Aryldialkylphosphatase

Last updated
Aryldialkylphosphatase
Identifiers
EC no. 3.1.8.1
CAS no. 117698-12-1
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO
Search
PMC articles
PubMed articles
NCBI proteins

Aryldialkylphosphatase (EC 3.1.8.1, also known as phosphotriesterase, organophosphatehydrolase, parathion hydrolase, paraoxon ase, and parathionarylesterase; systematic name aryltriphosphate dialkylphosphohydrolase) is a metalloenzyme that hydrolyzes the triester linkage [1] found in organophosphate insecticides:

Contents

Phosphotriesterase family
Structure of organophosphorus hydrolase.jpg
Structure of organophosphorus hydrolase
Identifiers
SymbolPTE
Pfam PF02126
InterPro IPR001559
PROSITE PDOC01026
SCOP2 1dpm / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
PDB 1bf6 B:2-292 1i0d B:44-359 1i0b B:44-359

1jgm A:44-359 1ez2 A:44-359 1dpm A:44-359 1psc A:44-359 1eyw A:44-359 1hzy B:44-359 1qw7 A:44-359 1pta :44-359 1p6c A:44-359 1p6b A:44-359 2d2h A:43-358 2d2j A:43-358

2d2g A:43-358
an aryl dialkyl phosphate + H2O dialkyl phosphate + an aryl alcohol

The gene (opd, for organophosphate-degrading) that codes for the enzyme is found in a large plasmid (pSC1, 51Kb) endogenous to Pseudomonasdiminuta, [2] although the gene has also been found in many other bacterial species such as Flavobacterium sp. (ATCC27551), where it is also encoded in an extrachromosomal element (pSM55, 43Kb). [2]

Organophosphate is the general name for esters of phosphoric acid and is one of the organophosphorus compounds. They can be found as part of insecticides, herbicides, and nerve gases, amongst others. Some less-toxic organophosphates can be used as solvents, plasticizers, and EP additives. The use of organophosphates accounts for approximately 38% of all pesticide use globally. [3]

Gene

Bacterial isolates capable of degrading organophosphate (OP) pesticides have been identified from soil samples from different parts of the world. [3] [4] The first organophosphate-degrading bacterial species was isolated from a soil sample from the Philippines in 1973, [5] which identified as Flavobacterium sp. ATCC27551. Since then, other species have demonstrated to have OP-degrading abilities, such as Pseudomonas diminuta (isolated from US soil sample), Agrobacterium radiobacter (isolated from Australian soil sample), Alteromonas haloplanktis (isolated from US soil sample), and Pseudomonas sp. WBC-3 (isolated from Chinese soil sample). [3]

The capacity to hydrolyze organophosphates is not unique to bacteria. A few fungi and cyanobacteria species have been found to also hydrolyze them. [3] Moreover, through sequence homology searches of whole genomes, several other bacterial species were identified that also contain sequences from the same gene family as opd, including pathogenic bacteria such as Escherichia coli (yhfV) and Mycobacterium tuberculosis . [3]

The gene sequence encoding the enzyme (opd) in Flavobacterium sp. ATCC27551 and Pseudomonas diminuta is highly conserved (100% sequence homology), [4] although the plasmids where the genes are found have very different sequences apart from a 5.1Kb [4] [6] conserved region where the gene is found. [2]

A closer look on the organization of the opd gene from Flavobacterium suggests a potential transposon-like architecture, which accounts for the widespread distribution of the gene among other microbial species that might have occurred through lateral DNA transfer. The opd gene is flanked by transposition insertion sequences, characteristic of Tn3 family of transposons. Moreover, a transposase-like sequence (homologous to TnpA) and a resolvase-like sequence (homologous to TnpR) were also identified in regions upstream of the opd gene, [4] which are characteristics of class II transposons such as Tn3.

