LETTERS

A role for the two-helix finger of the SecA ATPase inprotein translocationKarl J. Erlandson1, Stephanie B. M. Miller1, Yunsun Nam1, Andrew R. Osborne1{, Jochen Zimmer1

& Tom A. Rapoport1

An important step in the biosynthesis of many proteins is theirpartial or complete translocation across the plasma membrane inprokaryotes or the endoplasmic reticulum membrane in eukar-yotes1. In bacteria, secretory proteins are generally translocated aftercompletion of their synthesis by the interaction of the cytoplasmicATPase SecA and a protein-conducting channel formed by the SecYcomplex2. How SecA moves substrates through the SecY channel isunclear. However, a recent structure of a SecA–SecY complex raisesthe possibility that the polypeptide chain is moved by a two-helixfinger domain of SecA that is inserted into the cytoplasmic openingof the SecY channel3. Here we have used disulphide-bridge cross-linking to show that the loop at the tip of the two-helix finger ofEscherichia coli SecA interacts with a polypeptide chain right at theentrance into the SecY pore. Mutagenesis demonstrates that a tyr-osine in the loop is particularly important for translocation, but canbe replaced by some other bulky, hydrophobic residues. We proposethat the two-helix finger of SecA moves a polypeptide chain into theSecY channel with the tyrosine providing the major contact with thesubstrate, a mechanism analogous to that suggested for hexameric,protein-translocating ATPases.

SecA uses the energy of ATP hydrolysis to ‘push’ polypeptidesthrough the SecY channel4. The channel has an hourglass-shaped porethat consists of funnels on the cytoplasmic and external sides of themembrane5,6. The constriction of the pore is located near the middleof the membrane and is formed from a ‘pore ring’ of hydrophobic aminoacids that project their side chains radially inward. A short helix plugs theexternal funnel in the closed state of the channel5 and is displaced duringtranslocation7,8. The channel-interacting SecA ATPase contains twoRecA-like nucleotide-binding domains (NBD1 and NBD2) that bindthe nucleotide at their interface and move relative to one another duringthe ATP hydrolysis cycle. In addition, SecA contains a polypeptide-crosslinking domain (PPXD), a helical wing domain (HWD), and ahelical scaffold domain (HSD)9. In a recent structure of the SecA–SecY complex3, two helices of SecA’s HSD form a ‘two-helix finger’ (alsoreferred to as the intramolecular regulator of ATPase10) that is insertedinto the cytoplasmic funnel of the SecY channel. The loop connectingthe two helices is located right above the SecY pore, suggesting thatit interacts with a polypeptide chain and pushes it into the SecY pore3.

To test these ideas, we first investigated which residues of SecA’s two-helix finger are important for translocation. Because mutations in thisregion compromise translocation10–12, we performed a systematic ana-lysis by changing residues 788–803 individually to alanines. These resi-dues span the carboxy terminus of the first helix of the finger domain(residues 788–791), the entire loop between the helices (residues 792–798), and the amino terminus of the second helix (residues 799–803).The SecA mutants were purified and tested for translocation of thesubstrate proOmpA. In vitro synthesized 35S-labelled proOmpA was

