@article {2120,
	title = {Identification and structural characterization of a CBP/p300-binding domain from the ETS family transcription factor GABP alpha},
	journal = {Journal of Molecular Biology},
	volume = {377},
	number = {3},
	year = {2008},
	note = {ISI Document Delivery No.: 293ZPTimes Cited: 5Cited Reference Count: 60Kang, Hyun-Seo Nelson, Mary L. Mackereth, Cameron D. Scharpf, Manuela Graves, Barbara J. McIntosh, Lawrence P.},
	month = {Mar},
	pages = {636-646},
	type = {Article},
	abstract = {Using NMR spectroscopy, we identified and characterized a previously unrecognized structured domain near the N-terminus (residues 35-121) of the ETS family transcription factor GABP alpha. The monomeric domain folds as a five-stranded beta-sheet crossed by a distorted helix. Although globally resembling ubiquitin, the GABP(x fragment differs in its secondary structure topology and thus appears to represent a new protein fold that we term the OST (On-SighT) domain. The surface of the GABP alpha OST domain contains two predominant clusters of negatively-charged residues suggestive of electrostatically driven interactions with positively-charged partner proteins. Following a best-candidate approach to identify such a partner, we demonstrated through NMR-monitored titrations and glutathione S-transferase pulldown assays that the OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300. This provides a direct structural link between GABP and a central component of the transcriptional machinery. (C) 2008 Elsevier Ltd. All rights reserved.},
	keywords = {BACKBONE DYNAMICS, C-13-LABELED PROTEINS, CREB-BINDING-PROTEIN, ESCHERICHIA-COLI, HIGH-RESOLUTION, HYPOXIA-INDUCIBLE FACTOR-1-ALPHA, LARGER PROTEINS, NEUROMUSCULAR-JUNCTION, NMR, NMR EXPERIMENTS, protein-protein interaction, RESIDUAL DIPOLAR COUPLINGS, SPECTROSCOPY, TRANSCRIPTION FACTOR, UBIQUITIN},
	isbn = {0022-2836},
	url = {<Go to ISI>://000255374200006},
	author = {Kang, H. S. and Nelson, M. L. and Mackereth, C. D. and Scharpf, M. and Graves, B. J. and McIntosh, L. P.}
}
@article {976,
	title = {Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces},
	journal = {Journal of Molecular Biology},
	volume = {341},
	number = {1},
	year = {2004},
	note = {ISI Document Delivery No.: 841JCTimes Cited: 25Cited Reference Count: 65},
	month = {Jul},
	pages = {37-54},
	type = {Article},
	abstract = {S1 domains occur in four of the major enzymes of mRNA decay in Escherichia coli: RNase E, PNPase, RNase II, and RNase G. Here, we report the structure of the S1 domain of RNase E, determined by both X-ray crystallography and NMR spectroscopy. The RNase E S1 domain adopts an OB-fold, very similar to that found with PNPase and the major cold shock proteins, in which flexible loops are appended to a well-ordered five-stranded beta-barrel core. Within the crystal lattice, the protein forms a dimer stabilized primarily by intermolecular hydrophobic packing. Consistent with this observation, light-scattering, chemical crosslinking, and NMR spectroscopic measurements confirm that the isolated RNase E S1 domain undergoes a specific monomer-dimer equilibrium in solution with a K-D value in the millimolar range. The substitution of glycine 66 with serine dramatically destabilizes the folded structure of this domain, thereby providing an explanation for the temperature-sensitive phenotype associated with this mutation in full-length RNase E. Based on amide chemical shift perturbation mapping, the binding surface for a single-stranded DNA dodecamer (K-D = 160(+/-40) muM) was identified as a groove of positive electrostatic potential containing several exposed aromatic side-chains. This surface, which corresponds to the conserved ligand-binding cleft found in numerous OB-fold proteins, lies distal to the dimerization interface, such that two independent oligonucleotide-binding sites can exist in the dimeric form of the RNase E S1 domain. Based on these data, we propose that the S1 domain serves a dual role of dimerization to aid in the formation of the tetrameric quaternary structure of RNase E as described by Callaghan et al. in 2003 and of substrate binding to facilitate RNA hydrolysis by the adjacent catalytic domains within this multimeric enzyme. (C) 2004 Elsevier Ltd. All rights reserved.},
