ATPases substrate recognition

Clapier, C.R., Nightingale, K.P., and Becker, P.B. (2002) A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res. 30, 649-655. 

SWI/SNF, the ATPase subunit SWI2/SNF2 could be cross-linked to the unremodeled nucleosome but not the remodeled nucleosome or to naked DNA, indicating that the ATPase subunit was involved in nucleosome recognition. However, Sthl, the corresponding ATPase of the RSC complex, was not cross linked to either nucleosomal or free DNA, raising questions about whether direct interaction with the ATPase subunit is universally required for substrate recognition. 

Fig. 9.4. Hypothetical reaction cycle for the 26S proteasome. A polyubiquitylated substrate is delivered to a 26S hybrid proteasome in some cases by chaperones such as VCP/p97 (step 1). Substrate is bound by polyubiquitin recognition components within the regulatory complex (RC) until the polypeptide chain is engaged by the ATPases (step 2). As the...

The binding of ubiquitinylated substrates requires the 19S complex of the proteasome, which possesses a ubiquitin binding site and several ATPase sites. It is assumed that the recognition and ATP-dependent unfolding of the substrate protein occurs within the 19S complex. 

In every case, the chaperone substrates for ClpA and ClpX are also substrates for degradation by the respective ClpAP or ClpXP protease. For example, ClpXP degrades MuA, and ClpAP degrades RepA (Levchenko et al., 1995 Wickner et al., 1994). Thus the specificity of protein recognition resides on the ATPase component. 

A number of years ago, one of the first indications that the synthetic polyammonium macrocycles would be able to go beyond simple recognition of anionic substrates was published by Lehn, Mertes, and coworkers in 1983. The excitement surrounding the discovery of this chemistry was that these simple cyclic systems could mimic the naturally occurring ATPases by catalyzing the hydrolysis of ATP at physiological pHs in aqueous solution. The utility of these simple macrocycles can be attributed to several aspects (i) they operate in water, (ii) due to their cyclic nature the hosts are polyprotonated under physiological pH conditions, (iii) one of the reaction pathways involves a covalent intermediate as a result of the presence of an amine nucleophile, and (iv) the rates of reaction are enhanced upon the addition of certain metal ions as seen for the Mg +-dependence of the ATPases. ... 

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