Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
247  structures 1271  species 1  interaction 1651  sequences 13  architectures

Family: PTE (PF02126)

Summary: Phosphotriesterase family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Aryldialkylphosphatase". More...

Aryldialkylphosphatase Edit Wikipedia article

Phosphotriesterase
Identifiers
EC number 3.1.8.1
CAS number 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

Aryldialkylphosphatase (EC 3.1.8.1) (more commonly known as phosphotriesterase, and also organophosphate hydrolase, parathion hydrolase, paraoxonase, and parathion aryl esterase) is a metalloenzyme that hydrolyzes the triester linkage[1] found in organophosphate insecticides.

Phosphotriesterase family
Structure of organophosphorus hydrolase.jpg
Structure of organophosphorus hydrolase
Identifiers
Symbol PTE
Pfam PF02126
InterPro IPR001559
PROSITE PDOC01026
SCOP 1dpm
SUPERFAMILY 1dpm
an aryl dialkyl phosphate + H2O dialkyl phosphate + an aryl alcohol

Thus, the two substrates of this enzyme are aryldialkylphosphate and H2O, whereas its two products are dialkylphosphate and aryl alcohol.

The gene (opd, for organophosphate-degrading) that codes for the enzyme is found in a large plasmid (pSC1, 51Kb) endogenous to Pseudomonas diminuta,[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 OPs.[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.

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.

Minimal kinetic model for hydrolysis of organophosphates (S) by enzyme PTE (E)

Kinetics

The kinetic model proposed consists of a reversible binding step that takes place between the enzyme and the substrate, and the formation of the Michaelis complex (ES). An irreversible step follows, when the P–O bond is cleaved and the transient enzyme + product (EP) complex is formed. Lastly, the products are released and the free enzyme (E) is regenerated.[9]

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.

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.

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].

References

  1. ^ a b 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. 
  2. ^ a b c 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. PMC 204325Freely accessible. PMID 3202637. 
  3. ^ a b c d e f g h i j Singh BK (February 2009). "Organophosphorus-degrading bacteria: ecology and industrial applications". Nature Reviews. Microbiology. 7 (2): 156–64. doi:10.1038/nrmicro2050. PMID 19098922. 
  4. ^ a b c d e f g h 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. doi:10.1128/AEM.69.5.2533-2539.2003. PMC 154515Freely accessible. PMID 12732518. 
  5. ^ a b 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. ^ a b 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. PMC 238989Freely accessible. PMID 3015022. 
  7. ^ a b c d 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. 
  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. ^ a b 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. ^ a b 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. PMC 184103Freely accessible. 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 1169522Freely accessible. PMID 15995215. 
  12. ^ a b 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. 
  13. ^ a b 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. 
  14. ^ a b 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. ^ a b 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. 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. 
  17. ^ Ragnarsdottir KV (2000). "Environmental fate and toxicology of organophosphate pesticides". Journal of the Geological Society. 157 (4): 859–876. doi:10.1144/jgs.157.4.859. 

Further reading

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Phosphotriesterase family Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001559

Bacteria such as Brevundimonas diminuta (Pseudomonas diminuta) harbour a plasmid that carries the gene for phosphotriesterase (PTE also known as parathion hydrolase; EC). This enzyme has attracted interest because of its potential use in the detoxification of chemical waste and organophosphate warfare agents such as VX, soman, and sarin, and its ability to degrade agricultural pesticides such as parathion. It acts specifically on synthetic organophosphate triesters and phosphorofluoridates. It does not seem to have a naturally occuring substrate and may thus have optimally evolved for utilising paraoxon.

PTE exists as a homodimer with one active site per monomer. The active site is located next to a binuclear metal centre, at the C-terminal end of a TIM alpha- beta barrel motif. The native enzyme contains two zinc ions at the active site however these can be replaced with other metals such as cobalt, cadmium, nickel or manganese and the enzyme remains active [PUBMED:10858282, PUBMED:8396425, PUBMED:9314115, PUBMED:11170459, PUBMED:7867909].

PTE belongs to a family [PUBMED:9383406, PUBMED:9548740] of enzymes that possess a binuclear zinc metal centre at their active site. The two zinc ions are coordinated by six different residues, six of which being histidines. This family so far includes, in addition to the parathion hydrolase, the following proteins:

  • Sulfolobus solfataricus aryldialkylphosphatase that has a low paraoxonase activity [PUBMED:15909078].
  • E. coli php (phosphotriesterase homology) protein. The substrate of php is not yet known [PUBMED:9548740].
  • Mycobacterium tuberculosis phosphotriesterase homology protein Rv0230C.
  • Phospho-furanose lactonase from Mycoplasma [PUBMED:24955762].
  • Animal phosphotriesterase related protein (PTER) (RPR-1).

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan Amidohydrolase (CL0034), which has the following description:

This family includes a large family of metal dependent amidohydrolase enzymes [1].

The clan contains the following 14 members:

A_deaminase Amidohydro_1 Amidohydro_2 Amidohydro_3 DHOase DUF3604 Peptidase_M19 PHP PHP_C PTE RNase_P_p30 TatD_DNase Urease_alpha UxaC

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(3)
Full
(1651)
Representative proteomes UniProt
(4651)
NCBI
(7296)
Meta
(83)
RP15
(380)
RP35
(1025)
RP55
(1650)
RP75
(2419)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(3)
Full
(1651)
Representative proteomes UniProt
(4651)
NCBI
(7296)
Meta
(83)
RP15
(380)
RP35
(1025)
RP55
(1650)
RP75
(2419)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(3)
Full
(1651)
Representative proteomes UniProt
(4651)
NCBI
(7296)
Meta
(83)
RP15
(380)
RP35
(1025)
RP55
(1650)
RP75
(2419)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: IPR001559
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mian N , Bateman A , Griffiths-Jones SR
Number in seed: 3
Number in full: 1651
Average length of the domain: 298.40 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 93.07 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.4 22.4
Noise cut-off 22.3 22.3
Model length: 298
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There is 1 interaction for this family. More...

PTE

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PTE domain has been found. There are 247 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

Loading structure mapping...