Post on 15-Dec-2016
Mechanism of CuA assemblyLuciano A Abriata1,2, Lucia Banci2, Ivano Bertini2,Simone Ciofi-Baffoni2, Petros Gkazonis2,3,Georgios A Spyroulias3, Alejandro J Vila1 & Shenlin Wang2
Copper is essential for proper functioning of cytochromec oxidases, and therefore for cellular respiration in eukaryotesand many bacteria. Here we show that a new periplasmicprotein (PCuAC) selectively inserts Cu(I) ions into subunit II ofThermus thermophilus ba3 oxidase to generate a native CuAsite. The purported metallochaperone Sco1 is unable todeliver copper ions; instead, it works as a thiol-disulfidereductase to maintain the correct oxidation state of theCuA cysteine ligands.
CuA is a dinuclear copper site within the soluble domain of subunit II(Cox2) of bacterial and eukaryotic cytochrome c oxidases (CcOs),whose function is to convey electrons from a soluble cytochrome c tothe catalytic heme a3-CuB center of CcO (refs. 1,2). The properassembly of the CuA site is essential for the catalytic machinery of afunctional oxidase. Several proteins have been identified as keyplayers in the delivery of metal ions to the CuA site3, but thedetailed molecular mechanisms and the specific roles of eachprotein are poorly understood4. In prokaryotes two proteinfamilies have been proposed to be involved in CuA site formation.The first includes proteins that are able to bind Cu(I) throughmethionine and histidine residues arranged in a highly conservedH(M)X10MX21HXM motif 5 (referred to as periplasmic CuA chaper-one (PCuAC) hereafter). The second consists of the Sco proteins,whose mechanism of action in CuA assembly as thioredoxins ormetallochaperones is still debated6. These proteins (PCuAC and Sco)are often found in the same bacterial operon, and most of theidentified operons that encode Sco also contain a gene for Cox2(ref. 7). PCuAC and Sco proteins occur together in the Vibrio choleraebacterium (http://string.embl.de).
The CuA-containing subunit II from Thermus thermophilus ba3
oxidase (Tt CuA hereafter), T. thermophilus PCuAC (Tt PCuAC) andT. thermophilus Sco1 (Tt Sco1), which are all located in the bacterialperiplasm, were expressed as truncated soluble versions in which thetransmembrane helices (and the signal peptide region in Tt PCuAC)were not included, thus resulting in constructs of 136, 172 and 121amino acids, respectively (Supplementary Methods and Supplemen-tary Fig. 1 online).Tt PCuAC binds one equivalent of Cu(I), as also observed for the
homologous protein DR1885 (ref. 5). The Cu(I) binding affinity,measured by competition experiments with DTT followed by
1H-15N HSQC, is (2.2 ± 0.1) � 10�13 M (Supplementary Fig. 2,Supplementary Data and Supplementary Methods online). Uponaddition of Cu(I) up to a 1:1 metal/protein ratio, the most affectedregion includes residues His46, Met61, Met83 and His85 and theneighboring residues (Supplementary Fig. 2), thus defining thecopper binding ligands (similar to the Met3His ligand set found forDR1885 in homologous positions).
Sco proteins, in contrast to the Tt PCuAC protein family, are able tobind both Cu(I) and Cu(II) ions8–10. Cu(I) binding followed by NMRconfirmed the involvement of metal ligands conserved in all Sco1proteins (Cys47, Cys51 and His137) (Supplementary Fig. 2 andSupplementary Data). Apo-Tt Sco1 showed weaker Cu(I) bindingcapabilities compared with its eukaryotic homologs (a lower limit ofB10�10 M was estimated for the Kd of Cu(I)–Tt Sco1). Cu(II)–Tt Sco1presents spectroscopic features resembling those of the human andBacillus subtilis homologs8,10,11 (Supplementary Data and Supple-mentary Fig. 3 online).
The solution structures of apo-Tt PCuAC, Cu(I)–Tt PCuAC andapo-Tt Sco1 were determined using NMR-derived restraints (Supple-mentary Methods). The NMR spectra of apo- and Cu(I)–Tt PCuACvariants show two sets of signals in a 65:35 ratio (SupplementaryFig. 3) for 23 and 24 residues, respectively, which originate from acis-trans isomerization of the Gly13-Pro14 peptide bond. The twostructures resulting from this isomerism in both apo- and Cu(I)–TtPCuAC were obtained (Fig. 1a–d and Supplementary Tables 1 and2 online). The structural differences induced by this isomerization arelocalized in loops 1 and 8 and do not affect Cu(I) binding (Fig. 1a–d).Tt PCuAC is arranged in a cupredoxin-like fold (Fig. 1a–d), exceptthat strands b4 and b5 form an extended, flexible solvent-exposedb-hairpin that is longer than the one reported for the homologousDR1885 protein5. The Cu(I) ion is coordinated in a tetrahedralarrangement to the sulfur atoms of Met61 and Met85, the Nd1atom of His46 and the Ne2 atom of His83 (Fig. 1a,c). The structureof apo-Tt Sco1 in the reduced form adopts the thioredoxin-like foldalready observed for all Sco1 homologs12–16 (Fig. 1e and Supplemen-tary Table 3 online). Loop 8 (which includes the metal ligand His137)adopts an extended conformation in Tt Sco1 (Fig. 1e) resembling thatobserved for the human and yeast proteins, in contrast with theshorter (and less extended) loop 8 present in Bs Sco1. The cysteinemetal ligands are solvent exposed (as in other Sco1 proteins), which isin agreement with the observation of rapid air oxidation.
