PDBsum entry: 1hwt

Gene regulation/DNA

PDB-id: 1hwt

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Description

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References

PROCHECK

Protein chains

70 a.a. *

74 a.a. *

DNA/RNA

Metal ions

_ZN ×9

Waters ×58

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1hwt

Name:

Gene regulation/DNA

Title:

Structure of a hap1/DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein

Structure:

DNA (5'- d( Gp Cp Gp Cp Tp Ap Tp Tp Ap Tp Cp Gp Cp Tp Ap Tp Tp Ap Gp C)-3'). Chain: a, e. Fragment: upstream activation sequence. Synonym: uas cyc7. Engineered: yes. DNA (5'- d( Gp Cp Tp Ap Ap Tp Ap Gp Cp Gp Ap Tp Ap Ap Tp Ap Gp Cp Gp

Source:

Synthetic: yes. Other_details: sequence from saccharomyces cerevisiae. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: bwg-1-7a-dcyc1. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Chains C, G: P12351 (HAP1_YEAST)

Seq:
Struc:
	Seq:
	Struc:
Seq:
Struc:
	Seq:
	Struc:
Seq:
Struc:
	Seq:	1483 a.a.
	Struc:	70 a.a.

Chains D, H: P12351 (HAP1_YEAST)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

1483 a.a.

Struc:

74 a.a.

Key:

PfamA domain

Secondary structure

Resolution:

2.50Å

R-factor:

0.246

R-free:

0.291

Authors:

D.A.King,L.Zhang,L.Guarente,R.Marmorstein

Key ref:

D.A.King et al. (1999). Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein.. Nat Struct Biol, 6, 64-71. [PubMed id: 9886294] [DOI: 10.1038/4940]

Date:

17-Sep-98

Release date:

10-Nov-99

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Surface

Key reference

DOI no: 10.1038/4940

Nat Struct Biol 6:64-71 (1999)

PubMed id: 9886294

Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein.

D.A.King, L.Zhang, L.Guarente, R.Marmorstein.

ABSTRACT

HAP1 is a member of a family of fungal transcription factors that contain a Zn2Cys6 binuclear cluster domain and bind as homodimers to sequences containing two DNA half sites. We have determined the 2.5 A crystal structure of HAP1 bound to a cognate upstream activation sequence from the CYC7 gene. The structure reveals that HAP1 is bound in a dramatically asymmetric manner to the DNA target. This asymmetry aligns the Zn2Cys6 domains in a tandem head-to-tail fashion to contact two DNA half sites, positions an N-terminal arm of one of the protein subunits to interact with the inter-half site base pairs in the DNA minor groove, and suggests a mechanism by which DNA-binding facilitates asymmetric dimerization by HAP1. Comparisons with the DNA complexes of the related GAL4, PPR1 and PUT3 proteins illustrate how a conserved protein domain can be reoriented to recognize DNA half sites of different polarities and how homodimeric proteins adopt dramatically asymmetric structures to recognize cognate DNA targets.

Selected figure(s)

Figure 4.
Figure 4. Protein−DNA contacts in the HAP1−DNA complex. a, Protein−DNA contacts mediated by the right Zn[2]Cys[6] domain. For clarity, the DNA is shown in red and only the C tracing of the protein (blue) is shown, except for the side chains that contact the functional groups of the bases (yellow) and backbone groups of the DNA (green). Dashed lines indicate salt links and hydrogen bonds between protein and DNA. The metal ions are indicated as steel gray spheres. Van der Waals contacts mediated between Lys 71R and bases 1L and 2L are omitted for clarity. b, Protein−protein and protein−DNA contacts at the dimerization interface and N-terminal arm of HAP1. Relevant regions of the left and right subunits are shown as a C trace (left subunit, royal blue; right subunit, light blue). A subset of hydrophobic side chains at the interface is shown in yellow. Main and side chain atoms of residues involved in hydrogen-bonding interactions with DNA are shown in green with a water molecule represented as a violet sphere. Backbone NH groups that contact the DNA are indicated by green balls. c, Schematic diagram summarizing all the HAP1−DNA contacts. Water-mediated contacts are indicated with black circles.

Figure 5.
Figure 5. Mapping PC mutations onto the DNA-binding domain of HAP1. Space filling model of the HAP1 dimer bound to DNA showing the location of PC mutations (yellow). The right and left HAP1 subunits are indicated in light and royal blue respectively, with the DNA in red. Prepared using GRASP^55.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 64-71) copyright 1999.

Figures were selected by the author.