incubated with E. coli SecA, ATP and proteoliposomes containingpurified E. coli SecY complex, and translocation of proOmpA wasdetermined by protease digestion (Fig. 1a; quantification in Fig. 1b).The results show that two residues in the helices are particularly impor-tant for translocation: Leu 791 at the end of the first helix (Fig. 1a, lane 9versus lane 1), which probably interacts with the SecY loop betweentransmembrane (TM) segments 6 and 7 (ref. 3), and Pro 799 at thebeginning of the second helix (lane 23), which may serve to cap thehelix. Glu 802 and Tyr 803 in the second helix are also required for fullactivity (lanes 29 and 31), perhaps because they stabilize the structure ofthe two-helix finger13. Within the loop, the only important residue isTyr 794 (Fig. 1a, lane 15; Fig. 1b). Similar results were obtained withcysteine mutations in the loop region (Supplementary Fig. 1). We thenmutated the tyrosine residue to different amino acids. The transloca-tion rates obtained with purified SecA mutants show that the tyrosinecan be replaced by a few other amino acids with bulky, hydrophobicside chains (Tyr . Phe . Leu > Trp > Met . His . Val), whereas allamino acids with small or charged side chains have very low activity(Fig. 1c). The tyrosine residue is found in 80.3% of all SecA proteins(601 out of 748 SecA proteins listed in the database), but other bulky,hydrophobic residues are occasionally observed (SupplementaryTables 1 and 2; the infrequently found histidines might be unchargedat appropriate pH). Interestingly, 18 listed SecA proteins have small orhydrophilic amino acids at the critical position that would be expectedto cause low translocation activity, but in all but one case (a SecA withan arginine) there is another SecA in the same organism with a con-ventional bulky, hydrophobic residue (Supplementary Table 3). InStreptococcus gordonii, the non-conventional SecA (SecA2) has a threo-nine and cooperates with a specialized SecY channel and other factorsto export just one substrate, a 3,072-residue, serine-rich cell surfaceadhesin that is glycosylated in the cytosol before secretion; the conven-tional SecA1 has a tyrosine and is responsible for the export of all othersubstrates14. A similar situation may apply to other bacteria that containboth a conventional and non-conventional SecA15.

Next we used disulphide crosslinking to investigate whether theloop at the tip of the two-helix finger of SecA interacts with a poly-peptide chain during translocation. Because SecA interacts ratherpromiscuously with polypeptide chains in solution (Y.N. andK.J.E., unpublished results), we developed a strategy that allowedus to study interactions of a truly translocating polypeptide chain.We introduced two cysteines into the substrate proOmpA, one thatwould crosslink to the SecY channel, and another one that wouldcrosslink to SecA (Fig. 2a). Double crosslinks of proOmpA to bothSecY and SecA would indicate interactions of a polypeptide chainthat has engaged both translocation components.

We first determined the positions at which cysteines in proOmpAwould crosslink to a cysteine introduced into the pore ring of E. coli

1Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA. {Present address:Department of Pathology, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, Illinois 60611, USA.

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SecY (position 282). ProOmpA fragments of 206 amino acids, eachcontaining a single cysteine, were synthesized by in vitro translation of atruncated messenger RNA in the presence of 35S-methionine. With nostop codon in the mRNA, the nascent polypeptide chain remainsassociated with the ribosome as peptidyl-transfer RNA, and can bereleased from the ribosome by treatment with urea (proOmpA–tRNA)16. These proOmpA–tRNA substrates were then incubated withE. coli SecA lacking the endogenous cysteines17,18, ATP, and proteoli-posomes containing purified SecY complex. The bulky tRNA at the Cterminus of the substrates prevents their complete translocation intothe vesicles, thus generating translocation intermediates (Fig. 2a)19. Anoxidant was added and the formation of a disulphide bridge wasanalysed by non-reducing SDS–polyacrylamide gel electrophoresis

(PAGE) and autoradiography (Fig. 2b). Crosslinks betweenproOmpA and the pore residue of SecY were only seen in the presenceof ATP, when the polypeptide chain was translocated by SecA into thechannel (Fig. 2b). The strongest crosslinks were seen with cysteines atpositions 186–196 of proOmpA (lanes 1–20; see quantification inFig. 2c); residues that were closer than ten residues from the C terminusgave only weak or no crosslinks, consistent with the idea that the tRNAmoiety prevents the final residues from moving into the pore.

ProOmpA residues not yet translocated into the SecY pore may beexpected to interact with the two-helix finger of SecA, which is locatedright above the pore entrance3 (Fig. 2a). We therefore used aproOmpA–tRNA substrate that contained a cysteine at position 194for crosslinking to the pore position 282 in SecY (see Fig. 2b), and acysteine at position 201 for crosslinking to position 797 near the tip ofthe two-helix finger of SecA. After incubation in the presence or absenceof ATP, disulphide bridge formation was induced with an oxidant.A prominent double crosslink was generated (Fig. 3a, lane 8), inaddition to the single crosslinks to SecY and SecA. The double cross-links to SecY and SecA and the single crosslinks to SecY were dependenton the presence of ATP, whereas crosslinks to SecA were nucleotideindependent (Fig. 3a, lane 8 versus 7), reflecting the promiscuous inter-action of SecA with non-translocating substrate. Double crosslinks toSecY and SecA were not observed when either SecY or SecA lacked acysteine (Fig. 3a, lanes 1–6). The identity of the crosslinked band wasfurther confirmed by immunoprecipitation experiments; the high-molecular-mass band could be precipitated with either SecA or SecYantibodies (Fig. 3b, lanes 6 and 8).