Furthermore, another open reading frame was identified downstream of opd and encodes a protein that further degrades p-nitrophenol, one of the byproducts of OP degradation. This protein is believed to work as a complex with PTE, since a dramatic increase in activity is observed when PTE is present. [4]

Therefore, the characteristic architectural organization of the opd gene region suggests that different species acquired the gene through horizontal transfer through transposition and plasmid transfer.

Protein

Structure

Phosphotriesterase (PTE) belongs to a family metalloenzymes that has two catalytic Zn2+ metal atoms, bridged via a common ligand and coordinated by imidazole side chains of histidine residues that are clustered around the metal atoms. [7] The protein forms a homodimer. [8] The overall structure consists of an α/β-barrel motif, also present in other 20 catalytic proteins. The active sites of these proteins is located at the C-terminal portion of the β-barrel, which is where the active site of PTE is also located. [7]

Reaction schematic of enzyme-catalyzed hydrolysis of paraoxon into diethyl phosphoric acid and p-nitrophenol. Reaction schematic.png
Reaction schematic of enzyme-catalyzed hydrolysis of paraoxon into diethyl phosphoric acid and p-nitrophenol.

Catalysis

Catalysis of organophosphates occurs via a nucleophilic substitution with inversion of configuration (SN2 mechanism) about the phosphorus centre of the substrate. [7] In the active site, the metal cations aid in catalysis by further polarizing the P–O bond of the substrate, which makes it more susceptible to a nucleophilic attack. Furthermore, a basic residue abstracts a proton from a water molecule, and the hydroxide ion produced bridges the two divalent cations and acts as the nucleophile. The OH− then attacks the phosphorus centre of the substrate, followed by a proton transfer event. The P–O bond is broken, and the products are released from the active site. [9] The turnover rate (kcat) of phosphotriesterase is nearly 104 s−1 for the hydrolysis of paraoxon, [10] and the products are p-nitrophenol and diethyl phosphoric acid.


Species

Phosphotriesterase is present in two species, Pseudomonas diminuta and Flavobacterium sp. ATCC27551. Other gene variants that also encode organophosphate-degrading enzymes are present in other species. The list includes bacterial species such as the radioresistant Deinococcus radiodurans, pathogens Mycobacterium tuberculosis and Mycobacterium bovis, the anaerobic bacterium Desulfatibacillum alkenivorans, the thermophilic bacteria Geobacillus sp. and Thermoanaerobacter sp. X514, Escherichia coli (yhfV) and many other groups of bacteria, [3] and also some Archaea such as Sulfolobus acidocaldarius. [11]

Schematic diagram of cell wall of Gram-negative bacteria (Pseudomonas) showing the inner membrane where PTE is anchored and the periplasmic space. Gram negative cell wall.svg
Schematic diagram of cell wall of Gram-negative bacteria (Pseudomonas) showing the inner membrane where PTE is anchored and the periplasmic space.

Subcellular localization

Phosphotriesterase is a membrane-associated protein that is translated with a 29 amino acid-long target peptide (Tat motif), [12] [10] [13] which is then cleaved from the mature protein after insertion in the plasma membrane. [1] The protein is anchored to the inner membrane of the cell, facing the periplasm. [14]

Function

The enzyme phosphotriesterase hydrolyzes organophosphate compounds by cleaving the triester linkage in the substrate.

Organophosphate compounds that serve as substrates for enzyme-catalyzed hydrolysis by PTE. Organophosphates susceptible to cleavage by PTE.png
Organophosphate compounds that serve as substrates for enzyme-catalyzed hydrolysis by PTE.

