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PDBsum entry 1dpm
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1dpm

 

 

 

 

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Contents
Protein chains
329 a.a. *
Ligands
EBP ×4
FMT ×2
Metals
_ZN ×4
Waters ×263
* Residue conservation analysis
PDB id:
1dpm
Name: Hydrolase
Title: Three-dimensional structure of the zinc-containing phosphotriesterase with bound substrate analog diethyl 4-methylbenzylphosphonate
Structure: Phosphotriesterase. Chain: a, b
Source: Brevundimonas diminuta. Organism_taxid: 293
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.154    
Authors: J.L.Vanhooke,M.M.Benning,F.M.Raushel,H.M.Holden
Key ref:
J.L.Vanhooke et al. (1996). Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate. Biochemistry, 35, 6020-6025. PubMed id: 8634243 DOI: 10.1021/bi960325l
Date:
13-Feb-96     Release date:   20-Aug-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P0A434  (OPD_BREDI) -  Parathion hydrolase from Brevundimonas diminuta
Seq:
Struc: 		365 a.a.
329 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.8.1  - aryldialkylphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An aryl dialkyl phosphate + H2O = dialkyl phosphate + an aryl alcohol
aryl dialkyl phosphate
 + H2O
 = dialkyl phosphate
 + aryl alcohol
      Cofactor: Divalent cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1021/bi960325l Biochemistry 35:6020-6025 (1996)
PubMed id: 8634243  
 
 
Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate.
J.L.Vanhooke, M.M.Benning, F.M.Raushel, H.M.Holden.
 
