1H1H correlation via isotropic mixing of 13C magnetization, a new three-dimensional approach for assigning 1H and 13C spectra of 13C-enriched proteins

Bax, Ad; Clore, G. Marius; Gronenborn, Angela M.

doi:10.1016/0022-2364(90)90202-k

Cited by 341 publications

(335 citation statements)

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“…Using a combination of 3D triple-resonance CBCANH and CBCA(C0)NH (Grzesiek & Bax, 1992a, 1992b, doubleresonance HCCH-TOCSY (Bax et al, 1990b;Clore et al, 1990), 3D "N TOCSY-HMQC , and various 2D experiments, we have assigned almost all of the 'H, I'N, and "C signals of the 92-residue DNA-binding domain of HSF from Kluyveromyces lactis ( Table 1). The CBCANH, CBCA (CO)NH, and HCCH-TOCSY experiments rely primarily on strong 1-and 2-bond coupling constants, which allow for assignment of the NMR signals without reference to the secondary structure of the protein as in more traditional methods (Wuthrich, 1986).…”

Section: Discussionmentioning

confidence: 99%

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Solution structure of the DNA‐binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy

et al. 1994

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The solution structure of the 92-residue DNA-binding domain of the heat shock transcription factor from Kluyveromyces fuctis has been determined using multidimensional NMR methods. Three-dimensional (3D) triple resonance, 'H-'3C-'3C-'H total correlation spectroscopy, and I5N-separated total correlation spectroscopyheteronuclear multiple quantum correlation experiments were used along with various 2D spectra to make nearly complete assignments for the backbone and side-chain 'H, "N, and I3C resonances. Five-hundred eighty-three NOE constraints identified in 3D I3C-and "N-separated NOE spectroscopy (N0ESY)-heteronuclear multiple quantum correlation spectra and a 4-dimensional I3C/l3C-edited NOESY spectrum, along with 35 6, 9 xI , and 30 hydrogen bond constraints, were used to calculate 30 structures by a hybrid distance geometry/simulated annealing protocol, of which 24 were used for structural comparison. The calculations revealed that a 3-helix bundle packs against a small 4-stranded antiparallel P-sheet. The backbone RMS deviation (RMSD) for the family of structures was 1.03 * 0.19 A with respect to the average structure. The topology is analogous to that of the C-terminal domain of the catabolite gene activator protein and appears to be in the helix-turn-helix family of DNAbinding proteins. The overall fold determined by the NMR data is consistent with recent crystallographic work on this domain (Harrison CJ, Bohm AA, Nelson HCM, 1994, Science 263:224) as evidenced by RMSD between backbone atoms in the NMR and X-ray structures of 1.77 k 0.20 A. Several differences were identified some of which may be due to protein-protein interactions in the crystal.

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Section: Discussionmentioning

confidence: 99%

“…3D-HCCH-TOCSY (Bax et al, 1990b;Clore et al, 1990) and 3D-I3C-separated NOESY-HMQC spectra (Ikura et al, 1990) were recorded using uniformly '3C/'SN-labeled HSF samples in 99.96% D'O. Quadrature detection was achieved using the States-TPPI method (Marion et al, 1989b).…”

Section: "C-separated 3 0 Experimentsmentioning

confidence: 99%

Solution structure of the DNA‐binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy

et al. 1994

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“…Sequence-specific assignment of backbone resonances of c RES, c Snu17p-c Bud13p, c Snu17p-c Pml1p as well as monomeric c Bud13p and c Snu17p was achieved through 3D HNCA, HNCOCA, HNCACB, HNCO and 15 N-edited NOESY-HSQC experiments 56 . For the side chain assignment of the three subunits in the c RES trimer 3D HcCH-TOCSY, HBCBCGCDHD, and aliphatic and aromatic 13 C-edited NOESY-HSQC were recorded [56][57][58] . Intermolecular contacts were extracted from three 13 C-15 N F1-filtered/ 13 C F3-edited NOESY-HSQC experiments recorded on c RES trimer samples in which c Snu17p, c Bud13p or c Pml1p was 13 C- 15 N labeled, and the other two subunits were at natural abundance 59 .…”