To confirm that the N- and C-terminal cysteines of proOmpAcontact SecY and SecA, respectively, we varied the spacing betweenthe two cysteines in proOmpA (Fig. 3c). As before, we used a SecAmutant with a cysteine at position 797 in the two-helix finger and aSecY mutant with a cysteine at position 282. The proOmpA sub-strates contained a cysteine at position 194 and a second cysteine

a

ATP:Triton:

G788A

I789A

P799A

D798A

K797A

Q796A

Y794A

G793A

R792A

L791

A

H790A

Y803A

E802A

Q801A

K800A

Cys–

Cys–SecA:

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33

pOA30 kDa20 kDa14 kDa

b 2.5

SecA:

G788A

I789A

P799A

D798A

K797A

Q796A

Y794A

G793A

R792A

L791

A

H790A

Y803A

E802A

Q801A

K800A

Cys–

0.5

1.0

1.5

2.0

Tran

sloc

atio

n ac

tivity

(nor

mal

ized

to

Cys

– at

5 m

in)

c

0 0.5 1.0 2.5 5.0

Y

F

VCTQNASRDKPEG

0

0.2

0.4

0.6

0.8

1.0

Tran

sloc

atio

n ac

tivity

(nor

mal

ized

to

Cys

– at

5 m

in)

Incubation time (min)

Amino acid at 794

0

Helix 1 Helix 2Loop

LWMH

+ – + – + – + – + – + – + – + – + – + – + – + – + – + – + – + – ++

Figure 1 | An essential tyrosine at the tip of the two-helix finger. a, Residuesin SecA’s two-helix finger were individually mutated to alanines. Position795 is an alanine in the wild type and cysteine-lacking (Cys2) proteins andtherefore remained unchanged. Residues in the helices and loops areindicated in the scheme on top and loop residues are also highlighted in bold.The mutants were purified and tested for translocation activity byincubation for 5 min at 37 uC in the presence or absence of ATP with in vitrosynthesized 35S-labelled proOmpA (pOA) and proteoliposomes containingpurified SecY complex. After treatment with proteinase K, the samples wereseparated by SDS–PAGE and analysed by autoradiography. The Cys2

mutant served as a positive control. For each mutant, samples were alsotreated with protease in the presence of Triton X-100 to disrupt themembrane (shown here in lane 33 for the Cys2 mutant). b, Quantificationof three experiments performed as in a (mean and standard errors). The datawere normalized with respect to the Cys2 mutant. c, Translocation kineticsof SecA mutants in which Tyr 794 was replaced with other residues (in one-letter amino acid code). Shown are the mean and standard deviation of threeexperiments, normalized to the 5-min data point of the Cys2 mutant, whichhas the wild-type tyrosine (Y) in the loop.

SecA

tRNA

Two-helix finger

CC

CC

Sec

Y

pOA

a c 25

20

15

10

5

0

Cro

sslin

ked

to

Sec

Y (%

)

