Crystal Structure of Adenylylsulfate Reductase fromDesulfovibrio gigasSuggests a Potential Self-Regulation Mechanism Involving the C Terminus of the β-Subunit

Abstract

Adenylylsulfate reductase (adenosine 5-phosphosulfate [APS] reductase [APSR]) plays a key role in catalyzing APS to sulfite in dissimilatory sulfate reduction. Here, we report the crystal structure of APSR from Desulfovibrio gigas at 3.1-Å resolution. Different from the ␣ 2 ␤ 2 -heterotetramer of the Archaeoglobus fulgidus, the overall structure of APSR from D. gigas comprises six ␣␤-heterodimers that form a hexameric structure. The flavin adenine dinucleotide is noncovalently attached to the ␣-subunit, and two gigas and A. fulgidus shows the largest differences toward the C termini of the ␤-subunits, and structural comparison reveals notable differences at the C termini, activity sites, and other regions. The disulfide comprising Cys156 to Cys162 stabilizes the C-terminal loop of the ␤-subunit and is crucial for oligomerization. Dynamic light scattering and ultracentrifugation measurements reveal multiple forms of APSR upon the addition of AMP, indicating that AMP binding dissociates the inactive hexamer into functional dimers, presumably by switching the C terminus of the ␤-subunit away from the active site. The crystal structure of APSR, together with its oligomerization properties, suggests that APSR from sulfatereducing bacteria might self-regulate its activity through the C terminus of the ␤-subunit.Sulfate-reducing bacteria (SRB) are a special group of prokaryotes that are found in sulfate-rich environments because of their ability to metabolize sulfate. SRB use sulfate as the final electron acceptor in various anaerobic environments, such as soil, oil fields, the sea, or the innards of animals or even human beings (10,11,19,25,33). Their ability to degrade sulfate offers protection against environmental pollution. SRB can remove sulfate and toxic heavy atoms from factory waste waters (12). The Desulfovibrio species is a much-studied representative of SRB, and Desulfovibrio gigas has been studied under many diverse conditions to elucidate metabolic pathways (23,35).Sulfate reduction is one of the oldest forms of cellular metabolism. The reduction can be either assimilatory or dissimilatory. Sulfate is the terminal electron acceptor in dissimilatory reduction and the raw material for the biosynthesis of cysteine in assimilatory reduction. The latter type of reduction occurs in archaebacteria, bacteria, fungi, and plants via various pathways (17). For example, in Escherichia coli, the reduction initially catalyzes sulfate to adenosine 5Ј-phosphosulfate (APS) by ATP sulfurylase. APS is then phosphorylated by APS kinase to 3Ј-phosphate APS, which is then further reduced to sulfite by 3Ј-phosphate APS reductase (APSR). Finally, sulfite is reduced by sulfite reductase to sulfide, which condenses with O-acetylserine by O-acetylserine lyase to form cysteine. For comparison, in dissimilatory sulfate reduction, sulfate is first catalyzed by ATP sulfurylase to APS, which is then directly reduced by APSR to sulfite. Sulfite is subsequently reduced by dissimilatory sulfite reductase to the following three possible pro...

The Sulfate-Rich and Extreme Saline Sediment of the Ephemeral Tirez Lagoon: A Biotope for Acetoclastic Sulfate-Reducing Bacteria and Hydrogenotrophic Methanogenic Archaea

“…We defined two regions of unambiguously aligned aa, the first one located in the N-terminal domain (137 aas) for the α subunit of AprA (AprA_alpha_N), and the second one located in the C-terminal domain (139 aas) of the α subunit of McrA (MrcA_alpha_C), both of them containing some of the catalytic sites involved in their metabolic role (supplementary material, Figures S2 and S3, resp.). It is important to note that not only the phylogenetic topologies obtained for the AprA_alpha_N and McrA_alpha_C sequences are robust, as can be seen by the significant bootstrap values in the main clustering branches, but also the internal groups are supported by the expected clustering of the McrA and AprA crystals previously characterized for (a) the McrA in Methanosarcina barkeri belonging to Methanosarcinales [ 50 ], Methanothermobacter thermoautotrophicus from Methanobacteriales [ 51 ] and Methanopyrus kandleri in Methanopyrales [ 52 ]; (b) the AprA from Archaeoglobus fulgidus in Euryarchaeota [ 16 ], and Desulfovibrio gigas in Deltaproteobacteria [ 49 ].…”

“…The N-terminal domain of the α -subunit of the AprA (AprA_alpha_N) harbors the FAD cofactor-binding domain (aa positions: 2–261 and 394–487) and the capping domains (aa positions: 262–393). These functional domains have been characterized from Archaeoglobus fulgidus in the reduced state (FAD red -APS, PDB ID: 1JNR) [ 16 ] and in the oxidized state (FAD ox -APS, PDB ID: 2FJA) [ 48 ] as well as in Desulfovibrio gigas (PDB ID: 3GYX) [ 49 ]. Thus, a total of 100 aa sequences were included in the AprA alignment, where 23 phylotypes are derived from this work.…”

Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation

“…k00394 and k00395 encode adenylylsulfate reductase, which catalyzes APS to sulfite 33 , 34 , the second reaction of sulfate reduction 31 . There was a higher abundance of k00394 and k00395 in the yeast extract and tryptone groups than in the glucose and lactate groups.…”

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

“…APS reductase (AprBA) is a heterodimeric iron-sulphur flavoprotein that catalyses the reductive cleavage of APS to sulphite and AMP (Lampreia, Pereira, & Moura, 1994;Parey, Fritz, et al, 2013). Two crystal structures have been determined for AprBA from SRP, one from A. fulgidus (Fritz, Roth, et al, 2002) and one from Desulfovibrio gigas (Chiang et al, 2009). The AprA subunit is a flavoprotein that binds an FAD cofactor and has a fold similar to the fumarate reductase/aspartate oxidase family, while the AprB subunit binds two [4Fe-4S] 2+/1+ clusters in a ferredoxin-like domain (Fritz, Büchert, & Kroneck, 2002;Fritz, Roth, et al, 2002).…”