scholarly journals The Solution Structure of YbcJ from Escherichia coli Reveals a Recently Discovered αL Motif Involved in RNA Binding

2003 ◽  
Vol 185 (14) ◽  
pp. 4204-4210 ◽  
Author(s):  
Laurent Volpon ◽  
Carine Lievre ◽  
Michael J. Osborne ◽  
Shaifali Gandhi ◽  
Pietro Iannuzzi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Solution Structure ◽  
Rna Binding ◽  
Bacterial Proteins ◽  
Binding Domains ◽  
Rna Binding Domains ◽  
Nuclear Magnetic

ABSTRACT The structure of the recombinant Escherichia coli protein YbcJ, a representative of a conserved family of bacterial proteins (COG2501), was determined by nuclear magnetic resonance. The fold of YbcJ identified it as a member of the larger family of S4-like RNA binding domains. These domains bind to structured RNA, such as that found in tRNA, rRNA, and a pseudoknot of mRNA. The structure of YbcJ revealed a highly conserved patch of basic residues, comprising amino acids K26, K38, R55, K56, and K59, which likely participate in RNA binding.

scholarly journals Nuclear Magnetic Resonance Solution Structure of the Escherichia coli DNA Polymerase III θ Subunit

2005 ◽  
Vol 187 (20) ◽  
pp. 7081-7089 ◽  
Author(s):  
Geoffrey A. Mueller ◽  
Thomas W. Kirby ◽  
Eugene F. DeRose ◽  
Dawei Li ◽  
Roel M. Schaaper ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Dna Polymerase ◽  
Solution Structure ◽  
Conformational Exchange ◽  
Dna Polymerase Iii ◽  
Catalytic Core ◽  
Polymerase Iii ◽  
Nuclear Magnetic

ABSTRACT The catalytic core of Escherichia coli DNA polymerase III holoenzyme contains three subunits: α, ε, and θ. The α subunit contains the polymerase, and the ε subunit contains the exonucleolytic proofreading function. The small (8-kDa) θ subunit binds only to ε. Its function is not well understood, although it was shown to exert a small stabilizing effect on the ε proofreading function. In order to help elucidate its function, we undertook a determination of its solution structure. In aqueous solution, θ yielded poor-quality nuclear magnetic resonance spectra, presumably due to conformational exchange and/or protein aggregation. Based on our recently determined structure of the θ homolog from bacteriophage P1, named HOT, we constructed a homology model of θ. This model suggested that the unfavorable behavior of θ might arise from exposed hydrophobic residues, particularly toward the end of α-helix 3. In gel filtration studies, θ elutes later than expected, indicating that aggregation is potentially responsible for these problems. To address this issue, we recorded 1H-15N heteronuclear single quantum correlation (HSQC) spectra in water-alcohol mixed solvents and observed substantially improved dispersion and uniformity of peak intensities, facilitating a structural determination under these conditions. The structure of θ in 60/40 (vol/vol) water-methanol is similar to that of HOT but differs significantly from a previously reported θ structure. The new θ structure is expected to provide additional insight into its physiological role and its effect on the ε proofreading subunit.

scholarly journals Solution Structure, Determined by Nuclear Magnetic Resonance, of the b30-82 Domain of Subunit b of Escherichia coli F1Fo ATP Synthase

2009 ◽  
Vol 191 (24) ◽  
pp. 7538-7544 ◽  
Author(s):  
Ragunathan Priya ◽  
Goran Biuković ◽  
Shovanlal Gayen ◽  
Subramanian Vivekanandan ◽  
Gerhard Grüber
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Solution Structure ◽  
Hydrophobic Surface ◽  
Surface Pattern ◽  
Dimerization Domain ◽  
Binding Domains ◽  
Α Helix ◽  
Soluble Part ◽  
Nuclear Magnetic

ABSTRACT Subunit b, the peripheral stalk of bacterial F1Fo ATP synthases, is composed of a membrane-spanning and a soluble part. The soluble part is divided into tether, dimerization, and δ-binding domains. The first solution structure of b30-82, including the tether region and part of the dimerization domain, has been solved by nuclear magnetic resonance, revealing an α-helix between residues 39 and 72. In the solution structure, b30-82 has a length of 48.07 Å. The surface charge distribution of b30-82 shows one side with a hydrophobic surface pattern, formed by alanine residues. Alanine residues 61, 68, 70, and 72 were replaced by single cysteines in the soluble part of subunit b, b22-156. The cysteines at positions 61, 68, and 72 showed disulfide formation. In contrast, no cross-link could be formed for the A70C mutant. The patterns of disulfide bonding, together with the circular dichroism spectroscopy data, are indicative of an adjacent arrangement of residues 61, 68, and 72 in both α-helices in b22-156.

scholarly journals Carbon 13 Nuclear Magnetic Resonance of Pentapeptides of Glycine Containing Central Residues of Aliphatic Amino Acids

1973 ◽  
Vol 248 (17) ◽  
pp. 6104-6113 ◽  
Author(s):  
Philip Keim ◽  
Robert A. Vigna ◽  
Robert C. Marshall ◽  
Frank R.N. Gurd
Keyword(s):  
Amino Acids ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Nuclear Magnetic
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