186 187 188 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206

Cysteine position in pOA

186C

187C

188C

190C

191C

192C

193C

194C

195C

196C

197C

198C

199C

200C

201C

202C

203C

204C

205C

206C

– + – + – + –+ – + – + – + – + – + – + – + – + – + – + – + – + – + – + – + – +

pOA

ATP

45 kDa

30 kDa20 kDa

pOAxSecY

pOA

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40

b

Figure 2 | Contact of a translocation intermediate with the pore of SecY.a, Scheme of the crosslinking strategy. A tRNA-associated fragment of 35S-proOmpA (pOA) was synthesized in vitro and translocated by SecA into theSecY channel. The bulky tRNA prevents complete translocation. Twocysteines (C) were introduced into proOmpA, one for crosslinking to acysteine in the two-helix finger of SecA and one for crosslinking to a cysteinein SecY. b, Translocation substrates (proOmpA–tRNA) of 206 residuescontaining single cysteines at the indicated positions were incubated in theabsence or presence of ATP with a cysteine-free SecA and proteoliposomescontaining purified SecY complex. SecY carried a single cysteine in the porering at position 282. After oxidation with Cu21-phenanthroline, the sampleswere treated with NEM and RNaseA, and analysed by non-reducingSDS–PAGE and autoradiography. The positions of free and crosslinkedproOmpA (pOA and pOAxSecY) are indicated. c, Quantification of threeexperiments performed as in b (mean and standard deviation).

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in a more C-terminal position. The samples were incubated in theabsence or presence of ATP, the membranes were sedimented, anddisulphide bridge formation was induced with an oxidant. Doublecrosslinks were observed when the second cysteine in proOmpA wasplaced at positions 201–205 (Fig. 3c, lanes 7–17), indicating that thefinal residues of proOmpA contact SecA’s two-helix finger. Positionsfurther towards the N terminus did not give double crosslinks (posi-tions 198–200; lanes 1–6), consistent with the expectation that theyhave already passed the two-helix finger of SecA and are locatedfurther inside the SecY channel.

Next, we determined the region of the two-helix finger that contactsthe proOmpA substrate. We placed single cysteines at various positionsin the finger of SecA and used a proOmpA substrate with cysteines atpositions 194 and 201. The most prominent double crosslinks wereobserved with positions 795, 797 and 798 (Fig. 3d, lanes 8, 10 and 12).These positions are located at the tip of the two-helix finger, preciselywhere a polypeptide chain is predicted to pass according to the SecA–SecY structure3. Positions in the two helices, which are further away

from the fingertip, did not give crosslinks (Fig. 3d, lanes 4, 14 and 16).Although some of the SecA mutants translocated proOmpA moreslowly than wild-type SecA (Supplementary Fig. 1), the incubation timewas sufficient to generate translocation intermediates, as indicated bythe appearance of ATP-dependent SecY crosslinks (Fig. 3d). Replace-ment of the tyrosine at the fingertip with cysteine severely compromisedtranslocation (Supplementary Fig. 1), and therefore only weak SecY andno SecY–SecA double crosslinks were observed (Fig. 3d, lane 6).However, because the mutant is not entirely inactive, in some experi-ments weak SecY and double crosslinks were seen (data not shown),indicating that this position also contacts the polypeptide chain. Takentogether, these results indicate that a translocating polypeptide chainpasses from the tip of the two-helix finger into the SecY pore. Becausethe double crosslinks could be generated when the two cysteines inproOmpA were only seven residues apart (Fig. 3c; residues 201 and194), the translocating polypeptide chain must be in an extended con-formation to span the distance of 20–25 A between the fingertip of SecAand the pore ring of SecY. Given that even the most C-terminal residuesof proOmpA can crosslink to the two-helix finger, it seems that most ofthe polypeptide chain has been pushed into the channel.

Our crosslinking experiments show that a translocating polypep-tide chain passes directly from the tip of the two-helix finger into theSecY pore (Fig. 4). The polypeptide chain is probably positionedabove the pore entrance by a clamp generated by the PPXD, theNBD2 and the HSD3 (Fig. 4). We propose that the finger domainmoves up and down during the ATP hydrolysis cycle and pushes thepolypeptide into the SecY channel. The finger could interact with thepolypeptide chain on ATP binding to SecA, and release the chain andreset after ATP hydrolysis. In support of this mechanism, the ADP-bound state of SecA allows a polypeptide chain to slide back into thecytosol20. We propose that the essential tyrosine (or other bulky,hydrophobic residue) in the loop at the tip of the finger domaincontacts and drags the polypeptide chain, probably by interactingwith amino acid side chains in the substrate. In the case of non-conventional SecA proteins (SecA2 proteins), a small or hydrophilicamino acid might make specific contact with special features in theirunique substrates, while at the same time preventing the transport ofordinary substrates. The proposed mechanism of SecA function isanalogous to the one proposed for hexameric RecA-like ATPases,such as ClpX, ClpA, HslU, the 19S subunit of the proteasome,FtsH and p97 (refs 21–25). In these cases, each monomer has a loopwith a conserved tyrosine at its tip (tryptophan or phenylalanine inthe case of p97 and FtsH, respectively), which contacts the polypep-tide and transports it by moving up and down inside the central pore.As in the case of SecA, the aromatic residue in the loop can be

