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Reca-Like Motor Atpases—Lessons from Structures

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Reca-Like Motor Atpases—Lessons from Structures View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1659 (2004) 1–18 http://www.elsevier.com/locate/bba Review RecA-like motor ATPases—lessons from structures Jiqing Yea,1, Andrew R. Osbornea,1, Michael Grollb, Tom A. Rapoporta,* a Department of Cell Biology, Harvard Medical School, HHMI, 240 Longwood Ave., LHRRB 613, Boston, MA 02115, USA b Institut fuer Physiologische Chemie, Ludwig Maximilians Universitaet Muenchen, Butenandtstr. 5, Haus B, 81377 Muenchen, Germany Received 5 March 2004; received in revised form 15 June 2004; accepted 16 June 2004 Available online 6 July 2004 Abstract A large class of ATPases contains a RecA-like structural domain and uses the energy of nucleotide binding and hydrolysis to perform mechanical work, for example, to move polypeptides or nucleic acids. These ATPases include helicases, ABC transporters, clamp loaders, and proteases. The functional units of the ATPases contain different numbers of RecA-like domains, but the nucleotide is always bound at the interface between two adjacent RecA-like folds and the two domains move relative to one another during the ATPase cycle. The structures determined for different RecA-like motor ATPases begin to reveal how they move macromolecules. D 2004 Elsevier B.V. All rights reserved. Keywords: ATPase; RecA; Structure; Motor protein; Oligomerization 1. Introduction example, a hexameric ring of ATPases is located at the base of the 19S regulatory subunit of the proteosome and moves Many ATPases that use the energy of nucleotide binding polypeptides into the 20S proteolytic subunit. Similarly, in and hydrolysis for mechanical work have a common struc- bacteria, the ATPase rings of ClpA or HslU (ClpY) move tural domain first seen in RecA, an E. coli protein involved polypeptides into the proteolytic chambers formed by ClpP in DNA recombination [1]. A large number of these or HslV (ClpQ), respectively. The list includes SecA, an enzymes move macromolecules or move along macromole- ATPase that transports polypeptides across the bacterial cules; in both situations, the ATPase is moving relative to membrane, the ABC transporter PrtD that exports metal- the macromolecule with either the former or the latter being loproteases from Erwinia chrysanthemi,andTrwB,an stationary. Classic molecular motors, such as myosin or ATPase that moves DNA across the bacterial membrane kinesin, move along a polymeric filament formed from during conjugation. We have also listed several examples actin or tubulin, but—with the exception of dynein—the for which the movement of macromolecules is more spec- RecA-like motor ATPases use nonfilamentous polypeptide ulative. For example, the disassembly of protein aggregates chains or nucleic acid strands as substrates. Some RecA-like by Hsp104 might occur by moving a polypeptide chain ATPases perform just a single round of mechanical work, through the central pore of the hexameric ring of the ATPase e.g., they ‘‘pull’’ on a protein or ‘‘pry’’ apart an oligomeric and releasing it on the other side of the ring in an unfolded assembly of proteins. conformation. The ATPase p97 may ‘‘pull’’ proteins out of Several prominent members of the RecA-like motor the endoplasmic reticulum membrane and move them into ATPases are listed in Table 1. The list contains several the cytosol. The list contains F1 ATPase, which differs from proteases with associated ATPases that move a polypeptide all other examples by being a rotary motor; the g-subunit substrate into a proteolytic chamber for degradation. For rotates in the central pore of the hexameric arrangement, either generating ATP from a trans-membrane proton gra- dient, or vice versa, generating a proton gradient from ATP * Corresponding author. Tel.: +1-617-432-0676; fax: +1-617-432-1190. hydrolysis. Another special case is dynein, a molecular E-mail address: [email protected] (T.A. Rapoport). motor that moves cargo along microtubules. We also include 1 These authors contributed equally to this work. the clamp loader, an ATPase that opens a dimeric protein 0005-2728/$ - see front matter D 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.bbabio.2004.06.003 2 J. Ye et al. / Biochimica et Biophysica Acta 1659 (2004) 1–18 Table 1 Table 1 (continued) RecA-like motor ATPase ATPase Subfamily Function ATPase Subfamily Function FtsH AAA protease, [100,101] Dimera retrotranslocation PcrA Helicase DNA helicase [6] of membrane superfamily I proteins Rep Helicase DNA helicase [84] HslU(ClpY) AAA + protein [18,19] superfamily I unfolding and SecA Helicase protein [8,9] translocation superfamily II translocation Dyneinb AAA + microtubule [72] HCV NS3 Helicase RNA helicase [7,85,86] associated motor superfamily II Cdc6/Cdc18c AAA + assembly of [102] RecG Helicase DNA helicase [87] prereplication superfamily II complex UvrB Helicase DNA helicase [88–90] SV40 Large Helicase DNA helicase [50] superfamily II T antigen superfamily III T7 gp4 Helicase DNA helicase [15,16] ABC dimer superfamily III Rad50 ABC family involved in [10] RepA Helicase DNA helicase [49] double superfamily III strand break RuvB Helicase DNA branch [103] repair superfamily III migration MalK ABC family Maltose importer [38,91] MutS ABC family mismatch repair [92–95] Dodecamer MJ1267 ABC family branched-chain [48] P97 AAA membrane fusion, [25,26] amino acid ER protein importer degradation MJ0796 ABC family Unknown [11] NSF AAA membrane fusion [54] SMC ABC family sister chromatid [96] ClpA AAA + protein unfolding [28] cohesion, and translocation chromosome into the ClpP condensation proteolytic chamber MsbA ABC family multiple drug [56,57] ClpB AAA + protein unfolding [30] exporter, Hsp104b AAA + protein chaperone lipid flippase a Two RecA domains in one polypeptide chain. BtuCD ABC family Vitamin B [45] b X-ray structure unknown. importer c Oligomerization state unclear. TAP ABC family antigen peptide [47] presentation HlyB ABC family RTX-toxin [46] ring, the clamp, for DNA to enter; the clamp subsequently translocation slides along the DNA, allowing the bound replicative b PrtD ABC family metalloprotease polymerase to be processive over long distances. The table translocation also contains several helicases that move along nucleic acid Pentamer strands and displace a second strand, thereby unwinding Clamp loader AAA + Loads clamp [12,97] base-paired duplexes. A special case is Rho transcription onto DNA terminator, an RNA/DNA helicase that loads onto mRNA, translocates to the site of transcription, and disengages the Hexamer F1-ATPase F- and V-type proton gradient [13,31,61] polymerase. The list of RecA-like motor ATPases is much ATPase/Rho formation longer than shown in Table 1, and in many cases the Rho F- and V-type Transcriptional [17] functions of the ATPases remain unclear. ATPase/Rho termination, RNA helicase 19S regulatory AAA translocation of subunitb protein into 2. The RecA-like core structure the proteosome chamber At the primary sequence level, the RecA-like motor TrwB AAA translocation [14] ATPases belong to different classes of P-loop ATPases. of DNA These include the AAA+ family (which contains the sub- across membranes HP0525 AAA translocation of [98,99] family AAA), the ABC family, and helicase superfamilies I, DNA across II, and III (Table 1) [2,3]. The overall sequence similarity membranes between proteins with the same RecA-like fold is low, confined to short sequence motifs that make up the ATPase site. J. Ye et al. / Biochimica et Biophysica Acta 1659 (2004) 1–18 3 The RecA-like fold is characterized by a central h- aspartate, polarizes the attacking water molecule. The posi- sheet (the strand order in RecA is 51432) flanked by a- tion of important residues can be seen in the structure of F1 helices (Fig. 1A) [1,4]. A highly conserved sequence ATPase bound to ADP:AlF4 which may represent the motif (A/GxxxxGKT/S, where x is any amino acid) is transition state or a state shortly thereafter (Fig. 2B and C) located at the tip of the h1-strand, between h1 and the [31]. The conserved lysine in the Walker A motif (h Lys162) following a-helix (shown in red), and is called the P-loop and an arginine from a neighboring subunit (a Arg373) (phosphate loop) or Walker A motif. It is responsible for interact with the h- and g-phosphate groups. The attacking coordination of the g-phosphate of ATP during the hy- water is polarized by a glutamic acid residue (h Glu188) drolysis reaction (see below). The less conserved Walker which, in contrast to most other ATPases, is not located in the B motif (ffffDE, where f is a hydrophobic residue) is Walker B motif but at the tip of a neighboring h-strand. An located in the h3-strand (in blue) [5]. It coordinates the Mg2+ ion also participates in the stabilization of the transi- magnesium ion and activates the attacking water molecule tion state. It is coordinated by negatively charged residues at (see below). Other conserved motifs are discussed in the the end of the Walker B strand (h3), and by the side chain following sections. hydroxyl group of the Thr/Ser residue in the Walker A motif. Fig. 1B shows an alignment of the structures of several Ala158 has also been implicated in stabilizing the transition members of the RecA-like motor ATPases with the core state [32]. structure of RecA (the left figures show the alignment, the In all RecA-like motor ATPases, the nucleotide is right ones the localization of the RecA-like domains in the bound primarily to one RecA-like domain, with the respective complete molecules). The comparison shows that phosphates always positioned in a similar manner by the the h-sheet and the loops in the active site are highly Walker A motif. However, hydrolysis requires residues conserved, whereas the a-helices on the outside show larger from a neighboring RecA-like domain, explaining why the deviations.
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