title: Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition.
abstract: The crystal structure of a DNA-binding domain of PHO4 complexed with DNA at 2.8 A resolution revealed that the domain folds into a basic-helix-loop-helix (bHLH) motif with a long but compact loop that contains a short alpha-helical segment. This helical structure positions a tryptophan residue into an aromatic cluster so as to make the loop compact. PHO4 binds to DNA as a homodimer with direct reading of both the core E-box sequence CACGTG and its 3'-flanking bases. The 3'-flanking bases GG are recognized by Arg2 and His5. The residues involved in the E-box recognition are His5, Glu9 and Arg13, as already reported for bHLH/Zip proteins MAX and USF, and are different from those recognized by bHLH proteins MyoD and E47, although PHO4 is a bHLH protein.
authors.affiliation: Department of Molecular Biology, Nara Institute of Science and Technology, Ikoma, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Shimizu
authors.forename: A
authors.initials: A
authors.lastname: Toumoto
authors.forename: K
authors.initials: K
authors.lastname: Ihara
authors.forename: M
authors.initials: M
authors.lastname: Shimizu
authors.forename: Y
authors.initials: Y
authors.lastname: Kyogoku
authors.forename: N
authors.initials: N
authors.lastname: Ogawa
authors.forename: Y
authors.initials: Y
authors.lastname: Oshima
authors.forename: T
authors.initials: T
authors.lastname: Hakoshima
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D018360:Crystallography, X-Ray; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004563:Electrochemistry; D004926:Escherichia coli / Q000235:genetics; D018257:Helix-Loop-Helix Motifs; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D028061:Phosphate Transport Proteins; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics
chemical_list: D004271:DNA, Fungal; D026901:Membrane Transport Proteins; D028061:Phosphate Transport Proteins; D011994:Recombinant Proteins; C055831:phosphate permease