PDBsum entry 2adr

Transcription regulation

PDB id: 2adr

Contents

Protein chain

60 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

2adr

Name:

Transcription regulation

Title:

Adr1 DNA-binding domain from saccharomyces cerevisiae, nmr, 25 structures

Structure:

Adr1. Chain: a. Fragment: DNA-binding domain. Engineered: yes. Mutation: yes

Source:

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

NMR struc:

25 models

Authors:

P.M.Bowers,R.E.Kleivt

Key ref:

P.M.Bowers et al. (1999). A folding transition and novel zinc finger accessory domain in the transcription factor ADR1. Nat Struct Biol, 6, 478-485. PubMed id: 10331877 DOI: 10.1038/8283

Date:

20-Mar-98 Release date: 17-Jun-98

Protein chain

P07248  (ADR1_YEAST) -  Regulatory protein ADR1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1323 a.a.

Struc: 60 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/8283

Nat Struct Biol 6:478-485 (1999)

PubMed id: 10331877

A folding transition and novel zinc finger accessory domain in the transcription factor ADR1.

P.M.Bowers, L.E.Schaufler, R.E.Klevit.

ABSTRACT

The region responsible for sequence-specific DNA binding by the transcription factor ADR1 contains two Cys2-His2 zinc fingers and an additional N-terminal proximal accessory region (PAR). The N-terminal (non-finger) PAR is unstructured in the absence of DNA and undergoes a folding transition on binding the DNA transcription target site. We have used a set of HN-HN NOEs derived from a perdeuterated protein-DNA complex to describe the fold of ADR1 bound to the UAS1 binding site. The PAR forms a compact domain consisting of three antiparallel strands that contact A-T base pairs in the major groove. The three-strand domain is a novel fold among all known DNA-binding proteins. The PAR shares sequence homology with the N-terminal regions of other zinc finger proteins, suggesting that it represents a new DNA-binding module that extends the binding repertoire of zinc finger proteins.

Selected figure(s)

Figure 6.
Figure 6. An NMR spectrum and diagram of the observed and inferred intermolecular contacts. a, A strip-plot highlighting intermolecular NOE contacts between the N-terminal region of ADR1-DBD and the UAS1 binding site taken from the perdeuterated ADR1-DBD−UAS1 3D ^15N-edited NOESY spectrum. The NOE contacts demonstrate that the N-terminal residues are in close proximity to base pairs A[3] and T[4], but do not shed light on the specific contacts made by side chains. Selection assays show a preference for a T base at position 4, indicating that specific side-chain contacts as yet undetermined are made to this base. b, Protein−DNA contacts elucidated from change-of-specificity experiments (- - - - -) and observed NOE contacts (——) in each AGAGG nucleotide-binding site. Conserved residues in the -helices of each finger are believed to contact the GAGG nucleotides. The close spatial proximity of the N-terminal residues to base pairs A[3] and T[4], as determined from NOE contacts, does not provide information about base-specific contacts with side chains.

Figure 7.
Figure 7. A model of ADR1-DBD bound to the UAS1, showing both zinc fingers and the N-terminal region. The position of the zinc fingers on the GAGG binding site is modeled from the Zif268−DNA complex and specific base contacts determined from change-of-specificity experiments^1, ^3. The structure of the N-terminal region is the average structure taken from the global fold of ADR1-DBD and positioned with relation to the binding site on the basis of NOE contacts observed in the 3D ^15N-edited NOESY spectra.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 478-485) copyright 1999.

Figures were selected by an automated process.