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PDBsum entry 2adr
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Transcription regulation
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PDB id
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2adr
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References listed in PDB file
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Key reference
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Title
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A folding transition and novel zinc finger accessory domain in the transcription factor adr1.
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Authors
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P.M.Bowers,
L.E.Schaufler,
R.E.Klevit.
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Ref.
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Nat Struct Biol, 1999,
6,
478-485.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(1999,
6,
478-485)
copyright 1999.
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Secondary reference #1
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Title
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A disorder-To-Order transition couled to DNA binding in the essential zinc-Finger DNA-Binding of yeast adr1 elucidated by backbone dynamics and proton exchange
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Authors
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D.E.Hyre,
R.E.Klevit.
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Ref.
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TO BE PUBLISHED ...
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Secondary reference #2
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Title
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Nmr chemical shift perturbation mapping of DNA binding by a zinc-Finger domain from the yeast transcription factor adr1.
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Authors
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M.Schmiedeskamp,
P.Rajagopal,
R.E.Klevit.
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Ref.
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Protein Sci, 1997,
6,
1835-1848.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. N-HQCspectra ofADRlz and ADRlz-DNA. TheHSQCspectrum of ADRlz uniformlylabeledwith I5N isshowninred,
that DNA-bound ADRlz in blue.ThefreespectrumwasacquiredatpH .4, 30°C; the ound pectrumwasacquiredatpH 7.0,
37°C. Thesedifferences in temperatureandpH alonedo not permrbthespectrum of free ADRlz significantly(datanotshow).
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Figure 7.
Fig. 7. Perturbationsto ADRlz 'H chemical shifts upon DNA binding.Resduesareclassifiedasseverelyperturbed (red), oderately
perturbed (green), or unperturbed (blue). Seetextfordefinitonsofcategories. A: Classificationsareshownascoloredcirclesunder
thesequenceof Bracketsinicatetheextent f theshortestsequencethatbinds NA withighaffinityandthelongest
sequenethatfailstobind DNA. he site ofthe suppressormutation, R91K, iscircled.Conservedresiduesarecolored orange inthe
sequene.Arrowsmarknon-conservedresidueswheremutationsdeleteriousto NA bindinghavebeenidentified.Thosearrowsthat
are redmarkthe sites ofsuspectedbase-specificcontcts. : Thesamedata are shownonbackbonetraces of azincfinger,witha
comparison to direct DNA contactsmade by Zif268. C, D: Thesameperturbationdataaredisplayedonathree-dimensionalmodel of
thefingers of ADRl boundto DNA. Themodelwasgeneratedbysubstitutingfingers2and 3 ofthe Zif268co-crystal structure with
theanalogoussequenceof ADRI. DNA is coloredcyan in panelsC and D. StructuresarerenderedusingtheMOLSCRIPTprogram
(Kraulis, 1991).
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The above figures are
reproduced from the cited reference
with permission from the Protein Society
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