The availability of the NMR resonance assignments of the apo andthe metallated forms of the two possible copper donors,as well as that of the CuA-containing soluble fragment of theT. thermophilus ba3 oxidase, allowed us to investigate, throughNMR, copper uptake by the CuA fragment. We simultaneouslymonitored the occurrence of copper transfer and the formation of
Received 7 May; accepted 8 August; published online 31 August 2008; doi:10.1038/nchembio.110
1Instituto de Biologıa Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Cientıficas y Tecnicas, Facultad de Ciencias Bioquımicas y Farmaceuticas,Universidad Nacional de Rosario, Suipacha 531, (S2002LRK) Rosario, Argentina. 2Magnetic Resonance Center CERM and Department of Chemistry, University ofFlorence, Scientific Campus, 50019, Sesto Fiorentino, Florence, Italy. 3Department of Pharmacy, University of Patras, Panepistimioupoli-Rion, GR-26504 Patras,Greece. Correspondence should be addressed to I.B. (ivanobertini@cerm.unifi.it).
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the correct metallated form, and also identified the copper donorprotein, by detecting the resulting apo state of the protein that hadtransferred the copper ions. This strategy also allows the identificationof possible transient intermediates.
Addition of Cu(I) to reduced 15N apo-Tt CuA under anaerobic condi-tions gives rise to the fully metallated protein in the reduced state (Sup-plementary Data and Supplementary Fig. 4 online). Exposure of thisspecies to oxygen resulted in the formation of a purple species with thecharacteristic electronic spectrum and 1H NMR signals of the oxidized,mixed-valence CuA center (Supplementary Fig. 4)17. This indicates thatthe CuA center can be formed in vitro without the assistance of anyprotein when the cysteine residues of the CuA center are reduced. Theaffinity of both copper ions in Tt CuA is in the femtomolar range basedon competition studies with DTT (Supplementary Methods) and isthus higher than that of Tt PCuAC and Tt Sco1. However, because Cu(I)is not freely available in the periplasmic space, a Cu(I) chaperone isneeded to deliver two Cu(I) ions to the apo-CuA protein.
We initially explored the possible role of Sco1 as a Cu(I) or Cu(II)donor to apo-CuA. No evidence of copper uptake by the CuA proteinor of metal depletion of Tt Sco1 was observed, which suggests that TtSco1 is not responsible for the direct delivery of Cu(I) or Cu(II) ionsinto apo-Tt CuA.
Genomic studies have suggested that Tt PCuAC homologs could beinvolved in copper transport in the periplasmic space of bacteria5,18,and we decided to test this previously unexplored hypothesis. Whenapo-Tt CuA was added to a solution of 15N Cu(I)–Tt PCuAC, a new setof resonances corresponding to apo-Tt PCuAC was observed (Fig. 2a).A step-wise titration led to the progressive disappearance of the signalscorresponding to Cu(I)–Tt PCuAC, with the concomitant increase ofsignals from the apo form (Fig. 2a). This process was complete at a TtCuA/Tt PCuAC ratio of 1:2 (Fig. 2a). The complementary experimentto characterize the metallated species was performed by adding twoequivalents of unlabeled Cu(I)–Tt PCuAC to 15N apo-Tt CuA, which
led to the typical 1H-15N HSQC pattern of native Cu(I)2–Tt CuA
(Fig. 2b). A step-wise titration disclosed the formation of an inter-mediate species when less than one equivalent of Cu(I)–Tt PCuAC wasadded to the CuA domain (Fig. 2b,c). This species then converted intothe dimetallated Cu(I)2–Tt CuA upon further addition of the donorprotein (Fig. 2c). This intermediate species displayed resonances withchemical shifts differing from those of both the apo- and the fullymetallated species (Fig. 2b), and it did not show any line broadeningwith respect to the other forms of the CuA domain. This behavior,together with the observation that no intermediate was identified bymonitoring the copper release from Cu(I)–Tt PCuAC to apo-Tt CuA,allowed us to rule out the detection of a possible complex between thetwo proteins, and suggested that this intermediate corresponds to asingly metallated CuA species. We conclude that Tt PCuAC is capable oftransferring two Cu(I) ions to the reduced apo-Tt CuA site sequentially,thereby eliciting the formation of the binuclear CuA center in thereduced state (Fig. 2c). Aerobic oxidation of this mixture leads to themixed-valence, oxidized CuA center, as revealed by its characteristicelectronic spectrum (Supplementary Fig. 4).
