Crystal Structure of the Bifunctional ATP Sulfurylase – APS kinase from the Chemolithotrophic Thermophile Aquifex aeolicus

Yu, Zhihao; Lansdon, E.B.; Segel, Irwin H.; Fisher, A.J.

doi:10.1016/j.jmb.2006.10.035

Cited by 31 publications

(61 citation statements)

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“…Calorimetric, Crystallographic, and Mutagenesis Analysis of P-loop Recognition of Oxyanions-The above results, along with crystal structures of APSK from a variety of sources (25)(26)(27)(28)(29)(30), suggests that the P-loop (Fig. 1B) plays a role in nucleotide binding specificity at the ATP/ADP site of AtAPSK.…”

Section: Calorimetric Analysis Of Nucleotide Binding To Atapsk-tomentioning

confidence: 77%

“…At the interface of the two nucleotide-binding sites in AtAPSK (Fig. 6) and the enzyme from other species (25)(26)(27)(28)(29)(30), the P-loop (Ser 110 -Thr 116 ) is essential for ATP/ADP binding and residues from the ␣3 helix provide critical contacts with APS. In particular, Arg 141 forms chargecharge interactions with the phosphosulfate group of APS and Asp 138 provides a bidentate interaction with the hydroxyl groups of the APS ribose and serves as a general base in the reaction mechanism (25,29).…”

Section: Pre-bound Nucleotidementioning

confidence: 99%

“…1B) and P. chrysogenum, the APSK domain from human PAPS synthetase, and the bifunctional ATP sulfurylase-APSK from Aquifex aeolicus and Thiobacillus denitrificans (25)(26)(27)(28)(29)(30) show that the overall fold of APSK is highly conserved across a variety of organisms. Two nucleotide-binding sites (i.e.…”

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confidence: 99%

“…In multiple crystal structures, AMP-PNP and ADP interact with residues in the P-loop (Fig. 5), which provides a driving force for nucleotide recognition as it forms nine hydrogen bonds with the ␤-phosphate compared with two hydrogen bonds made between the rest of the nucleotide and protein (23)(24)(25)(26)(27)(28)(29)(30). Comparable interactions are observed for SO 4 2Ϫ bound in the AtAPSK⅐APS⅐SO 4 2Ϫ complex (Fig.…”

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confidence: 99%

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Nucleotide Binding Site Communication in Arabidopsis thaliana Adenosine 5′-Phosphosulfate Kinase

Ravilious

Jez

2012

Journal of Biological Chemistry

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Background: Adenosine 5Ј-phosphosulfate kinase (APSK) catalyzes the synthesis of phosphoadenosine 5Ј-phosphosulfate, but how APSK coordinates binding of phosphonucleotides is unclear. Results: Using calorimetry, crystallography, and mutagenesis, this study provides new insight on nucleotide binding in APSK. Conclusion:The P-loop and a critical aspartate integrate dynamic structural and nucleotide recognition features. Significance: These results suggest how structural changes guide the order of nucleotide addition for catalysis.

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Section: Calorimetric Analysis Of Nucleotide Binding To Atapsk-tomentioning

confidence: 77%

Section: Pre-bound Nucleotidementioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Nucleotide Binding Site Communication in Arabidopsis thaliana Adenosine 5′-Phosphosulfate Kinase

Ravilious

Jez

2012

Journal of Biological Chemistry

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“…The reaction sequence suggested by kinetic studies of the APSK from Penicillium chrysogenum, E. coli, and A. thaliana follows an ordered mechanism with substrate inhibition by APS (28)(29)(30). Although no structural information for a plant APSK is available, X-ray crystal structures of the P. chrysogenum APSK and bifunctional ATP sulfurylase-APSK from human, Aquifex aeolicus, and Thiobacillus denitrificans have been determined and reveal a canonical α/β purine nucleotide binding fold (31)(32)(33)(34)(35)(36). For the bifunctional human enzyme, the substrate inhibition by APS on APSK activity is linked to an approximately 20-aa N-terminal loop of low sequence homology (36) (Fig.…”

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confidence: 99%

Structural basis and evolution of redox regulation in plant adenosine-5′-phosphosulfate kinase