SecY –CysSecY 282CSecA –CysSecA 797C

ATP

220 kDa

97 kDa66 kDa

45 kDa

30 kDa

20 kDa14 kDa

pOAxSecYxSecApOAxSecA

pOAxSecY

pOA

ATP

Input(20%)

Antibodies toSecY SecA–

– + – + – + – +220 kDa

97 kDa

66 kDa

45 kDa

30 kDa

20 kDa

+ + – – + +

+ ++ ++ + + +

+ + + ++ + + +

– –– – – –

– – – –– – – –– – – –

1 2 3 4 5 6 7 8

pOAxSecYxSecA

pOAxSecA

pOAxSecY

pOA

– + – + – + – + – + – + – + – +x1

98C

x199

C

x200

C

x201

C

x202

C

x203

C

x204

C

x205

C

ATP

220 kDa

97 kDa66 kDa

45 kDa

30 kDa

20 kDa1 2 3 4 5 6 7 8 10 11 12 13 14 15 16 17

pOAxSecYxSecApOAxSecA

pOAxSecY

pOA

pOAxSecYxSecApOAxSecA

pOAxSecY

pOA

– + – + – + – + – + – + – + – +–C

ysI78

9CY79

4C

A759C

K797C

D798C

O801C

E802CSecA

ATP

220 kDa

97 kDa66 kDa45 kDa

30 kDa20 kDa

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

a

b

c

d

1 2 3 4 5 6 7 8

pOA 194CFigure 3 | The two-helix finger of SecA interacts with a translocatingsubstrate. a, A translocation substrate (proOmpA–tRNA) of 206 residuescontaining cysteines at positions 194 and 201 was incubated with SecA andproteoliposomes containing SecY complex in the absence or presence ofATP. The SecA proteins either lacked a cysteine or contained a cysteine at thetip of the two-helix finger (position 797). SecY lacked a cysteine or containeda cysteine in the pore ring (position 282). After oxidation with Cu21-phenanthroline, the samples were treated with NEM and RNaseA, andanalysed by non-reducing SDS–PAGE and autoradiography. The positionsof free and crosslinked proOmpA (pOA, pOAxSecY, pOAxSecA andpOAxSecYxSecA) are indicated. b, As in a, but the proteoliposomes weresedimented before addition of the oxidant. SecA contained a cysteine atposition 797. After solubilization in DDM, 20% of each sample was analyseddirectly (lanes 1 and 2), whereas the remainder was incubated with protein Gbeads either without antibody or with SecA or SecY antibodies (lanes 3–8).c, As in a, but the proteoliposomes containing SecY with a cysteine atposition 282 were incubated with a SecA mutant containing a single cysteineat position 797 and proOmpA–tRNA with a cysteine at position 194 and asecond cysteine at the indicated position. The samples were sedimentedbefore addition of the oxidant. d, As in c, but the proteoliposomescontaining SecY with a cysteine at position 282 were incubated withproOmpA–tRNA containing cysteines at positions 194 and 201 and SecAmutants containing single cysteines at the indicated positions.

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changed to other bulky, hydrophobic residues, but not to smallamino acids22,23,26,27. These similarities suggest that polypeptidemovement occurs by a conserved, general mechanism.

METHODS SUMMARYPoint mutants of the N95 fragment of E. coli SecA, which lacks the non-essential

C terminus, were generated by polymerase chain reaction (PCR) mutagenesis.The proteins were C-terminally His-tagged and purified by Ni21-chelating chro-

matography. SecY complexes were purified19 and reconstituted with E. coli polar

lipids into phospholipid vesicles19,28. Cysteine mutants were generated in a

proOmpA fragment that lacked residues 175–296 and all endogenous cysteines.