Sco1 is able to bind Cu(II) ions. The possible direct transfer of Cu(II)ions was explored by following the titration of a sample of 15N-labeledCu(II)–Tt Sco1 with unlabeled apo-Tt CuA. There was no evidence ofthe formation of apo-Tt Sco1 in the 1H-15N HSQC spectra, thusrevealing the inability of this protein to transfer Cu(II) ions to the CuA
domain. When 2 equivalents of unlabeled Cu(I)–Tt PCuAC wereadded to the mixture of 15N-labeled Cu(II)–Tt Sco1 and 15N-labeled
H137C51
C47
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e Figure 1 Solution structures of apo-Tt PCuAC, Cu(I)–Tt PCuAC and apo-Tt
Sco1. (a–d) The trans (a,b) and cis (c,d) conformations resulting from Pro14
isomerization in Tt PCuAC are shown for each protein. The methionine and
histidine residues that bind the metal are shown as purple sticks in Tt
PCuAC. The Cu(I) ion is rendered as a golden sphere. The inset highlights the
metal binding site of Cu(I)–Tt PCuAC. Residues experiencing double confor-
mations in Tt PCuAC as a consequence of cis-trans proline isomerization are
shown in cyan, and those displaying fast backbone motions at 298 K are
shown in red. (e) The metal ligands Cys47, Cys51 and His137 of apo-Tt
Sco1 are shown as purple sticks, and loops 3 and 8 are shown in green.
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Figure 2 Cu(I) transfer reaction between Cu(I)–Tt PCuAC and apo-Tt CuA.
(a) Titration of 15N-labeled Cu(I)–Tt PCuAC with unlabeled apo-Tt CuA
followed by 1H-15N HSQC experiments. In the insets, residues followed to
map the metal exchange reaction are shown. (b) Overlay of the 1H-15N
HSQC spectra of 15N apo-Tt CuA (red), and after addition of one (green) and
two (blue) equivalents of unlabeled Cu(I)–Tt PCuAC. Some residues
indicating the formation of Cu(I)2–Tt CuA and of a partially metallated CuA
species are labeled. (c) Plot showing the relative concentrations of Cu(I)2–Tt
CuA (green), the partially metallated CuA protein (red) and apo-Tt CuA
(black) as a function of the Tt PCuAC/Tt CuA molar ratio. The signals of
residues Cys153 (solid symbols) and Gly162 (open symbols) (whose 1H-15N
chemical shifts substantially change depending on the metallation state of
Tt CuA) have been selected to evaluate the molar fractions of Tt CuA forms.
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apo-Tt CuA, the reduced Cu(I)2–Tt CuA center was formed (Supple-mentary Fig. 5 online). This result indicates that (i) the presence ofCu(II)–Tt Sco1 does not prevent Cu(I)–Tt PCuAC from transferringCu(I), and (ii) as the final product is the reduced Cu(I)2–Tt CuA
center, the mechanism cannot involve the concerted action of bothCu(II)–Tt Sco1 and Cu(I)–Tt PCuAC, which would give rise to amixed-valence, oxidized CuA site.
Sco1, which has already been shown to be essential for copper uploadinto the CuA site in B. subtilis19, is characterized by a thioredoxin-likefold. We therefore investigated the possible thiol-disulfide oxidoreduc-tase activity of Tt Sco1 during copper uptake. Oxidized apo-Tt CuA, inwhich the two cysteine ligands had been aerobically oxidized to forma disulphide bond (ox-apo-Tt CuA hereafter), was not able to bindcopper ions when Cu(I)–Tt PCuAC was added. However, when15N-labeled ox-apo-Tt CuA was titrated with a 2:1 mixture of Cu(I)–Tt PCuAC and reduced apo-Tt Sco1, the backbone resonances ofthe native Cu(I)2–Tt CuA appeared (Fig. 3a). Exposure of thereaction sample to atmospheric oxygen allowed the development ofthe typical UV-vis spectrum of the oxidized, mixed-valence CuA center,which confirmed that the native site had formed. A 4-acetamide-4¢-amleimidylstilbene-2,2¢-disulfonic acid, disodium salt (AMS)-reactedSDS gel of the reaction mixture (run under nonreducing conditions,Supplementary Methods) indicated that, at a Tt CuA/Tt Sco1/TtPCuAC ratio of 1:1:2, Tt Sco1 is mostly in the oxidized state(Fig. 3b). Similarly, in a 1:1 Tt CuA/Tt Sco1 mixture, Tt Sco1 isessentially in an oxidized state, whereas Tt CuA is in a reduced state(Fig. 3b). These experiments show that Tt Sco1 is able to reduce thedisulfide bond of ox-apo-Tt CuA protein, which demonstrates that thisprotein behaves as a thiol-disulfide reductase in in vitro CuA assembly.