Ravilious

Nguyen

Francois

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

101

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Adenosine-5′-phosphosulfate (APS) kinase (APSK) catalyzes the phosphorylation of APS to 3′-phospho-APS (PAPS). In Arabidopsis thaliana, APSK is essential for reproductive viability and competes with APS reductase to partition sulfate between the primary and secondary branches of the sulfur assimilatory pathway; however, the biochemical regulation of APSK is poorly understood. The 1.8-Å resolution crystal structure of APSR from A. thaliana (AtAPSK) in complex with β,γ-imidoadenosine-5′-triphosphate, Mg 2+ , and APS provides a view of the Michaelis complex for this enzyme and reveals the presence of an intersubunit disulfide bond between Cys86 and Cys119. Functional analysis of AtAPSK demonstrates that reduction of Cys86-Cys119 resulted in a 17-fold higher k cat / K m and a 15-fold increase in K i for substrate inhibition by APS compared with the oxidized enzyme. The C86A/C119A mutant was kinetically similar to the reduced WT enzyme. Gel-and activity-based titrations indicate that the midpoint potential of the disulfide in AtAPSK is comparable to that observed in APS reductase. Both cysteines are invariant among the APSK from plants, but not other organisms, which suggests redox-control as a unique regulatory feature of the plant APSK. Based on structural, functional, and sequence analyses, we propose that the redox-sensitive APSK evolved after bifurcation of the sulfur assimilatory pathway in the green plant lineage and that changes in redox environment resulting from oxidative stresses may affect partitioning of APS into the primary and secondary thiol metabolic routes by having opposing effects on APSK and APS reductase in plants.enzyme kinetics | sulfur metabolism | X-ray crystallography | metabolic evolution S ulfur is an essential element for all living organisms and is required for the biosynthesis of a diverse array of metabolites and macromolecules (1-4). Plants and prokaryotes are the primary assimilatory organisms that convert inorganic sulfate (SO 4 2− ), the predominant form of environmental sulfur, into physiologically useful forms of sulfur (5, 6). The metabolic organization of sulfur assimilation varies among plants and microbes ( Fig. 1) (1-8). In yeast, fungi, and enterobacteria, including Escherichia coli, sulfate is incorporated into adenosine-5′-phosphate (APS), then converted to 3′-phospho-APS (PAPS) as a biologically "activated" compound that is reduced to sulfide (6, 7). In other sulfate-assimilating bacteria, such as Pseudomonas aeruginosa, APS can be used for reduction of sulfide (8). Plants possess bifurcated thiol metabolism pathways, which may reflect the metabolic needs of sessile organisms adapted to a range of environmental stresses and nutrient fluctuations (Fig. 1) (5). These pathways branch after formation of APS. The primary sulfur metabolic route in plants uses APS as the activated highenergy compound for sulfur reduction and the production of cysteine, which is crucial for the synthesis of proteins, methionine, iron-sulfur clusters, vitamin cofactors, and compounds that prote...

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Aminoacyl‐tRNA synthetases and the evolution of coded peptide synthesis: the Thioester World

Jakubowski

2016

FEBS Letters

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Edited by Michael IbbaCoded peptide synthesis must have been preceded by a prebiotic stage, in which thioesters played key roles. Fossils of the Thioester World are found in extant aminoacyl-tRNA synthetases (AARSs). Indeed, studies of the editing function reveal that AARSs have a thiol-binding site in their catalytic modules. The thiol-binding site confers the ability to catalyze aminoacylc oenzyme A thioester synthesis and peptide bond formation. Genomic comparisons show that AARSs are structurally related to proteins involved in sulfur and coenzyme A metabolisms and peptide bond synthesis. These findings point to the origin of the amino acid activation and peptide bond synthesis functions in the Thioester World and suggest that the present-day AARSs had originated from ancestral forms that were involved in noncoded thioesterdependent peptide synthesis.

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Crystal Structure of the Bifunctional ATP Sulfurylase – APS kinase from the Chemolithotrophic Thermophile Aquifex aeolicus

Cited by 31 publications

References 50 publications

Nucleotide Binding Site Communication in Arabidopsis thaliana Adenosine 5′-Phosphosulfate Kinase

Nucleotide Binding Site Communication in Arabidopsis thaliana Adenosine 5′-Phosphosulfate Kinase

Structural basis and evolution of redox regulation in plant adenosine-5′-phosphosulfate kinase

Aminoacyl‐tRNA synthetases and the evolution of coded peptide synthesis: the Thioester World

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