Crystal Structure of the Bacillus subtilis Phosphodiesterase PhoD Reveals an Iron and Calcium-containing Active Site

Rodriguez, Fernanda; Lillington, James; Johnson, Steven; Timmel, Christiane R.; Lea, Susan M.; Berks, Ben C.

doi:10.1074/jbc.m114.604892

Cited by 62 publications

(74 citation statements)

References 46 publications

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“…In this respect, Rv0805i sd istinguished from other metallohydrolases that requireC a II as an essential cofactorf or enzymatic activity (such as extra-cytoplasmic alkaline phosphatases that may require as many as three Ca II ions in their active state). [23,24] This mechanism, whereby Rv0805c an alter the level of itsr eactivityd epending on the presence or absence of Ca II may be important for the biological function of this enzyme because Ca II is an important mediatoro fs ignal transductions. [17,19,41] www.chemeurj.org asignificant change in the activity of Rv0805, which greatlyimpacts on the concentration of cyclic nucleotides within the cell.…”

Section: Resultsmentioning

confidence: 99%

“…[17][18][19][20][21][22] Of particular interesti nc ontext of dinuclear metallohydrolases is the complex dependence of ag roup of extra-cytoplasmic alkaline phosphataseso nC a II .O ne of these enzymes, PhoD,i sc losely relatedt oP AP and also accommodates aF e III in its actives ite. [23] However,P hoD also requires two closely spaced Ca II ions where one (i.e.,C aA) occupies as itee quivalent to that accommodating ad ivalent transition metal ion in PAP. [23] Another membero ft his group of alkaline phosphatases, PhoA, contains two Zn II and one Ca II in the active site whereas at hird member,P hoX, contains two Fe III and three Ca II ions.…”

Section: Introductionmentioning

confidence: 99%

“…[23] However,P hoD also requires two closely spaced Ca II ions where one (i.e.,C aA) occupies as itee quivalent to that accommodating ad ivalent transition metal ion in PAP. [23] Another membero ft his group of alkaline phosphatases, PhoA, contains two Zn II and one Ca II in the active site whereas at hird member,P hoX, contains two Fe III and three Ca II ions. [24] Although it was speculated that the presence of Ca II ions in these alkaline phosphatases may be areflection of the bioavailability at least in the case of Rv0805, Ca II may play ar egulatory function.…”

Section: Introductionmentioning

confidence: 99%

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Ca^II Binding Regulates and Dominates the Reactivity of a Transition‐Metal‐Ion‐Dependent Diesterase from Mycobacterium tuberculosis

Pedroso

Larrabee

Ely

et al. 2015

Chemistry A European J

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The diesterase Rv0805 from Mycobacterium tuberculosis is a dinuclear metallohydrolase that plays an important role in signal transduction by controlling the intracellular levels of cyclic nucleotides. As Rv0805 is essential for mycobacterial growth it is a promising new target for the development of chemotherapeutics to treat tuberculosis. The in vivo metal-ion composition of Rv0805 is subject to debate. Here, we demonstrate that the active site accommodates two divalent transition metal ions with binding affinities ranging from approximately 50 nm for Mn(II) to about 600 nm for Zn(II) . In contrast, the enzyme GpdQ from Enterobacter aerogenes, despite having a coordination sphere identical to that of Rv0805, binds only one metal ion in the absence of substrate, thus demonstrating the significance of the outer sphere to modulate metal-ion binding and enzymatic reactivity. Ca(II) also binds tightly to Rv0805 (Kd ≈40 nm), but kinetic, calorimetric, and spectroscopic data indicate that two Ca(II) ions bind at a site different from the dinuclear transition-metal-ion binding site. Ca(II) acts as an activator of the enzymatic activity but is able to promote the hydrolysis of substrates even in the absence of transition-metal ions, thus providing an effective strategy for the regulation of the enzymatic activity.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Ca^II Binding Regulates and Dominates the Reactivity of a Transition‐Metal‐Ion‐Dependent Diesterase from Mycobacterium tuberculosis

Pedroso

Larrabee

Ely

et al. 2015

Chemistry A European J

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“…phoD-F733 anneals to the conserved region that consists of the amino acid residues WDDHE, which contribute to the coordination of two Ca 2ϩ cofactors (24). In addition, the fragment targeted by phoD-F733/phoD-R18083 includes two conserved arginine residues.…”