Fragments of 206 amino acids in length (numbering for the deletion construct)

were synthesized by in vitro translation in rabbit reticulocyte lysate in the pres-

ence of 35S-methionine. The substrates (proOmpA–tRNA) were precipitated

and dissolved in 8 M urea. For crosslinking, proOmpA–tRNA was incubated

for 15 min at 37 uC with SecY reconstituted into proteoliposomes, SecA and

ATP19. In indicated cases, the membranes were sedimented before adding the

oxidant. Oxidation was performed with Cu21-phenanthroline, followed by

N-ethylmaleimide (NEM) and RNaseA treatment. After solubilization in 1%

dodecylmaltoside (DDM), the samples were subjected to non-reducing SDS–

PAGE. For immunoprecipitation, the solubilized samples were incubated with

protein G beads containing pre-bound SecY or SecA antibodies6. Translocation

assays were performed as described20.

Full Methods and any associated references are available in the online version ofthe paper at www.nature.com/nature.

Received 2 June; accepted 19 September 2008.

1. Rapoport, T. A. Protein translocation across the eukaryotic endoplasmicreticulum and bacterial plasma membranes. Nature 450, 663–669 (2007).

2. Brundage, L., Hendrick, J. P., Schiebel, E., Driessen, A. J. M. & Wickner, W. Thepurified E. coli integral membrane protein SecY/E is sufficient for reconstitution ofSecA-dependent precursor protein translocation. Cell 62, 649–657 (1990).

3. Zimmer, J., Nam, Y. & Rapoport, T. A. Structure of a complex of the ATPase SecAand the protein-translocation channel. Nature doi:10.1038/nature07335 (thisissue).

4. Economou, A. & Wickner, W. SecA promotes preprotein translocation byundergoing ATP-driven cycles of membrane insertion and deinsertion. Cell 78,835–843 (1994).

5. van den Berg, B. et al. X-ray structure of a protein-conducting channel. Nature 427,36–44 (2004).

6. Cannon, K. S., Or, E., Clemons, W. M. Jr, Shibata, Y. & Rapoport, T. A. Disulfidebridge formation between SecY and a translocating polypeptide localizes thetranslocation pore to the center of SecY. J. Cell Biol. 169, 219–225 (2005).

7. Harris, C. R. & Silhavy, T. J. Mapping an interface of SecY (PrlA) and SecE (PrlG)by using synthetic phenotypes and in vivo cross-linking. J. Bacteriol. 181,3438–3444 (1999).

8. Tam, P. C., Maillard, A. P., Chan, K. K. & Duong, F. Investigating the SecY plugmovement at the SecYEG translocation channel. EMBO J. 24, 3380–3388 (2005).

9. Hunt, J. F. et al. Nucleotide control of interdomain interactions in theconformational reaction cycle of SecA. Science 297, 2018–2026 (2002).

10. Karamanou, S. et al. A molecular switch in SecA protein couples ATP hydrolysis toprotein translocation. Mol. Microbiol. 34, 1133–1145 (1999).

11. Jarosik, G. P. & Oliver, D. B. Isolation and analysis of dominant secA mutations inEscherichia coli. J. Bacteriol. 173, 860–868 (1991).

12. Vrontou, E., Karamanou, S., Baud, C., Sianidis, G. & Economou, A. Global co-ordination of protein translocation by the SecA IRA1 switch. J. Biol. Chem. 279,22490–22497 (2004).

13. Osborne, A. R., Clemons, W. M. Jr & Rapoport, T. A. A large conformationalchange of the translocation ATPase SecA. Proc. Natl Acad. Sci. USA 101,10937–10942 (2004).

14. Bensing, B. A., Takamatsu, D. & Sullam, P. M. Determinants of the streptococcalsurface glycoprotein GspB that facilitate export by the accessory Sec system. Mol.Microbiol. 58, 1468–1481 (2005).

