, X-Ray , DNA-Binding Proteins/chemistry , Drosophila melanogaster/chemistry , Hydrogen Bonding , Models, Molecular , Molecular Sequence Data , Protein Binding , Sequence Homology, Amino AcidABSTRACT
Structural studies are essential to understand mechanisms of non-sequence-specific DNA binding used by chromosomal proteins. A non-histone high-mobility group (HMG) chromosomal protein from Drosophila melanogaster, HMG-D, binds duplex DNA in a non-sequence-specific fashion. The DNA-binding domain of HMG-D has been co-crystallized with a duplex DNA fragment in the primitive orthorhombic space group P2(1)2(1)2(1), with unit-cell dimensions a = 43.74, b = 53.80, c = 86.84 A. Data have been collected to 2.20 A at 99 K, with diffraction observed to at least 2.0 A. Heavy-atom derivative crystals have been obtained by co-crystallization with oligonucleotides halogenated at major-groove positions near the end of the DNA.