	keywords = {BACILLUS-SUBTILIS, C-13-LABELED PROTEINS, CELLULOMONAS-FIMI, CENC, CHEMICAL-SHIFT, COLD-SHOCK PROTEIN, ESCHERICHIA-COLI, MACROMOLECULAR STRUCTURES, MESSENGER-RNA, OB-fold, protein structure, RNA binding, RNase E, ROTATIONAL DIFFUSION, S1 domain, SELECTIVE H-1-N-15 CORRELATIONS},
	isbn = {0022-2836},
	url = {<Go to ISI>://000222925100005},
	author = {Schubert, M. and Edge, R. E. and Lario, P. and Cook, M. A. and Strynadka, N. C. J. and Mackie, G. A. and McIntosh, L. P.}
}
@article {389,
	title = {The solution structure and interactions of CheW from Thermotoga maritima},
	journal = {Nature Structural Biology},
	volume = {9},
	number = {2},
	year = {2002},
	note = {ISI Document Delivery No.: 516PHTimes Cited: 35Cited Reference Count: 34},
	month = {Feb},
	pages = {121-125},
	type = {Article},
	abstract = {Using protein from the hyperthermophile Thermotoga maritima, we have determined the solution structure of CheW, an essential component in the formation of the bacterial chemotaxis signaling complex. The overall fold is similar to the regulatory domain of the chemotaxis kinase CheA. In addition, interactions of CheW with CheA were monitored by nuclear magnetic resonance (NMR) techniques. The chemical shift perturbation data show the probable contacts that CheW makes with CheA. In combination with previous genetic data, the structure also suggests a possible binding site for the chemotaxis receptor. These results provide a structural basis for a model in which CheW acts as a molecular bridge between CheA and the cytoplasmic tails of the receptor.},
	keywords = {BACTERIAL CHEMOTAXIS, BINDING DOMAIN, C-13-LABELED PROTEINS, ESCHERICHIA-COLI, HISTIDINE KINASE, KINASE CHEA, NMR EXPERIMENTS, RESONANCE ASSIGNMENTS, SECONDARY STRUCTURE, SIGNAL-TRANSDUCTION},
	isbn = {1072-8368},
	url = {<Go to ISI>://000173562000015},
	author = {Griswold, I. J. and Zhou, H. J. and Matison, M. and Swanson, R. V. and McIntosh, L. P. and Simon, M. I. and Dahlquist, F. W.}
}
@article {4745,
	title = {Structure and binding specificity of the second N-terminal cellulose-binding domain from Cellulomonas fimi endoglucanase C},
	journal = {Biochemistry},
	volume = {39},
	number = {10},
	year = {2000},
	note = {ISI Document Delivery No.: 294HFTimes Cited: 31Cited Reference Count: 74},
	month = {Mar},
	pages = {2445-2458},
	type = {Article},
	abstract = {The 1,4-beta-glucanase CenC from Cellulomonas fimi contains two cellulose-binding domains, CBDN1 and CBDN2, arranged in tandem at its N-terminus. These homologous CBDs are distinct in their selectivity for binding amorphous and not crystalline cellulose. Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the tertiary structure of CBDN2 in the presence of saturating amounts of cellopentaose. A total of 1996 experimental restraints were used to calculate an ensemble of 21 final structures for the protein. CBDN2 is composed of 11 beta-strands, folded into two antiparallel beta-sheets, with a topology of a jellyroll beta-sandwich. On the basis of patterns of chemical shift perturbations accompanying the addition of cellooligosaccharides, as well as the observation of intermolecular protein-sugar NOE interactions, the cellulose-binding site of CBDN2 was identified as a cleft that lies across one face of the beta-sandwich. The thermodynamic basis for the binding of cellooligosaccharides was investigated using isothermal titration calorimetry and