The enzyme has a very broad substrate specificity, [12] and is very efficient in catalyzing the reaction: PTE hydrolyzes paraoxon at a rate approaching the diffusion limit, [15] which indicates that the enzyme is optimally evolved for using this substrate. [13] It acts specifically on synthetic organophosphate triesters and phosphorofluoridates. [3] It does not seem to have a natural occurring substrate and may thus have optimally evolved for utilizing paraoxon and other common agricultural pesticides. [15]

The products of the reaction are diethyl phosphoric acid and p-nitrophenol. [4] The latter product is further degraded by an enzyme encoded 750bp downstream of the opd gene, and encodes a 29kDa putative hydrolase that may be involved in degrading aromatic compounds, and works in concert with PTE. [4] This enzyme is homologous to hydrolases in Pseudomonas putida, Pseudomonas azelaica, Rhodococcus sp., and P. fluorescens. [4]

Organophosphates are not toxic to bacteria, but they act as acetylcholinesterase inhibitors in animals. [16] Some species of bacteria are also able to utilize organophosphates as a nutrient and carbon source. [14]

Environmental significance

Phosphotriesterases are considered a strong candidate biocatalyst for bioremediation purposes. [7] Its wide substrate specificity and catalytic efficiency makes it an attractive target for the potential use of microbes containing the opd gene in detoxifying soils that are toxic due to pesticide overuse. [3] Moreover, organophosphates act as acetylcholinesterase (AChE) inhibitors. The AChE neurotransmitter is a vital component of the central nervous system (CNS) in insects in animals, and the inhibition of the proper turnover of this neurochemical results in overstimulation of the CNS, which ultimately results in death of insects and mammals. [3] [17] As a result, the use of organophosphate-degrading microorganisms is a potentially effective, low-cost, and environmentally friendly method of removing these toxic compounds from the environment. [3]

History

Bacterial species that had the ability to degrade organophosphate pesticides have been isolated from soil samples from different parts of the world. The first bacterial strain identified to be able to hydrolyze organophosphates was Flavobacterium sp. ATCC 27551, found by Sethunathan and Yoshida in 1973 from a soil sample originally from the Philippines. [5] Since then, other species were found to also have organophosphate-degrading enzymes similar to that found in Flavobacterium [6] .

Related Research Articles

<i>Pseudomonas putida</i> Species of bacterium

Pseudomonas putida is a Gram-negative, rod-shaped, saprophytic soil bacterium. It has a versatile metabolism and is amenable to genetic manipulation, making it a common organism used in research, bioremediation, and synthesis of chemicals and other compounds.

<span class="mw-page-title-main">Nitrilase</span> Class of enzymes

Nitrilase enzymes catalyse the hydrolysis of nitriles to carboxylic acids and ammonia, without the formation of "free" amide intermediates. Nitrilases are involved in natural product biosynthesis and post translational modifications in plants, animals, fungi and certain prokaryotes. Nitrilases can also be used as catalysts in preparative organic chemistry. Among others, nitrilases have been used for the resolution of racemic mixtures. Nitrilase should not be confused with nitrile hydratase which hydrolyses nitriles to amides. Nitrile hydratases are almost invariably co-expressed with an amidase, which converts the amide to the carboxylic acid. Consequently, it can sometimes be difficult to distinguish nitrilase activity from nitrile hydratase plus amidase activity.

Paenarthrobacter ureafaciens KI72, popularly known as nylon-eating bacteria, is a strain of Paenarthrobacter ureafaciens that can digest certain by-products of nylon 6 manufacture. It uses a set of enzymes to digest nylon, popularly known as nylonase.

<span class="mw-page-title-main">Flavobacteriia</span> Class of bacteria

The class Flavobacteriia is composed of a single class of environmental bacteria. It contains the family Flavobacteriaceae, which is the largest family in the phylum Bacteroidota. This class is widely distributed in soil, fresh, and seawater habitats. The name is often spelt Flavobacteria, but was officially named Flavobacteriia in 2012.

Paucimonas lemoignei, formerly [Pseudomonas lemoignei], is a Gram-negative soil bacterium. It is aerobic, motile, and rod-shaped.

