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PMID: 9303313 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition.

The EMBO journal ·Vol. 16 ·No. 15 ·1997-08-01 ·Pages 4689-97

Shimizu T, Toumoto A, Ihara K, Shimizu M, Kyogoku Y, Ogawa N, Oshima Y, Hakoshima T

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.

MeSH Terms
Amino Acid Sequence Base Sequence Binding Sites/genetics Crystallography, X-Ray DNA, Fungal/chemistry,genetics,metabolism Electrochemistry Escherichia coli/genetics Helix-Loop-Helix Motifs Membrane Transport Proteins/chemistry,genetics,metabolism Models, Molecular Molecular Sequence Data Molecular Structure Nucleic Acid Conformation Phosphate Transport Proteins Protein Conformation Recombinant Proteins/chemistry,genetics,metabolism Saccharomyces cerevisiae/enzymology,genetics
Chemicals
DNA, Fungal Membrane Transport Proteins Phosphate Transport Proteins Recombinant Proteins phosphate permease
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Shimizu T
Department of Molecular Biology, Nara Institute of Science and Technology, Ikoma, Japan.
Toumoto A
Ihara K
Shimizu M
Kyogoku Y
Ogawa N
Oshima Y
Hakoshima T
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Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
DOI
10.1093/emboj/16.15.4689
Published
1997-08-01
Pages
4689-97
Language
English
Region
England
NLM ID
8208664
PMCID
PMC1170095
Subset
IM
External Links
PubMed source DOI: 10.1093/emboj/16.15.4689 PMC Full Text View journal details
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