Section: Methodsmentioning

confidence: 99%

phoD Alkaline Phosphatase Gene Diversity in Soil

Ragot

Kertesz

Bünemann

2015

Appl Environ Microbiol

239

151

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bPhosphatase enzymes are responsible for much of the recycling of organic phosphorus in soils. The PhoD alkaline phosphatase takes part in this process by hydrolyzing a range of organic phosphoesters. We analyzed the taxonomic and environmental distribution of phoD genes using whole-genome and metagenome databases. phoD alkaline phosphatase was found to be spread across 20 bacterial phyla and was ubiquitous in the environment, with the greatest abundance in soil. To study the great diversity of phoD, we developed a new set of primers which targets phoD genes in soil. The primer set was validated by 454 sequencing of six soils collected from two continents with different climates and soil properties and was compared to previously published primers. Up to 685 different phoD operational taxonomic units were found in each soil, which was 7 times higher than with previously published primers. The new primers amplified sequences belonging to 13 phyla, including 71 families. The most prevalent phoD genes identified in these soils were affiliated with the orders Actinomycetales (13 to 35%), Bacillales (1 to 29%), Gloeobacterales (1 to 18%), Rhizobiales (18 to 27%), and Pseudomonadales (0 to 22%). The primers also amplified phoD genes from additional orders, including Burkholderiales, Caulobacterales, Deinococcales, Planctomycetales, and Xanthomonadales, which represented the major differences in phoD composition between samples, highlighting the singularity of each community. Additionally, the phoD bacterial community structure was strongly related to soil pH, which varied between 4.2 and 6.8. These primers reveal the diversity of phoD in soil and represent a valuable tool for the study of phoD alkaline phosphatase in environmental samples. P hosphorus (P) is an essential macronutrient for all living cells (1). Despite its relative abundance in soils, P is one of the main limiting nutrients for terrestrial organisms (2). P is present in organic and inorganic forms in soil, but only the inorganic orthophosphate ions in soil solutions are readily available for plants (3). To sustain crop productivity, large amounts of P fertilizers are therefore used in agriculture, both as inorganic fertilizers (e.g., triple super phosphate) and organic fertilizers (e.g., manure). After application, some of the inorganic P is rapidly taken up by plants and microorganisms, while the remaining P is immobilized as insoluble and bound P forms in the soil. Microorganisms can access and recycle P from these recalcitrant P forms by solubilization of inorganic P and by mineralization of organic P via enzymatic processes mediated primarily by phosphatases, which hydrolyze the orthophosphate group from organic compounds (3). When facing P scarcity, microorganisms upregulate expression of functional genes coding for phosphatases (phosphomonoesterases, phosphodiesterases, phytases), high-affinity phosphate transporters, and enzymes for phosphonate utilization, which together constitute the Pho regulon (4). The phosphomonoesters which are hydrolyzed ...

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“…Furthermore, marine bacteria contain more iron per unit biomass than phytoplankton, and thus, bacterial iron assimilation may constitute another constraint on iron availability to phytoplankton (646). Iron is also a key resource limiting microbial N 2 fixation, phosphate acquisition, and, thus, productivity in the ocean (181,(647)(648)(649). It has been proposed that iron may control productivity in half of the world's oceans (650,651) and may have accounted for onequarter of the decrease in the atmospheric CO 2 concentration during the Earth's historical glacial maxima (652).…”

Section: Cheating: It Happens In the Microbial World Toomentioning

confidence: 99%

Microbial Surface Colonization and Biofilm Development in Marine Environments

Dang

Lovell

2016

Microbiol Mol Biol Rev

837

636

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SUMMARYBiotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

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Crystal Structure of the Bacillus subtilis Phosphodiesterase PhoD Reveals an Iron and Calcium-containing Active Site

Cited by 62 publications

References 46 publications

Ca^II Binding Regulates and Dominates the Reactivity of a Transition‐Metal‐Ion‐Dependent Diesterase from Mycobacterium tuberculosis

Ca^II Binding Regulates and Dominates the Reactivity of a Transition‐Metal‐Ion‐Dependent Diesterase from Mycobacterium tuberculosis

phoD Alkaline Phosphatase Gene Diversity in Soil

Microbial Surface Colonization and Biofilm Development in Marine Environments

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Crystal Structure of the Bacillus subtilis Phosphodiesterase PhoD Reveals an Iron and Calcium-containing Active Site

Cited by 62 publications

References 46 publications

CaII Binding Regulates and Dominates the Reactivity of a Transition‐Metal‐Ion‐Dependent Diesterase from Mycobacterium tuberculosis

CaII Binding Regulates and Dominates the Reactivity of a Transition‐Metal‐Ion‐Dependent Diesterase from Mycobacterium tuberculosis

phoD Alkaline Phosphatase Gene Diversity in Soil

Microbial Surface Colonization and Biofilm Development in Marine Environments

Contact Info

Product

Resources

About

Ca^II Binding Regulates and Dominates the Reactivity of a Transition‐Metal‐Ion‐Dependent Diesterase from Mycobacterium tuberculosis

Ca^II Binding Regulates and Dominates the Reactivity of a Transition‐Metal‐Ion‐Dependent Diesterase from Mycobacterium tuberculosis