<span class="mw-page-title-main">Atrazine chlorohydrolase</span>

Atrazine Chlorohydrolase (AtzA) is an enzyme (E.C.3.8.1.8), which catalyzes the conversion of atrazine to hydroxyatrazine. Bacterial degradation determines the environmental impact and efficacy of an herbicide or pesticide. Initially, most pesticides are highly effective and show minimal bacterial degradation; however, bacteria can rapidly evolve and gain the ability to metabolize potential nutrients in the environment. Despite a remarkable structural similarity, degradation of atrazine by bacteria capable of melamine degradation was rare; however, since its introduction as a pesticide in the United States, bacteria capable of atrazine degradation have evolved. Currently, Pseudomonas sp. strain ADP seems to be the optimal bacterial strain for atrazine degradations, which appears to be the sole nitrogen source for the bacteria.

Poly(3-hydroxybutyrate) depolymerase (EC 3.1.1.75, PHB depolymerase, systematic name poly[(R)-3-hydroxybutanoate] hydrolase) is an enzyme used in the degradation processes of a natural polyester poly(3-hydroxyburate). This enzyme has growing commercialization interests due to it implications in biodegradable plastic decomposition.

The enzyme tannase (EC 3.1.1.20) catalyzes the following reaction:

<span class="mw-page-title-main">Lactonase</span>

Lactonase (EC 3.1.1.81, acyl-homoserine lactonase; systematic name N-acyl-L-homoserine-lactone lactonohydrolase) is a metalloenzyme, produced by certain species of bacteria, which targets and inactivates acylated homoserine lactones (AHLs). It catalyzes the reaction

<span class="mw-page-title-main">Paraoxonase</span> Class of enzymes

Paraoxonases are a family of mammalian enzymes with aryldialkylphosphatase activity. There are three paraoxonase isozymes, which were originally discovered for their involvement in the hydrolysis of organophosphates.

<span class="mw-page-title-main">Plasmid-mediated resistance</span> Antibiotic resistance caused by a plasmid

Plasmid-mediated resistance is the transfer of antibiotic resistance genes which are carried on plasmids. Plasmids possess mechanisms that ensure their independent replication as well as those that regulate their replication number and guarantee stable inheritance during cell division. By the conjugation process, they can stimulate lateral transfer between bacteria from various genera and kingdoms. Numerous plasmids contain addiction-inducing systems that are typically based on toxin-antitoxin factors and capable of killing daughter cells that don't inherit the plasmid during cell division. Plasmids often carry multiple antibiotic resistance genes, contributing to the spread of multidrug-resistance (MDR). Antibiotic resistance mediated by MDR plasmids severely limits the treatment options for the infections caused by Gram-negative bacteria, especially family Enterobacteriaceae. The global spread of MDR plasmids has been enhanced by selective pressure from antimicrobial medications used in medical facilities and when raising animals for food.

Organophosphorus acid anhydrolase (OPAA) is an enzyme that been shown to be particularly effective in detoxifying organophosphorus-containing compounds, such as deadly nerve gas used in chemical warfare. The enzyme is found in a diverse range of organisms, including protozoa, squid and clams, mammals, and soil bacteria. A highly active form of the enzyme is typically isolated from the marine bacteria Alteromonas undina for laboratory study. This form is both halophilic and thermophilic, making it particularly useful for detoxification applications. A slightly less active variant of OPAA has also been isolated in mung beans and slime mold duckweed.

The enzyme cocaine esterase (EC 3.1.1.84, CocE, hCE2, hCE-2, human carboxylesterase 2; systematic name cocaine benzoylhydrolase) catalyses the reaction

The enzyme pyrethroid hydrolase (EC 3.1.1.88, pyrethroid-hydrolyzing carboxylesterase, pyrethroid-hydrolysing esterase, pyrethroid-hydrolyzing esterase, pyrethroid-selective esterase, pyrethroid-cleaving enzyme, permethrinase, PytH, EstP; systematic name pyrethroid-ester hydrolase) catalyses the reaction

Acidobacterium capsulatum is a bacterium. It is an acidophilic chemoorganotrophic bacterium containing menaquinone. It is gram-negative, facultative anaerobic, mesophilic, non-spore-forming, capsulated, saccharolytic and rod-shaped. It is also motile by peritrichous flagella. Its type strain is JCM 7670.