15. Siboo, I. R., Chaffin, D. O., Rubens, C. E. & Sullam, P. M. Characterization of theaccessory Sec system of Staphylococcus aureus. J. Bacteriol. 190, 6188–6196(2008).

16. Matlack, K. E. S., Plath, K., Misselwitz, B. & Rapoport, T. A. Protein transport bypurified yeast Sec complex and Kar2p without membranes. Science 277, 938–941(1997).

17. Matsuyama, S., Kimura, E. & Mizushima, S. Complementation of two overlappingfragments of SecA, a protein translocation ATPase of Escherichia coli, allows ATPbinding to its amino-terminal region. J. Biol. Chem. 265, 8760–8765 (1990).

18. Or, E., Navon, A. & Rapoport, T. Dissociation of the dimeric SecA ATPase duringprotein translocation across the bacterial membrane. EMBO J. 21, 4470–4479(2002).

19. Osborne, A. R. & Rapoport, T. A. Protein translocation is mediated by oligomers ofthe SecY complex with one SecY copy forming the channel. Cell 129, 97–110(2007).

20. Erlandson, K. J., Or, E., Osborne, A. R. & Rapoport, T. A. Analysis of polypeptidemovement in the SecY channel during SecA-mediated protein translocation. J.Biol. Chem. 283, 15709–15715 (2008).

21. Wang, J. et al. Crystal structures of the HslVU peptidase-ATPase complex revealan ATP-dependent proteolysis mechanism. Structure 9, 177–184 (2001).

22. Siddiqui, S. M., Sauer, R. T. & Baker, T. A. Role of the processing pore of the ClpXAAA1 ATPase in the recognition and engagement of specific protein substrates.Genes Dev. 18, 369–374 (2004).

23. Hinnerwisch, J., Fenton, W. A., Furtak, K. J., Farr, G. W. & Horwich, A. L. Loops inthe central channel of ClpA chaperone mediate protein binding, unfolding, andtranslocation. Cell 121, 1029–1041 (2005).

24. DeLaBarre, B., Christianson, J. C., Kopito, R. R. & Brunger, A. T. Central poreresidues mediate the p97/VCP activity required for ERAD. Mol. Cell 22, 451–462(2006).

25. Martin, A., Baker, T. A. & Sauer, R. T. Diverse pore loops of the AAA1 ClpXmachine mediate unassisted and adaptor-dependent recognition of ssrA-taggedsubstrates. Mol. Cell 29, 441–450 (2008).

26. Yamada-Inagawa, T., Okuno, T., Karata, K., Yamanaka, K. & Ogura, T. Conservedpore residues in the AAA protease FtsH are important for proteolysis and itscoupling to ATP hydrolysis. J. Biol. Chem. 278, 50182–50187 (2003).

27. Park, E. et al. Role of the GYVG pore motif of HslU ATPase in protein unfolding andtranslocation for degradation by HslV peptidase. J. Biol. Chem. 280,22892–22898 (2005).

28. Collinson, I. et al. Projection structure and oligomeric properties of a bacterial coreprotein translocase. EMBO J. 20, 2462–2471 (2001).

Supplementary Information is linked to the online version of the paper atwww.nature.com/nature.

Acknowledgements We thank B. DeLaBarre and B. Burton for critical reading of themanuscript, and R. Sauer, T. Baker and A. Horwich for discussion. The work wassupported by an NIH grant. T.A.R. is a HHMI investigator. Y.N. was supported bythe Damon Runyon Cancer Research Foundation (DRG 1953-07).

Author Information Reprints and permissions information is available atwww.nature.com/reprints. Correspondence and requests for materials should beaddressed to T.A.R. (tom_rapoport@hms.harvard.edu).

SecA

SecE

SecY

SecG

794795

282

798797

Figure 4 | Model of SecA translocating a polypeptide into the SecYchannel. A segment of a translocation substrate was modelled in orange inthe Thermotoga maritima SecA–SecY complex structure (TM2b andresidues 72–76 were removed for clarity)3. The segment from the tip of thetwo-helix finger of SecA to the pore ring of SecY is shown as a solid line; theother segments as broken lines. Translocating proOmpA containing twocysteines could be double-crosslinked to position 282 of SecY (yellow) and toSecA positions in blue at the tip of the two-helix finger (brown). Theessential tyrosine in the loop between the two helices is shown in red. SecY isshown as a space-filling model and SecA as a cartoon. The numberscorrespond to the positions in E. coli SecA and SecY. The membraneboundaries are indicated.