Section: Competing Financial Interestsmentioning

confidence: 99%

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Wysoczanski

Schneider

Munari

et al. 2014

Nat Struct Mol Biol

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1 1 a r t i c l e sSplicing entails the removal of introns from pre-mRNAs to generate exon-only mRNA, which is exported out of the nucleus for translation 1 . The splicing process is driven and controlled by a large and dynamic RNA-protein complex, the spliceosome 1,2 . The composition and structure of the spliceosome undergoes multiple rearrangements during a splicing reaction, in which a set of distinct structural and compositional states, designated as E, A, B act , B* and C complexes, can be defined 1 . As part of this process, small nuclear ribonucleoprotein (snRNP) particles and non-snRNP splice factors are recruited and released 1,2 . Although the organization of snRNP components of the spliceosome has received considerable attention in recent years, very little is known about the assembly, structure and dynamics of non-snRNP multimeric complexes.The non-snRNP RES complex is present in humans and yeast 3,4 . Deletion of RES genes slows splicing and leads to pre-mRNA leakage into the cytoplasm 3-5 . Distinct introns exhibit RES-dependent splicing 5-9 , as do pre-mRNAs encoding proteins functioning in RNA-nucleotide metabolism 8,10 . Components of the RES complex are found in B and C complexes of the spliceosome, in which RES can interact with U2 snRNP 4,11,12 . In yeast, the RES complex is composed of three proteins, snRNP-associated protein 17 (Snu17p, also known as Ist3p), pre-mRNA-leakage protein 1 (Pml1p) and bud siteselection protein 13 (Bud13p) 3,4 . Snu17p and Bud13p have been implicated directly in splicing 3,5,13 , whereas Pml1p has been linked to the retention of unspliced pre-mRNA in the nucleus 3,5 . Caenorhabditis elegans Bud13p is involved in embryogenesis 14 .Sequence analysis has indicated that Snu17p is a 148-residue (17.1-kDa) noncanonical member of the RRM family of proteins with a long C-terminal part, which exhibits low sequence similarity to published RRM structures 4 . Snu17p binds with nanomolar affinity to the 266-residue (30.5-kDa), natively disordered protein Bud13p 15 . The interaction has been postulated to involve a C-terminal UHM-ligand motif (ULM) in Bud13p that interacts with a U2AF-homology motif (UHM) in the RRM domain of Snu17p 13,15,16 . The only other identified domain encompasses a stretch of lysine residues at the N terminus of Bud13p. Binding of the third component, the 204-residue (23.4-kDa) Pml1p, occurs through its 50 N-terminal disordered residues. The remainder of Pml1p folds as a forkhead-associated domain 13,15,17 , which could potentially bind phosphopeptides 17 . Biochemical evidence has suggested that Snu17p acts as the central binding platform, which interacts with disordered parts of Bud13p and Pml1p 13,15,16 . The precise molecular architecture of the RES complex, however, has been elusive, and its RNA binding capabilities have remained unexplored.Here we solved the three-dimensional structure of the core of the RES complex and demonstrated that its assembly is driven by cooperativity that increases the binding affinity of the components of the complex ...

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“…In addition, a semi-constant-time version was performed with a shorter tI evolution period, enhancing its sensitivity. H(C)CH-TOCSY experiments were recorded on the D 2 0 sample using FLOPSY-8 (Mohebbi & Shaka, 1991) spin-lock sequences with durations of 6.6 and 19.8 ms, according to Bax et al (1990a), with the following modifications. The indirect proton evolution period followed by the INEPT transfer was concatenated into a semi-constant-time ' H evolution period.…”

Section: Nmr Spectroscopymentioning

confidence: 99%

¹H, ¹³C, and ¹⁵N resonance assignments of Fusarium solani pisi cutinase and preliminary features of the structure in solution

et al. 1997

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Essentially complete (96%) sequence-specific assignments were made for the backbone and side-chain 'H, I3C, and "N resonances of Fusarium solanipisi cutinase, produced as a 214-residue heterologous protein in Escherichia coli, using heteronuclear NMR techniques. Three structural features were noticed during the assignment. (1) The secondary structure in solution corresponds mostly with the structure from X-ray diffraction, suggesting that both structures are globally similar. (2) The HN of Ala3' has a strongly upfield-shifted resonance at 3.97 ppm, indicative of an amidearomatic hydrogen bond to the indole ring of Trp69 that stabilizes the N-terminal side of the parallel @-sheet. (3) The NMR data suggest that the residues constituting the oxyanion hole are quite mobile in the free enzyme in solution, in contrast to the existence of a preformed oxyanion hole as observed in the crystal structure. Apparently, cutinase forms its oxyanion hole upon binding of the substrate like true lipases.Keywords: amide-aromatic hydrogen bond; cutinase; heteronuclear 3D NMR; protein; resonance assignment; secondary structure Fusarium solani pisi cutinase belongs to a group of homologous enzymes capable of degrading cutin (Kolattukudy et al., 1984), the insoluble lipid-polyester matrix covering the surface of plants. Cutinases are produced by several phytopathogenic fungi and pollen, enabling them to gain entry into the plant by enzymatic digestion of its cuticle. Moreover, these enzymes catalyze the hydrolysis of ester bonds of triglycerides (de Geus et al., 1990;Egmond et al., 1994aEgmond et al., , 1994bvan der Hijden et al., 1994). In true lipases, the hydrophobic binding site is buried by a flap region, which supposedly helps to avoid aggregation by hiding the binding site from the solvent. During adsorption to a lipid layer, a significant rearrangement of this flap increases the hydrophobic surface at the lipid-binding region, improving adsorption and allowing binding of the substrate (Brzozowski et al., 1991;Derewenda et al., 1992;van Tilbeurgh et al., 1993). E solanipisi cutinase does not possess a pronounced flap region covering the active site (Martinez et al.,

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1H1H correlation via isotropic mixing of 13C magnetization, a new three-dimensional approach for assigning 1H and 13C spectra of 13C-enriched proteins

Cited by 341 publications

References 5 publications

Solution structure of the DNA‐binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy

Solution structure of the DNA‐binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

¹H, ¹³C, and ¹⁵N resonance assignments of Fusarium solani pisi cutinase and preliminary features of the structure in solution

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1H1H correlation via isotropic mixing of 13C magnetization, a new three-dimensional approach for assigning 1H and 13C spectra of 13C-enriched proteins

Cited by 341 publications

References 5 publications

Solution structure of the DNA‐binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy

Solution structure of the DNA‐binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

1H, 13C, and 15N resonance assignments of Fusarium solani pisi cutinase and preliminary features of the structure in solution

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¹H, ¹³C, and ¹⁵N resonance assignments of Fusarium solani pisi cutinase and preliminary features of the structure in solution