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Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues*

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Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues* Lawrence Berkeley National Laboratory Recent Work Title Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues. Permalink https://escholarship.org/uc/item/5xd9v469 Journal The Journal of biological chemistry, 291(17) ISSN 0021-9258 Authors Youngblut, Matthew D Tsai, Chi-Lin Clark, Iain C et al. Publication Date 2016-04-01 DOI 10.1074/jbc.m116.714618 Peer reviewed eScholarship.org Powered by the California Digital Library University of California crossmark THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 291, NO. 17, pp. 9190–9202, April 22, 2016 Published in the U.S.A. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues*□S Received for publication, January 8, 2016, and in revised form, February 19, 2016 Published, JBC Papers in Press, March 3, 2016, DOI 10.1074/jbc.M116.714618 Matthew D. Youngblut‡1, Chi-Lin Tsai§1, Iain C. Clark‡, Hans K. Carlson‡, Adrian P. Maglaqui‡, Phonchien S. Gau-Pan‡, Steven A. Redford‡, Alan Wong‡, John A. Tainer§¶2, and John D. Coates‡ʈ3 From the ‡Energy Biosciences Institute and ʈDepartment of Plant and Microbial Biology, University of California, Berkeley, California 94720, §Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and ¶Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030 Perchlorate is an important ion on both Earth and Mars. Per- recently documented widespread distribution in both terres- chlorate reductase (PcrAB), a specialized member of the dime- trial and extraterrestrial planetary and non-planetary samples thylsulfoxide reductase superfamily, catalyzes the first step of suggests that perchlorate is prevalent throughout our solar sys- microbial perchlorate respiration, but little is known about the tem (1, 2). To date, perchlorate is primarily recognized as a biochemistry, specificity, structure, and mechanism of PcrAB. groundwater contaminant resulting from Cold War munition Here we characterize the biophysics and phylogeny of this manufacturing (3). However, recent studies have additionally enzyme and report the 1.86-A˚ resolution PcrAB complex crystal determined a natural atmospheric source (1, 4). Widespread structure. Biochemical analysis revealed a relatively high per- perchlorate abundance has also been identified on Mars (5–7), ␮ ؍ chlorate affinity (Km 6 M) and a characteristic substrate inhi- on our moon, and in meteorites (2). On Mars, the unique per- bition compared with the highly similar respiratory nitrate chlorate physical chemistry is responsible for maintaining reductase NarGHI, which has a relatively much lower affinity for water in the liquid state regardless of the environmental ؍ perchlorate (Km 1.1 mM) and no substrate inhibition. Struc- extremes (8). Furthermore, Martian perchlorate may represent tural analysis of oxidized and reduced PcrAB with and without a significant energy and oxygen resource for human exploration 2؊ the substrate analog SeO3 bound to the active site identified (9). Although the exact abiotic mechanisms of natural perchlo- key residues in the positively charged and funnel-shaped sub- rate neogenesis are not completely understood, there are no strate access tunnel that gated substrate entrance and product known biogenic mechanisms. In contrast, terrestrial perchlo- release while trapping transiently produced chlorate. The struc- rate diagenesis primarily occurs biologically through microbial tures suggest gating was associated with shifts of a Phe residue respiration (10). between open and closed conformations plus an Asp residue Dissimilatory (per)chlorate-reducing bacteria can use per- carboxylate shift between monodentate and bidentate coordi- chlorate or chlorate (collectively (per)chlorate) as a terminal nation to the active site molybdenum atom. Taken together, electron acceptor during anaerobic respiration (11). Canonical structural and mutational analyses of gate residues suggest key dissimilatory (per)chlorate-reducing bacteria utilize a highly roles of these gate residues for substrate entrance and product conserved pathway that is phylogenetically distributed through release. Our combined results provide the first detailed struc- horizontal gene transfer (3, 12, 13). Perchlorate is sequentially tural insight into the mechanism of biological perchlorate reduced to chlorite by the perchlorate reductase (PcrAB), reduction, a critical component of the chlorine redox cycle on which is then dismutated into chloride and oxygen by the chlo- Earth. rite dismutase (Cld). The biogenic oxygen is respired by the same microorganism, generally through the use of a high affin- ity cytochrome cbb3 oxidase (3). Due to oxygen biogenesis, Perchlorate has