Pesticide degradation is the process by which a pesticide is transformed into a benign substance that is environmentally compatible with the site to which it was applied. Globally, an estimated 1 to 2.5 million tons of active pesticide ingredients are used each year, mainly in agriculture. Forty percent are herbicides, followed by insecticides and fungicides. Since their initial development in the 1940s, multiple chemical pesticides with different uses and modes of action have been employed. Pesticides are applied over large areas in agriculture and urban settings. Pesticide use, therefore, represents an important source of diffuse chemical environmental inputs.

Xenophilus azovorans is a bacterium from the genus Xenophilus which has been isolated from soil in Switzerland.

Sphingobacterium olei is a Gram-stain-negative, rod-shaped, and non-motile bacterium. It was first isolated from oil-contaminated soil in Daqing oil field, China. S. olei has been found to be able to degrade herbicides quizalofop-p-ethyl and diclofop-methyl. Before a name was given, S. olei was designated as strain HAL-9T. The species name olei means "of oil" in Latin.

Cytophaga hutchinsonii is a bacterial species in the genus Cytophaga. C. hutchinsonii is an aerobic, gram-negative, soil, microorganism that exhibits gliding motility, enabling it to move quickly over surfaces and is capable of cellulose degradation.

<span class="mw-page-title-main">Plastic degradation by marine bacteria</span> Ability of bacteria to break down plastic polymers

Plastic degradation in marine bacteria describes when certain pelagic bacteria break down polymers and use them as a primary source of carbon for energy. Polymers such as polyethylene(PE), polypropylene (PP), and polyethylene terephthalate (PET) are incredibly useful for their durability and relatively low cost of production, however it is their persistence and difficulty to be properly disposed of that is leading to pollution of the environment and disruption of natural processes. It is estimated that each year there are 9-14 million metric tons of plastic that are entering the ocean due to inefficient solutions for their disposal. The biochemical pathways that allow for certain microbes to break down these polymers into less harmful byproducts has been a topic of study to develop a suitable anti-pollutant.

