Kinetic studies on turtle pancreatic ribonuclease: a comparative study of the base specificities of the B2 and P0 sites of bovine pancreatic ribonuclease A and turtle pancreatic ribonuclease

Katoh, Hideo; Yoshinaga, Makkiko; Yanagita, Tamami; Ohgi, Kazuko; Irie, Masachika; Beintema, Jaap J.; Meinsma, Durk

doi:10.1016/0167-4838(86)90085-3

Cited by 32 publications

(26 citation statements)

References 17 publications

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“…One option that was explored in a study on RNase A (Beach et al 2005) reported by the Loria laboratory was to use a small unreactive molecule that mimics the contacts that are expected in the Michaelis complex. RNase A primarily catalyzes the cleavage of single stranded RNA between purines and pyrimidines (Katoh et al 1986). Determination of a x-ray structure (at 2·0 Å) of a complex between RNase A and the dinucleotide 5′-phosphotymidine (3′−5′) pyrophosphate adenosine 3′-phosphate (pTppAp) (Russo & Shapiro, 1999) established that this small molecule is a relevant mimic of the Michaelis complex for RNase A catalysis.…”

Section: Rnase Amentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

142

122

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Abstract. It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.

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Section: Rnase Amentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

142

122

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“…One sialic acid binds at a site very near to the active site, mainly by hydrogen bonds (site I), and the other near a loop consisting of amino acid residues 64 to 78 (RNase A numbering) via hydrophobic interactions (site II). The binding of the latter sialic acid was very weak as judged from the strate specificities have been performed on three frog RNases (RC liv., cSBL and jSBL) [27] and onconase [28], as well as on chicken RNase CL2 [5], turtle RNase [29] and iguana RNase [6]. Kinetic studies on the base specificities of three frog RNases (RC Liv., cSBL and jSBL) with eight dinucleoside phosphates showed that frog RNases are uracil-preferential RNases, since the rates of hydrolysis of the dinucleosdie phosphate UpX consistently exceeded that of CpX (X =A, G, U and C).…”

Section: Three-dimensional Structures Of Onconase and Csblmentioning

confidence: 99%

“…Experiments on iguana RNase with UpA, CpA, uridylic acid (cUMP) and cytidylic acid (cCMP) indicated that iguana RNase is also a uracil-preferential enzyme [6]. Separate experiments performed for turtle and chicken RNases indicated that both are essentially cytosine base-preferential, like RNase A (C preference) [5,29]. As regards the B 1 base recognition site of frog RNases, Thr45 is well conserved, and Phe120 is also conserved or replaced by Tyr (turtle) or Leu (chicken).…”

Section: Three-dimensional Structures Of Onconase and Csblmentioning

confidence: 99%

“…However, detailed studies of sub- 3c). In terms of B 2 site preferences in chicken RNase CL2 [5] and turtle RNase [29], guanine is preferred rather than adenine, as is the case in RNase A. Glu111 is substituted for Leu (chicken) and Val (turtle) in these RNases. Therefore, shortening of the loop around Asn71 might at least in part be responsible for the guanine preference of frog RNases.…”

Section: Base Specificity Of Frog Rnase In Comparison To Rnase Amentioning

confidence: 99%

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Biochemistry of frog ribonucleases

Irie

Nitta

Nonaka

1998

Cellular and Molecular Life Sciences (CMLS)

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Frogs have unique pyrimidine base-specific RNases, with structures similar to those of turtle, iguana and chicken RNases. Among the four frog RNases discussed here, three from Rana pipiens, R. catesbeiana and R. japonica oocyte cells show antitumour activity, and the latter two show lectin activity towards sialic acid-rich glycoproteins. In this review, (i) we compare their unique primary structures with respect to the locations of their disulphide bridges, three-dimensional structure, base specificity and heat stability as compared with RNase A, and (ii) we summarize current knowledge about the mode of action of lectin and the antitumour activities of the three frog RNases.