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©2008 Macmillan Publishers Limited. All rights reserved

METHODSMutagenesis and protein purification. Point mutants of E. coli SecA were

generated by using the cysteine-lacking N95 fragment with a C-terminal His

tag (pET30b, Novagen) as the template for QuickChange (Stratagene) site-direc-

ted mutagenesis. SecA expression in BL21 (DE3) cells was induced with 1 mM

isopropyl-b-D-thiogalactoside for 3 h at 37 uC. The proteins were purified with a

Ni21-chelating column, and dialysed against 50 mM Tris, pH 7.5, 100 mM NaCl,

and 5 mM dithiothreitol (DTT)13. SecY complexes were purified as before19 and

reconstituted with E. coli polar lipids into phospholipid vesicles, as described19,28.

All endogenous cysteines of proOmpA were mutated and an internal fragmentencoding residues 175–296 was deleted. For crosslinking, a fragment of 206 amino

acids in length (numbering for the deletion construct) was generated by PCR with

a 59 primer containing the SP6 promoter sequence and a 39 primer lacking a stop

codon. After in vitro transcription, proOmpA fragments were translated in rabbit

reticulocyte lysate in the presence of 35S-methionine (Perkin Elmer). The proteins

were precipitated with three volumes of 80% saturated ammonium sulphate

(pH 7.5), pelleted at 22,000g for 15 min, and resuspended in the original volume

with 8 M urea buffered with 50 mM HEPES/KOH, pH 7.0.

Crosslinking. Crosslinking was performed in 25ml reactions containing 50 mM

HEPES/KOH, pH 7.5, 50 mM KCl, 5 mM MgCl2, 0.5 mg ml21 BSA and 2.5 mM

ATP in the presence of 27 mg ml21 of SecY proteoliposomes, 40 mg ml21 of SecA

and 1ml of proOmpA–tRNA19. The samples were incubated for 15 min at 37 uCto form a translocation intermediate. For the indicated double-crosslinking

experiments, the membranes were sedimented in an Eppendorf microcentrifuge

for 15 min at 14,000 r.p.m. at 4 uC. Crosslinking was performed with 50 mM

Cu21-phenanthroline for 10 min at 37 uC, and the samples were treated with

NEM and RNaseA and solubilized in 1% DDM. After centrifugation for 3 min at

14,000 r.p.m. at room temperature, SDS sample buffer was added and the sam-ples were subjected to SDS–PAGE in 4–20% Tris-HCl gels (Bio-Rad). For immu-

noprecipitation, the DDM-solubilized samples were mixed with 20 ml of protein-

G-agarose beads pre-bound to SecY or SecA antibodies6. Bound material was

eluted in sample buffer.

Translocation assays. A proOmpA fragment, lacking both endogenous cysteines

and an internal fragment encoding residues 175–296 but containing the natural

stop codon, was synthesized in vitro. The substrate was precipitated by ammo-

nium sulphate and dissolved in urea. Translocation assays of 50 ml contained

50 mM Tris-HCl, pH 7.9, 50 mM KCl, 50 mM NaCl, 2.5 mM ATP, 5 mM MgCl2,

1 mM DTT, 0.1 mg ml21 BSA, 20mg ml21 SecA, 36 mg ml21 SecY proteolipo-

somes and 1ml of proOmpA. For the experiments in the absence of ATP,

22 mg ml21 hexokinase and 20 mM glucose were added. After incubation for

different time periods at 37 uC, the samples were incubated with 0.1 mg ml21

proteinase K for 40 min on ice. The samples were treated with 2 mM phenyl-

methanesulphonyl fluoride and precipitated with 10% trichloroacetic acid

before SDS–PAGE.

doi:10.1038/nature07439

©2008 Macmillan Publishers Limited. All rights reserved