NTPase

Since the pioneering work of Kleymann et al. (2002), Betz et al. (2002), Baumeister et al. (2007), and Crute et al. (2002), who showed that compounds identified as inhibitors of the helicase-primase enzyme complex could alleviate herpesvirus-induced disease in animal models, the attention of researchers developing antiviral compounds has been drawn more and more towards the virus-encoded helicases, particularly those of Herpes viruses and of RNA viruses such as Hepatitis C Virus (HCV) and SAKS coronavirus (SARS-CoV). Enzyme activity is usually assayed by measuring NTPase activity in the presence of an appropriate nucleic acid co-substrate although, more recently, novel fiuorimetric and luminescence principles have been applied to the measurement of strand unwinding and/or translocation of the protein along the nucleic acid (Frick 2003, 2006). 

In each of the three divisions of life, the most common fold is the P-loop NTPase. Four common folds, namely P-loop NTPases, Triose Phosphate Isomerase (TIM) barrels, ferredoxin-like domains, and Rossmann-fold domains, are see in the top-10 lists for all three divisions (Table IV). 

Fig. 7. Dependence of the relative abundance of the most common folds on the proteome size. Trend lines are shown for the P-loop and PP-loop NTPases.

A metal-nucleotide complex that exhibits low rates of ligand exchange as a result of substituting higher oxidation state metal ions with ionic radii nearly equal to the naturally bound metal ion. Such compounds can be prepared with chromium(III), cobalt(III), and rhodi-um(III) in place of magnesium or calcium ion. Because these exchange-inert complexes can be resolved into their various optically active isomers, they have proven to be powerful mechanistic probes, particularly for kinases, NTPases, and nucleotidyl transferases. In the case of Cr(III) coordination complexes with the two phosphates of ATP or ADP, the second phosphate becomes chiral, and the screw sense must be specified to describe the three-dimensional configuration of atoms. 

In addition to mitochondrial components, four cytosolic factors were characterized that contribute specifically to the maturation of extramitochondrial FeS proteins in S. cerevisiae. Cfdl (Roy et al. 2003) and Nbp35 (Hausmann et al. 2005) are essential soluble P-loop NTPases. They form a complex which acts as a scaffold for the formation of transient FeS clusters (Netz et al. 2007). A WD40 repeat protein named Cial then facilitates the incorporation of preassembled FeS clusters into their target proteins (Balk et al. 2005a), which... 

Hausmann A, Aguilar Netz DJ, Balk J, Pierik AJ, Muhlenhoff U, Lill R (2005) The eukaryotic P loop NTPase NBP35 An essential component of the cytosolic and nuclear iron-sulfur protein assembly machinery. Proc Natl Acad Sci USA 102 3266-3271 Henriquez FL, Richards , Roberts F, McLeod R, Roberts CW (2005) The unusual mitochondrial compartment of Cryptosporidium parvum. Trends Parasitol 21 68-74 Horner DS, Foster PG, Embley TM (2000) Iron hydrogenases and the evolution of anaerobic eukaryotes. Mol Biol Evol 17 1695-1709... 

PFO puruvateiferredoxin oxidoreductase, HCP hybrid cluster protein, PNO pyruvate NADH oxidoreductase, Nbp35 P-loop NTPase, Nar/Narf hydrogenase-like protein, Rli ATP-binding cassette protein... 

The molecular mechanisms underlying the detrimental effects caused by aluminum have yet to be fully understood [31]. The toxicological mechanisms of aluminum in plants or in animals probably involve alterations in many enzyme activities. There is a large number of proteins which requires nucleoside phosphates as substrates or is regulated by nucleoside phosphates, therefore aluminum can potentially interfere with the normal functions of these proteins [18]. Thus, it is important to understand some reactions that involve aluminum and nucleotides. In this review we are going to focus on the alterations caused by this metal in some enzymes that hydrolyze or transfer phosphate groups of nucleotides, like NTPases, NTPDases, and kinases. 

Plumpton M, McGarvey M, Beggs JD. A dominant negative mutation in the conserved RNA helicase motif SAT causes splicing factor PRP2 to stall in spliceosomes. EMBO J. 1994 13 879-887. Kim SH, Smith J, Claude A, Lin RJ. The purified yeast pre-mRNA sphcing factor PRP2 is an RNA-dependent NTPase. EMBO J. 1992 11 2319-2326. 

P-Loop NTPase Domains Are Present in a Range of Important Proteins... 

Figure 9.52. Three Proteins Containing P-Loop NTPase Domains. For the conserved domain, the inner surfaces of the ribbons are purple and the P-loops are green.

Like other members of the P-loop NTPase superfamily, proteins with ABC domains undergo conformational changes on ATP binding and hydrolysis. These structural changes are coupled within each dimeric transporter unit in a manner that allows these membrane proteins to drive the uptake or efflux of specific compounds or to act as gates for open membrane channels. 

Figure 24.3. Fe Protein. This protein is a dimer composed of two polypeptide chains linked by a 4Fe-4S cluster. Each monomer is a member of the P-loop NTPase family and contains an ATP-binding site.

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