Although it is possible that the in vivo pathway is more complex,the structural characterization of Tt PCuAC and of its copper bindingproperties and its ability to selectively and sequentially deliver twoCu(I) ions to apo-Tt CuA, thus giving rise to the native Cu(I)2–Tt CuA
site in vitro, strongly supports the annotation of this protein as aperiplasmic Cu(I) chaperone. Our data also indicate that Tt Sco1 isable to reduce the disulfide bond of the CuA center, thus allowing theCuA site to accept Cu(I) ions from Tt PCuAC. The mechanism ofbacterial CuA assembly therefore consists of a sequential insertion oftwo Cu(I) ions donated by a metallochaperone once the disulfide bondof the CuA center is reduced by a thioredoxin. In eukaryotes theassembly of the CuA site is different, as Scos have a larger affinity forCu(I) and may act as both chaperones and thioredoxins12,20–22.
Note: Supplementary information is available on the Nature Chemical Biology website.
ACKNOWLEDGMENTSThis work was supported by the European Commission (European Network ofResearch Infrastructures for Providing Access and Technological Advancements inBio-NMR contract n1 026145, SPINE2-Complexes contract n1 LSHG-CT-2006-031220 and Marie Curie host fellowships for early stage research training n1MEST-CT-2004-504391, NMR in Inorganic Structural Biology) and by a grantfrom Ente Cassa di Risparmio di Firenze. Work in Rosario (Argentina) wassupported by the US National Institutes of Health (R01-GM068682), the HowardHughes Medical Institute and Agencia Nacional de Promocion Cientıfica yTecnologica (PME2003-0026 and PICT2002-01-11625) grants to A.J.V. L.A.A.thanks Consejo Nacional de Investigaciones Cientıfıcas y Tecnicas for a doctoralfellowship. We thank D. Winge (Departments of Medicine and Biochemistry,University of Utah Health Sciences Center, University of Utah) for kindlyproviding the expression plasmid for Tt Sco1.
AUTHOR CONTRIBUTIONSL.A.A. cloned and expressed Tt Sco1 and Tt CuA proteins and contributed to theNMR structure of Tt Sco1 and NMR titrations; P.G. cloned and expressed PCuACprotein and performed redox experiments; S.W. solved the structures of PCuACand contributed to the NMR titrations and NMR structure of Tt Sco1; S.C.-B.supervised and coordinated the acquisition of NMR data and structures, and theperformance of titration experiments; I.B., L.B., G.A.S. and A.J.V. developed anddirected the project and contributed to the writing. All authors were involved inthe discussion of the biochemical meaning of the experiments.
Published online at http://www.nature.com/naturechemicalbiology/
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Figure 3 Cu(I) transfer from Cu(I)–Tt PCuAC to oxidized apo-Tt CuA in the presence of
reduced apo-Tt Sco1. (a) 1H-15N HSQC overlay of oxidized apo-Tt CuA (red), Cu(I)2–Tt
CuA (blue) and the final mixture of the titration between 15N-labeled oxidized apo-Tt
CuA and unlabeled, reduced apo-Tt Sco1 and Cu(I)–Tt PCuAC in a 1:1:2 ratio, in the absence of DTT (black). (b) Left panel: AMS-reacted, nonreducing SDS
gel of different aliquots from the NMR titration between 15N-labeled oxidized apo-Tt CuA and a 1:2 mixture of unlabeled, reduced apo-Tt Sco1 and Cu(I)–Tt
PCuAC (shown in a). Four steps of the NMR titration are reported. The band of Tt CuA protein at 14.8 kDa is very close to that of Tt PCuAC, which indeed
has a very similar molecular weight (13.2 kDa). Starting materials and the Tt PCuAC and Tt CuA proteins in their different redox states are also reported as a
reference. Right panel: AMS-reacted, nonreducing SDS gel of a protein mixture containing oxidized apo-Tt CuA and reduced apo-Tt Sco1 in a 1:1 ratio. The
proteins in their different redox states are also reported as a reference. Molecular weight markers are shown in first lanes.
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