NMR spectroscopy. Binding is enthalpically driven and consistent with a structural model involving hydrogen bonding between the equatorial hydroxyls of the glucopyranosyl rings and polar amino acid side chains lining the CBDN2 cleft. Affinity electrophoresis was used to determine that CBDN2 also binds soluble beta-1,4-linked polymers of glucose, including hydroxyethylcellulose and beta-1,3-1,4-glucans. This study complements a previous analysis of CBDN1 [Johnson, P. E., Joshi, M. D., Tomme, P., Kilburn, D. G., and McIntosh, L. P. (1996) Biochemistry 35, 14381-14394] and demonstrates that the homologous CBDs from CenC share very similar structures and sugar binding properties.},
	keywords = {3-DIMENSIONAL SOLUTION STRUCTURE, C-13-ENRICHED PROTEINS, C-13-LABELED PROTEINS, CHEMICAL-SHIFT, DISTANCE GEOMETRY, IMPROVED SENSITIVITY, INDEX, ISOTOPICALLY-ENRICHED PROTEINS, LARGER PROTEINS, NUCLEAR-MAGNETIC-RESONANCE, SIDE-CHAIN RESONANCES},
	isbn = {0006-2960},
	url = {<Go to ISI>://000085905300003},
	author = {Brun, E. and Johnson, P. E. and Creagh, A. L. and Tomme, P. and Webster, P. and Haynes, C. A. and McIntosh, L. P.}
}
@article {4406,
	title = {Assigning the NMR spectra of aromatic amino acids in proteins: analysis of two Ets pointed domains},
	journal = {Biochemistry and Cell Biology-Biochimie Et Biologie Cellulaire},
	volume = {76},
	number = {2-3},
	year = {1998},
	note = {ISI Document Delivery No.: 157QRTimes Cited: 11Cited Reference Count: 34},
	pages = {379-390},
	type = {Article},
	abstract = {The measurement of interproton nuclear Overhauser enhancements (NOEs) and dihedral angle restraints of aromatic amino acids is a critical step towards determining the structure of a protein. The complete assignment of the resonances from aromatic rings and the subsequent resolution and identification of their associated NOEs, however, can be a difficult task. Shown here is a strategy for assigning the H-1,C-13, and N-15 signals from the aromatic side chains of histidine, tryptophan, tyrosine, and phenylalanine using a suite of homo- and hetero-nuclear scalar and NOE correlation experiments, as well as selective deuterium isotope labelling. In addition, a comparison of NOE information obtained from homonuclear NOE spectroscopy (NOESY) and C-13-edited NOESY - heteronuclear single quantum correlation experiments indicates that high-resolution homonuclear two-dimensional NOESY spectra of selectively deuterated proteins are invaluable for obtaining distance restraints to the aromatic residues.},
	keywords = {ACTIVE-SITE, ANGLE, aromatic residue, BACKBONE H-1, C-13-LABELED PROTEINS, CHEMICAL-SHIFTS, dihedral, DNA-BINDING, HETERONUCLEAR NMR, HISTIDINE-RESIDUES, MAGNETIC-RESONANCE SPECTROSCOPY, NMR assignment, NOE, pH titration, PHENYLALANINE RESIDUES, TRANSCRIPTION FACTOR},
	isbn = {0829-8211},
	url = {<Go to ISI>://000078073600026},
	author = {Slupsky, C. M. and Gentile, L. N. and McIntosh, L. P.}
}
@article {3956,
	title = {High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response regulator, SpoOF: Implications for phosphorylation and molecular recognition},
	journal = {Biochemistry},
	volume = {36},
	number = {33},
	year = {1997},
	note = {ISI Document Delivery No.: XR735Times Cited: 45Cited Reference Count: 78},
	month = {Aug},
	pages = {10015-10025},
	type = {Article},