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“…, and RNaseA can cleave its preferred dinucleotide sequence even faster, from 15.2 to 675 s Ϫ1 , depending on the source of the enzyme (1,2). Site-specific hydrolytic cleavage of RNA by the RNA subunit of Bacillus RNaseP or the Tetrahymena self-splicing group I intron has been observed (3) or calculated (4) to be fast, in the range of 6 s Ϫ1 .…”

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confidence: 99%

Exceptionally fast self-cleavage by a Neurospora Varkud satellite ribozyme

Zamel

Poon

Jaikaran

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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Most of the small ribozymes, including those that have been investigated as potential therapeutic agents, appear to be rather poor catalysts. These RNAs use an internal phosphoester transfer mechanism to catalyze site-specific RNA cleavage with apparent cleavage rate constants typically <2 min ؊1 . We have identified variants of one of these, the Neurospora Varkud satellite ribozyme, that self-cleaves with experimentally measured apparent rate constants of up to 10 s ؊1 (600 min ؊1 ), Ϸ2 orders of magnitude faster than any previously characterized self-cleaving RNA. We describe structural features of the cleavage site loop and an adjacent helix that affect the apparent rate constants for cleavage and ligation and the equilibrium between them. These data show that the phosphoester transfer ribozymes can catalyze reactions with rate constants much larger than previously appreciated and in the range of those of protein enzymes that perform similar reactions. S equence-or structure-specific cleavage of RNA phosphodiester bonds by many protein enzymes is quite rapid: for example, ribonuclease III cleaves its target RNA structure with an apparent rate constant (k obs ) of 6.4 s Ϫ1, and RNaseA can cleave its preferred dinucleotide sequence even faster, from 15.2 to 675 s Ϫ1 , depending on the source of the enzyme (1, 2). Site-specific hydrolytic cleavage of RNA by the RNA subunit of Bacillus RNaseP or the Tetrahymena self-splicing group I intron has been observed (3) or calculated (4) to be fast, in the range of 6 s Ϫ1 . A rate constant of Ϸ10 s Ϫ1was measured for a ligase ribozyme obtained by in vitro selection to catalyze the attack of a 3Ј hydroxyl on a 5Ј triphosphate (5).In contrast, most ribozymes appear to be rather poor catalysts. The ''small ribozymes,'' comprising the naturally occurring hammerhead, hairpin, hepatitis delta virus, and Neurospora Varkud satellite (VS) ribozymes, catalyze a transesterification reaction, yielding cleavage products with 2Ј3Ј cyclic phosphate and 5Ј hydroxyl termini like those produced by many protein ribonucleases. The vast majority of ribozymes selected in vitro to cleave RNA phosphodiester bonds also use this same phosphoester transfer chemistry and, like their natural counterparts, have cleavage rate constants of ϽϷ2 min Ϫ1 (0.033 s Ϫ1 ) (6, 7). A variety of enzymological considerations that affect ribozyme reaction rates have been discussed (8), and it has been recently proposed that chemical principles may limit the rates of certain small ribozymes (9, 10).The VS ribozyme is found in RNA transcripts of a plasmid in the mitochondria of certain natural isolates of the fungus Neurospora (11). It catalyzes site-specific cleavage and ligation reactions, similar to those performed by hammerhead, hairpin, and hepatitis delta virus ribozymes that are involved in the replication of the RNAs that contain the ribozyme (reviewed in refs. 12 and 13). Cleavage in VS RNA occurs after nucleotide G620 in an internal loop between helices Ia and Ib (Fig. 1B) (14). Biophysical, crosslinking, mu...

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Kinetic studies on turtle pancreatic ribonuclease: a comparative study of the base specificities of the B2 and P0 sites of bovine pancreatic ribonuclease A and turtle pancreatic ribonuclease

Cited by 32 publications

References 17 publications

Protein dynamics and function from solution state NMR spectroscopy

Protein dynamics and function from solution state NMR spectroscopy

Biochemistry of frog ribonucleases

Exceptionally fast self-cleavage by a Neurospora Varkud satellite ribozyme

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