References

  1. 1 2 Pinjari AB, Pandey JP, Kamireddy S, Siddavattam D (July 2013). "Expression and subcellular localization of organophosphate hydrolase in acephate-degrading Pseudomonas sp. strain Ind01 and its use as a potential biocatalyst for elimination of organophosphate insecticides". Letters in Applied Microbiology. 57 (1): 63–8. doi:10.1111/lam.12080. PMID   23574004. S2CID   12006833.
  2. 1 2 3 Harper LL, McDaniel CS, Miller CE, Wild JR (October 1988). "Dissimilar plasmids isolated from Pseudomonas diminuta MG and a Flavobacterium sp. (ATCC 27551) contain identical opd genes". Applied and Environmental Microbiology. 54 (10): 2586–9. Bibcode:1988ApEnM..54.2586H. doi:10.1128/AEM.54.10.2586-2589.1988. PMC   204325 . PMID   3202637.
  3. 1 2 3 4 5 6 7 8 9 10 Singh BK (February 2009). "Organophosphorus-degrading bacteria: ecology and industrial applications". Nature Reviews. Microbiology. 7 (2): 156–64. doi:10.1038/nrmicro2050. PMID   19098922. S2CID   205497513.
  4. 1 2 3 4 5 6 7 8 Siddavattam D, Khajamohiddin S, Manavathi B, Pakala SB, Merrick M (May 2003). "Transposon-like organization of the plasmid-borne organophosphate degradation (opd) gene cluster found in Flavobacterium sp". Applied and Environmental Microbiology. 69 (5): 2533–9. Bibcode:2003ApEnM..69.2533S. doi:10.1128/AEM.69.5.2533-2539.2003. PMC   154515 . PMID   12732518.
  5. 1 2 Sethunathan N, Yoshida T (July 1973). "A Flavobacterium sp. that degrades diazinon and parathion". Canadian Journal of Microbiology. 19 (7): 873–5. doi:10.1139/m73-138. PMID   4727806.
  6. 1 2 Mulbry WW, Karns JS, Kearney PC, Nelson JO, McDaniel CS, Wild JR (May 1986). "Identification of a plasmid-borne parathion hydrolase gene from Flavobacterium sp. by southern hybridization with opd from Pseudomonas diminuta". Applied and Environmental Microbiology. 51 (5): 926–30. Bibcode:1986ApEnM..51..926M. doi:10.1128/AEM.51.5.926-930.1986. PMC   238989 . PMID   3015022.
  7. 1 2 3 4 Benning MM, Kuo JM, Raushel FM, Holden HM (December 1994). "Three-dimensional structure of phosphotriesterase: an enzyme capable of detoxifying organophosphate nerve agents". Biochemistry. 33 (50): 15001–7. doi:10.1021/bi00254a008. PMID   7999757. S2CID   9424327.
  8. ↑ Dong YJ, Bartlam M, Sun L, Zhou YF, Zhang ZP, Zhang CG, Rao Z, Zhang XE (October 2005). "Crystal structure of methyl parathion hydrolase from Pseudomonas sp. WBC-3". Journal of Molecular Biology. 353 (3): 655–63. doi:10.1016/j.jmb.2005.08.057. PMID   16181636.
  9. ↑ Aubert SD, Li Y, Raushel FM (May 2004). "Mechanism for the hydrolysis of organophosphates by the bacterial phosphotriesterase". Biochemistry. 43 (19): 5707–15. doi:10.1021/bi0497805. PMID   15134445.
  10. 1 2 Mulbry WW, Karns JS (February 1989). "Purification and characterization of three parathion hydrolases from gram-negative bacterial strains". Applied and Environmental Microbiology. 55 (2): 289–93. Bibcode:1989ApEnM..55..289M. doi:10.1128/AEM.55.2.289-293.1989. PMC   184103 . PMID   2541658.
  11. ↑ Chen L, Brügger K, Skovgaard M, Redder P, She Q, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk HP, Garrett RA (July 2005). "The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota". Journal of Bacteriology. 187 (14): 4992–9. doi:10.1128/JB.187.14.4992-4999.2005. PMC   1169522 . PMID   15995215.
  12. 1 2 Classen JJ, Engler CR, Kenerley CM, Whittaker AD (April 2000). "A logistic model of subsurface fungal growth with application to bioremediation". Journal of Environmental Science and Health, Part A. 35 (4): 465–488. doi:10.1080/10934520009376982. S2CID   98035446.
  13. 1 2 Caldwell SR, Newcomb JR, Schlecht KA, Raushel FM (July 1991). "Limits of diffusion in the hydrolysis of substrates by the phosphotriesterase from Pseudomonas diminuta". Biochemistry. 30 (30): 7438–7444. doi:10.1021/bi00244a010. ISSN   0006-2960. PMID   1649628.
  14. 1 2 Singh BK, Walker A (May 2006). "Microbial degradation of organophosphorus compounds". FEMS Microbiology Reviews. 30 (3): 428–71. doi: 10.1111/j.1574-6976.2006.00018.x . PMID   16594965.
  15. 1 2 Dumas DP, Caldwell SR, Wild JR, Raushel FM (November 1989). "Purification and properties of the phosphotriesterase from Pseudomonas diminuta". The Journal of Biological Chemistry. 264 (33): 19659–65. doi: 10.1016/S0021-9258(19)47164-0 . PMID   2555328.
  16. ↑ Lotti M (2002). "Promotion of organophosphate induced delayed polyneuropathy by certain esterase inhibitors". Toxicology. 181–182: 245–248. doi:10.1016/s0300-483x(02)00291-3. PMID   12505319.
  17. ↑ Ragnarsdottir KV (2000). "Environmental fate and toxicology of organophosphate pesticides". Journal of the Geological Society. 157 (4): 859–876. Bibcode:2000JGSoc.157..859R. doi:10.1144/jgs.157.4.859. S2CID   129950334.

Further reading

This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.