	abstract = {NMR has been employed for structural and dynamic studies of the bacterial response regulator, SpoOF. This 124-residue protein is an essential component of the sporulation phosphorelay signal transduction pathway in Bacillus subtilis. Three-dimensional H-1, N-15, and C-13 experiments have been used to obtain full side chain assignments and the 1511 distance, 121 dihedral angle, and 80 hydrogen bonding restraints required for generating a family of structures (14 restraints per residue). The structures give a well-defined (alpha/beta)(5) fold for residues 4-120 with average rms deviations of 0.59 Angstrom for backbone heavy atoms and 1.02 Angstrom for all heavy atoms. Analyses of backbone N-15 relaxation measurements demonstrate relative rigidity in most regions of regular secondary structure with a generalized order parameter (S-2) Of 0.9 +/- 0.05 and a rotational correlation time (tau(m)) of 7.0 +/- 0.5 ns, Loop regions near the site of phosphorylation have higher than average rms deviation values and T-1/T-2 ratios suggesting significant internal motion or chemical exchange at these sites, Additionally, multiple conformers are observed for the beta 4-alpha 4 loop and beta-strand 5 region, These conformers may be related to structural changes associated with phosphorylation and also indicative of the propensity this recognition surface has for differential protein interactions. Comparison of SpoOF structural features to those of other response regulators reveals subtle differences in the orientations of secondary structure in the putative recognition surfaces and the relative charge distribution of residues surrounding the site of phosphorylation, These may be important in providing specificity for protein-protein interactions and for determining the lifetimes of the phosphorylated state.},
	keywords = {3-DIMENSIONAL STRUCTURE, BACTERIAL CHEMOTAXIS, C-13 MAGNETIZATION, C-13-ENRICHED PROTEINS, C-13-LABELED PROTEINS, ESCHERICHIA-COLI, MAGNESIUM-BINDING, NUCLEAR-MAGNETIC-RESONANCE, PROTEIN SECONDARY STRUCTURE, SIGNAL-TRANSDUCTION},
	isbn = {0006-2960},
	url = {<Go to ISI>://A1997XR73500007},
	author = {Feher, V. A. and Zapf, J. W. and Hoch, J. A. and Whiteley, J. M. and McIntosh, L. P. and Rance, M. and Skelton, N. J. and Dahlquist, F. W. and Cavanah, J.}
}
@article {3800,
	title = {Secondary structure and NMR assignments of Bacillus circulans xylanase},
	journal = {Protein Science},
	volume = {5},
	number = {6},
	year = {1996},
	note = {ISI Document Delivery No.: UP617Times Cited: 23Cited Reference Count: 74},
	month = {Jun},
	pages = {1118-1135},
	type = {Article},
	abstract = {Bacillus circulans xylanase (BCX) is a member of the family of low molecular weight endo-beta-(1,4)-xylanases. The main-chain H-1, C-13, and N-15 resonances of this 20.4-kDa enzyme were assigned using heteronuclear NMR experiments recorded on a combination of selectively and uniformly labeled protein samples. Using chemical shift, NOE, J coupling, and amide hydrogen exchange information, 14 beta-strands, arranged in a network of three beta-sheets, and a single cy-helix were identified in BCX. The NMR-derived secondary structure and beta-sheet topology agree closely with that observed in the crystal structure of this protein. The H-N of Ile 118 has a strongly upfield-shifted resonance at 4.03 ppm, indicative of a potential amide-aromatic hydrogen bond to the indole ring of Trp 71. This interaction, which is conserved in all low molecular weight xylanases of known structure, may play an important role in establishing the active site conformation of these enzymes. Following hen egg white and bacteriophage T4 lysozymes, B. circulans xylanase represents the third family of beta-glycanases for which extensive NMR assignments have been reported. These assignments provide the background for detailed studies of the mechanism of carbohydrate recognition and hydrolysis by this bacterial xylanase.},
	keywords = {amide-aromatic hydrogen bond, AMINO-ACID, ASSIGNMENTS, BACKBONE AMIDE, beta-glycanase, C-13-LABELED PROTEINS, C-ALPHA, chemical shift index, CHEMICAL-SHIFTS, COUPLING-CONSTANTS, LARGER PROTEINS, NMR, NUCLEAR-MAGNETIC-RESONANCE, SECONDARY STRUCTURE, SIDE-CHAIN RESONANCES, SOLVENT, SUPPRESSION, XYLANASE},
	isbn = {0961-8368},
	url = {<Go to ISI>://A1996UP61700014},
	author = {Plesniak, L. A. and Wakarchuk, W. W. and McIntosh, L. P.}
}
