PDBsum entry 1a0a

Transcription/DNA

PDB id: 1a0a

Contents

Protein chains

63 a.a. *

DNA/RNA

Waters ×80

* Residue conservation analysis

PDB id:

1a0a

Name:

Transcription/DNA

Title:

Phosphate system positive regulatory protein pho4/DNA complex

Structure:

DNA (5'- d( Cp Tp Cp Ap Cp Ap Cp Gp Tp Gp Gp Gp Ap Cp Tp Ap G )-3'). Chain: c. Fragment: upstream activation site p2. Synonym: uasp2(17). Engineered: yes. DNA (5'- d( Cp Tp Ap Gp Tp Cp Cp Cp Ap Cp Gp Tp Gp Tp Gp Ap G )-3'). Chain: d.

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.80Å R-factor: 0.230 R-free: 0.284

Authors:

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

Key ref:

T.Shimizu et al. (1997). Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition. EMBO J, 16, 4689-4697. PubMed id: 9303313 DOI: 10.1093/emboj/16.15.4689

Date:

27-Nov-97 Release date: 18-Mar-98

Protein chains

P07270  (PHO4_YEAST) -  Phosphate system positive regulatory protein PHO4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 312 a.a.

Struc: 63 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

C-T-C-A-C-A-C-G-T-G-G-G-A-C-T-A-G 17 bases

C-T-A-G-T-C-C-C-A-C-G-T-G-T-G-A-G 17 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1093/emboj/16.15.4689

EMBO J 16:4689-4697 (1997)

PubMed id: 9303313

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

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

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.

Selected figure(s)

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.

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.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1997, 16, 4689-4697) copyright 1997.

Figures were selected by an automated process.