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Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA.
Foster MP
,
Wuttke DS
,
Clemens KR
,
Jahnke W
,
Radhakrishnan I
,
Tennant L
,
Reymond M
,
Chung J
,
Wright PE
.
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We report the NMR resonance assignments for a macromolecular protein/DNA complex containing the three amino-terminal zinc fingers (92 amino acid residues) of Xenopus laevis TFIIIA (termed zf1-3) bound to the physiological DNA target (15 base pairs), and for the free DNA. Comparisons are made of the chemical shifts of protein backbone 1HN, 15N, 13C alpha and 13C beta and DNA base and sugar protons of the free and bound species. Chemical shift changes are analyzed in the context of the structures of the zf1-3/DNA complex to assess the utility of chemical shift change as a probe of molecular interfaces. Chemical shift perturbations that occur upon binding in the zf1-3/DNA complex do not correspond directly to the structural interface, but rather arise from a number of direct and indirect structural and dynamic effects.
Berg,
Zinc finger domains: hypotheses and current knowledge.
1990, Pubmed
Berg,
Zinc finger domains: hypotheses and current knowledge.
1990,
Pubmed
Brodsky,
Solution structure of the HIV-2 TAR-argininamide complex.
1997,
Pubmed
Brüschweiler,
Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling.
1995,
Pubmed
,
Xenbase
Chen,
Mapping of the binding interfaces of the proteins of the bacterial phosphotransferase system, HPr and IIAglc.
1993,
Pubmed
Clemens,
Definition of the binding sites of individual zinc fingers in the transcription factor IIIA-5S RNA gene complex.
1992,
Pubmed
,
Xenbase
Delaglio,
NMRPipe: a multidimensional spectral processing system based on UNIX pipes.
1995,
Pubmed
Elrod-Erickson,
Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions.
1996,
Pubmed
Emerson,
Solution structure of the Ras-binding domain of c-Raf-1 and identification of its Ras interaction surface.
1995,
Pubmed
Engelke,
Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes.
1980,
Pubmed
,
Xenbase
Fairall,
Mapping of the sites of protection on a 5 S RNA gene by the Xenopus transcription factor IIIA. A model for the interaction.
1986,
Pubmed
,
Xenbase
Fairall,
The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition.
1993,
Pubmed
Foster,
Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA.
1997,
Pubmed
Garrett,
Identification by NMR of the binding surface for the histidine-containing phosphocarrier protein HPr on the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system.
1997,
Pubmed
Ginsberg,
Xenopus 5S gene transcription factor, TFIIIA: characterization of a cDNA clone and measurement of RNA levels throughout development.
1984,
Pubmed
,
Xenbase
Gronenborn,
Identification of the contact surface of a streptococcal protein G domain complexed with a human Fc fragment.
1993,
Pubmed
Grzesiek,
The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase.
1996,
Pubmed
Grzesiek,
Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins.
1993,
Pubmed
Guddat,
Protein-mediated nuclear export of RNA: 5S rRNA containing small RNPs in xenopus oocytes.
1990,
Pubmed
,
Xenbase
Hayes,
Structure of the TFIIIA-5 S DNA complex.
1992,
Pubmed
,
Xenbase
Honda,
Association of a 5S gene transcription factor with 5S RNA and altered levels of the factor during cell differentiation.
1980,
Pubmed
,
Xenbase
Houbaviy,
Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator.
1996,
Pubmed
Kay,
Correlation between dynamics and high affinity binding in an SH2 domain interaction.
1996,
Pubmed
Kay,
Field gradient techniques in NMR spectroscopy.
1995,
Pubmed
Kim,
A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA.
1996,
Pubmed
Lee,
A pulsed field gradient isotope-filtered 3D 13C HMQC-NOESY experiment for extracting intermolecular NOE contacts in molecular complexes.
1994,
Pubmed
Liao,
1H, 15N and 13C resonance assignments for the first three zinc fingers of transcription factor IIIA.
1994,
Pubmed
,
Xenbase
Liao,
Specific interaction of the first three zinc fingers of TFIIIA with the internal control region of the Xenopus 5 S RNA gene.
1992,
Pubmed
,
Xenbase
Miller,
Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes.
1985,
Pubmed
,
Xenbase
Nicholls,
Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.
1991,
Pubmed
Nilges,
Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities.
1995,
Pubmed
Orbons,
An NMR study of polymorphous behaviour of the mismatched DNA octamer d(m5C-G-m5C-G-A-G-m5C-G) in solution. The B-duplex and hairpin forms.
1987,
Pubmed
Otting,
Heteronuclear filters in two-dimensional [1H,1H]-NMR spectroscopy: combined use with isotope labelling for studies of macromolecular conformation and intermolecular interactions.
1990,
Pubmed
Pavletich,
Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A.
1991,
Pubmed
Pavletich,
Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers.
1993,
Pubmed
Pelham,
A specific transcription factor that can bind either the 5S RNA gene or 5S RNA.
1980,
Pubmed
,
Xenbase
Pieler,
TFIIIA: nine fingers--three hands?
1993,
Pubmed
,
Xenbase
Qian,
Nuclear magnetic resonance spectroscopy of a DNA complex with the uniformly 13C-labeled Antennapedia homeodomain and structure determination of the DNA-bound homeodomain.
1993,
Pubmed
Schmiedeskamp,
NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.
1997,
Pubmed
Shuker,
Discovering high-affinity ligands for proteins: SAR by NMR.
1996,
Pubmed
Slijper,
Simultaneous 13C and 15N isotope editing of biomolecular complexes. Application to a mutant lac repressor headpiece DNA complex.
1996,
Pubmed
Spolar,
Coupling of local folding to site-specific binding of proteins to DNA.
1994,
Pubmed
Veldhoen,
Contribution of individual base pairs to the interaction of TFIIIA with the Xenopus 5S RNA gene.
1994,
Pubmed
,
Xenbase
Wishart,
1H, 13C and 15N chemical shift referencing in biomolecular NMR.
1995,
Pubmed
Wishart,
The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data.
1994,
Pubmed
Wishart,
Chemical shifts as a tool for structure determination.
1994,
Pubmed
Wishart,
The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy.
1992,
Pubmed
Wong,
Linkage of protein assembly to protein-DNA binding.
1995,
Pubmed
Wuttke,
Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity.
1997,
Pubmed
,
Xenbase
van Nuland,
The NMR determination of the IIA(mtl) binding site on HPr of the Escherichia coli phosphoenol pyruvate-dependent phosphotransferase system.
1993,
Pubmed
van Nuland,
High-resolution structure of the phosphorylated form of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from NMR-NOE data.
1995,
Pubmed