recently gained notoriety because of the these unique chemotrophs represent a distinctive metabolic identified environmental prevalence of this exotic ion (1). Its juxtaposition between aerobic and anaerobic metabolisms. Although an impressive body of literature focuses on the bio- * The work on perchlorate and chlorate respiration in the laboratory of J. D. C. chemistry, genetics, and evolution of the Cld, relatively little is was supported by the Energy Biosciences Institute, University of California, Berkeley, and structural studies were supported by National Institute of known about the PcrAB. We have shown that PcrAB is an oxy- Health Project MINOS (Macromolecular INsights Optimized by Scattering) gen-sensitive heterodimeric periplasmic enzyme that catalyzes Grant R01GM105404. The authors declare that they have no conflicts of the 2eϪ reduction of perchlorate to chlorate, which is further interest with the contents of this article. The content is solely the respon- Ϫ sibility of the authors and does not necessarily represent the official views reduced by 2e to form chlorite (3, 14). The catalytic subunit of the National Institutes of Health. PcrA is phylogenetically closely related to the NarG subunit of □S This article contains supplemental Fig. S1 and Table S1. nitrate reductase (15). Both proteins are in the DMSO4 reduc- The atomic coordinates and structure factors (codes 4YDD, 5CH7, 5CHC, and tase superfamily and are strongly associated with intermediate 5E7O) have been deposited in the Protein Data Bank (http://wwpdb.org/). 1 Co-first authors. 2 Supported by a Robert A. Welch Distinguished Chair in Chemistry. 3 To whom correspondence should be addressed: Dept. of Plant and Micro- 4 The abbreviations used are: DMSO, dimethylsulfoxide; [Fe-S], iron-sulfur bial Biology, 271 Koshland Hall, University of California, Berkeley, CA 94720. cluster; [4Fe-4S], four-iron/four-sulfur cluster; [3Fe-4S], three-iron/four-sul- Tel.: 510-643-8455; Fax: 510-642-4995; E-mail: [email protected]. fur cluster; MGD, molybdopterin guanine dinucleotide; Ec, E. coli. This is an Open Access article under the CC BY license. 9190 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 291•NUMBER 17•APRIL 22, 2016 PcrAB Is Specialized for Scarce Perchlorate electron-shuttling protein subunits (PcrB and NarH, respec- trifugal concentrators with 100-kDa-molecular mass-cutoff fil- tively). Given the important and ancient roles of [Fe-S] clusters ters (Amicon) to Ͻ800 ␮l. The concentrated sample was loaded in biology and electron transfer, it is furthermore important to onto a HiPrep Sephacryl S-300 HR 16/60 size exclusion column consider the detailed structural relationships of the five [Fe-S] (GE Healthcare) that was equilibrated with anaerobic buffer C clusters in PcrAB and NarGH. (buffer A with 150 mM NaCl) at a flow rate of 0.25 ml/min. Here we perform an unprecedented structure and function PcrAB typically eluted at 50–60 ml. Fractions shown to be pure characterization of PcrAB. The crystal structures revealed all by SDS-PAGE were pooled and concentrated as described pre- metal ion cofactors along with a novel gating mechanism at the viously to 7 mg/ml, snap frozen in gasketed cryovials with liquid Ϫ active site that evidently endow the enzyme with unique bio- N2, and stored at 80 °C until use. Protein concentrations were physical characteristics. These, in addition to comparative phy- determined via the Bradford assay (Sigma). PcrAB containing logenetic and mutational studies, identified the evolutionary the PcrA W461E mutation was purified in the same manner as basis for this enzyme and revealed the unique and distinguish- wild-type PcrAB. ing features between PcrAB and the closely related NarGH res- Steady-state Kinetics—The cNarGHI from Escherichia coli piratory complex. was a generous gift from the Weiner laboratory (University of Alberta). Activity assays of PcrAB and EccNarGHI were per- Experimental Procedures formed in an anaerobic chamber by monitoring the substrate- Expression and Purification of PcrAB—Cells of wild-type or dependent oxidation of NADH (Sigma) with phenazine metho- mutant Azospira suillum PS were initially grown aerobically sulfate (Sigma) as an electron shuttle (14). 450 ␮M NADH was from single colonies in acetate, lactate, pyruvate growth incubated with 100 ␮M phenazine methosulfate and protein medium (12) in 5-ml cultures and incubated overnight at 37 °C sample in 50 mM MOPS, pH 7.2, and reactions were initiated by at 250 rpm. This culture was then used to inoculate 1 liter of the the addition of substrate. For reactions containing EccNarGHI, same growth medium and incubated at the previously listed the buffer was supplemented with 0.01% (v/v) Thesit detergent conditions. Anaerobic cultures were prepared by adding
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