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PDBsum entry 1a0a
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Transcription/DNA
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PDB id
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1a0a
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of pho4 bhlh domain-Dna complex: flanking base recognition.
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Authors
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T.Shimizu,
A.Toumoto,
K.Ihara,
M.Shimizu,
Y.Kyogoku,
N.Ogawa,
Y.Oshima,
T.Hakoshima.
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Ref.
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EMBO J, 1997,
16,
4689-4697.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 4.
Figure 4 Summary of contacts of PHO4 residues with DNA bases and
phosphate groups. Schematic summary of the base and phosphate
contacts made by each monomer. The DNA is represented as a
cylindrical projection with phosphates indicated by circles. The
E-box bases are stippled and recognized flanking bases are
hatched. Base pair recognitions are indicated by bold-lined
arrows, and phosphate recognitions by thin-lined arrows. The
weak interaction is shown by dashed-lined arrows. All contacts
are via side chains.
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Figure 7.
Figure 7 Surroundings of the 5'-flanking base in PHO4 (green)
and USF (white). A van der Waals contact shown by a dashed line
was observed between the methyl group of the flanking thymine
(at position 4L) and Val8 of USF. Glu3 (PHO4) and Ala3 (USF) are
far from the 5'-flanking base in PHO4 and USF.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1997,
16,
4689-4697)
copyright 1997.
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