  ABSTRACT  
 
Phosphotriesterase from Pseudomonas diminuta catalyzes the hydrolysis of paraoxon and related acetylcholinesterase inhibitors with rate enhancements that approach 10(12). The enzyme requires a binuclear metal center for activity and as isolated contains 2 equiv of zinc per subunit. Here we describe the three-dimensional structure of the Zn2+/Zn2+-substituted enzyme complexed with the substrate analog diethyl 4-methylbenzylphosphonate. Crystals employed in the investigation belonged to the space group C2 with unit cell dimensions of a = 129.6 A, b = 91.4 A, c = 69.4 A, beta = 91.9 degrees, and two subunits in the asymmetric unit. The model was refined by least-squares analysis to a nominal resolution of 2.1 A and a crystallographic R-factor of 15.4% for all measured X-ray data. As in the previously reported structure of the cadmium-containing enzyme, the bridging ligands are a carbamylated lysine residue (Lys 169) and a hydroxide. The zinc ions are separated by 3.3 A. The more buried zinc ion is surrounded by His 55, His 57, Lys 169, Asp 301, and the bridging hydroxide in a trigonal bipyramidal arrangement as described for the cadmium-substituted enzyme. Unlike the octahedral coordination observed for the more solvent-exposed cadmium ion, however, the second zinc is tetrahedrally ligated to Lys 169, His 201, His 230, and the bridging hydroxide. The diethyl 4-methylbenzylphosphonate occupies a site near the binuclear metal center with the phosphoryl oxygen of the substrate analog situated at 3.5 A from the more solvent-exposed zinc ion. The aromatic portion of the inhibitor binds in a fairly hydrophobic pocket. A striking feature of the active site pocket is the lack of direct electrostatic interactions between the inhibitor and the protein. This most likely explains the broad substrate specificity exhibited by phosphotriesterase. The position of the inhibitor within the active site suggests that the nucleophile for the hydrolysis reaction is the metal-bound hydroxide.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20890601 C.M.Theriot, and A.M.Grunden (2011).
Hydrolysis of organophosphorus compounds by microbial enzymes.
  Appl Microbiol Biotechnol, 89, 35-43.  
21485029 J.K.Raynes, F.G.Pearce, S.J.Meade, and J.A.Gerrard (2011).
Immobilization of organophosphate hydrolase on an amyloid fibril nanoscaffold: Towards bioremediation and chemical detoxification.
  Biotechnol Prog, 27, 360-367.  
21037279 L.Briseño-Roa, C.M.Timperley, A.D.Griffiths, and A.R.Fersht (2011).
Phosphotriesterase variants with high methylphosphonatase activity and strong negative trade-off against phosphotriesters.
  Protein Eng Des Sel, 24, 151-159.  
20650962 L.Briseño-Roa, Z.Oliynyk, C.M.Timperley, A.D.Griffiths, and A.R.Fersht (2011).
Highest paraoxonase turnover rate found in a bacterial phosphotriesterase variant.
  Protein Eng Des Sel, 24, 209-211.  
20868365 F.Ely, K.S.Hadler, L.R.Gahan, L.W.Guddat, D.L.Ollis, and G.Schenk (2010).
The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis.
  Biochem J, 432, 565-573.
PDB codes: 3ood 3oqe
19874798 B.Chen, C.Lei, Y.Shin, and J.Liu (2009).
Probing mechanisms for enzymatic activity enhancement of organophosphorus hydrolase in functionalized mesoporous silica.
  Biochem Biophys Res Commun, 390, 1177-1181.  
19353598 X.Zhang, R.Wu, L.Song, Y.Lin, M.Lin, Z.Cao, W.Wu, and Y.Mo (2009).
Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase.
  J Comput Chem, 30, 2388-2401.  
18688403 A.B.Curtiss, M.Bera, G.T.Musie, and D.R.Powell (2008).
Synthesis and characterization of mono- and micro6-sulfato hexanuclear zinc complexes of a new symmetric dinucleating ligand.
  Dalton Trans, (), 2717-2724.  
18369486 C.Neuhäuser, D.Domide, J.Mautz, E.Kaifer, and H.J.Himmel (2008).
Electron density controlled carbamate ligand binding mode: towards a better understanding of metalloenzyme activity.
  Dalton Trans, (), 1821-1824.  
18535849 R.E.Mirams, S.J.Smith, K.S.Hadler, D.L.Ollis, G.Schenk, and L.R.Gahan (2008).
Cadmium(II) complexes of the glycerophosphodiester-degrading enzyme GpdQ and a biomimetic N,O ligand.
  J Biol Inorg Chem, 13, 1065-1072.  
17575004 H.Jiang, C.Yang, H.Qu, Z.Liu, Q.S.Fu, and C.Qiao (2007).
Cloning of a novel aldo-keto reductase gene from Klebsiella sp. strain F51-1-2 and its functional expression in Escherichia coli.
  Appl Environ Microbiol, 73, 4959-4965.  
  17620708 M.Elias, J.Dupuy, L.Merone, C.Lecomte, M.Rossi, P.Masson, G.Manco, and E.Chabriere (2007).
Crystallization and preliminary X-ray diffraction analysis of the hyperthermophilic Sulfolobus solfataricus phosphotriesterase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 553-555.  
16088350 E.Efremenko, Y.Votchitseva, F.Plieva, I.Galaev, and B.Mattiasson (2006).
Purification of His6-organophosphate hydrolase using monolithic supermacroporous polyacrylamide cryogels developed for immobilized metal affinity chromatography.
  Appl Microbiol Biotechnol, 70, 558-563.  
16734778 I.Horne, X.Qiu, D.L.Ollis, R.J.Russell, and J.G.Oakeshott (2006).
Functional effects of amino acid substitutions within the large binding pocket of the phosphotriesterase OpdA from Agrobacterium sp. P230.
  FEMS Microbiol Lett, 259, 187-194.  
16327895 C.J.Jackson, J.W.Liu, M.L.Coote, and D.L.Ollis (2005).
The effects of substrate orientation on the mechanism of a phosphotriesterase.
  Org Biomol Chem, 3, 4343-4350.  
15593246 F.J.Stevens, C.Kuemmel, G.Babnigg, and F.R.Collart (2005).
Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: application.
  J Mol Recognit, 18, 150-157.  
16284925 L.L.Lin, W.H.Hsu, W.Y.Hsu, S.C.Kan, and H.Y.Hu (2005).
Phylogenetic analysis and biochemical characterization of a thermostable dihydropyrimidinase from alkaliphilic Bacillus sp. TS-23.
  Antonie Van Leeuwenhoek, 88, 189-197.  
15103151 L.Sun, Y.Dong, Y.Zhou, M.Yang, C.Zhang, Z.Rao, and X.E.Zhang (2004).
Crystallization and preliminary X-ray studies of methyl parathion hydrolase from Pseudomonas sp. WBC-3.
  Acta Crystallogr D Biol Crystallogr, 60, 954-956.  
12505981 A.D.Griffiths, and D.S.Tawfik (2003).
Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization.
  EMBO J, 22, 24-35.  
12757939 I.Horne, X.Qiu, R.J.Russell, and J.G.Oakeshott (2003).
The phosphotriesterase gene opdA in Agrobacterium radiobacter P230 is transposable.
  FEMS Microbiol Lett, 222, 1-8.  
12548728 J.Koca, C.G.Zhan, R.C.Rittenhouse, and R.L.Ornstein (2003).
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics.
  J Comput Chem, 24, 368-378.  
12837777 Z.Xu, Y.Liu, Y.Yang, W.Jiang, E.Arnold, and J.Ding (2003).
Crystal structure of D-Hydantoinase from Burkholderia pickettii at a resolution of 2.7 Angstroms: insights into the molecular basis of enzyme thermostability.
  J Bacteriol, 185, 4038-4049.
PDB code: 1nfg
11916726 C.M.Cho, A.Mulchandani, and W.Chen (2002).
Bacterial cell surface display of organophosphorus hydrolase for selective screening of improved hydrolysis of organophosphate nerve agents.
  Appl Environ Microbiol, 68, 2026-2030.  
11840523 D.Rochu, and P.Masson (2002).
Multiple advantages of capillary zone electrophoresis for exploring protein conformational stability.
  Electrophoresis, 23, 189-202.  
12057683 F.M.Raushel (2002).
Bacterial detoxification of organophosphate nerve agents.
  Curr Opin Microbiol, 5, 288-295.  
12089017 I.Horne, T.D.Sutherland, R.L.Harcourt, R.J.Russell, and J.G.Oakeshott (2002).
Identification of an opd (organophosphate degradation) gene in an Agrobacterium isolate.
  Appl Environ Microbiol, 68, 3371-3376.  
11775695 D.Walther, C.Fugger, H.Schreer, R.Kilian, and H.Görls (2001).
Reversible fixation of carbon dioxide at nickel(0) centers: a route for large organometallic rings, dimers, and tetramers.
  Chemistry, 7, 5214-5221.  
11435114 E.I.Scharff, J.Koepke, G.Fritzsch, C.Lücke, and H.Rüterjans (2001).
Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris.
  Structure, 9, 493-502.
PDB codes: 1e1a 2iao 2iap 2iaq 2iar 2ias 2iat 2iau
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
11295437 J.Hartleib, and H.Rüterjans (2001).
Insights into the reaction mechanism of the diisopropyl fluorophosphatase from Loligo vulgaris by means of kinetic studies, chemical modification and site-directed mutagenesis.
  Biochim Biophys Acta, 1546, 312-324.  
11170460 M.Chen-Goodspeed, M.A.Sogorb, F.Wu, and F.M.Raushel (2001).
Enhancement, relaxation, and reversal of the stereoselectivity for phosphotriesterase by rational evolution of active site residues.
  Biochemistry, 40, 1332-1339.  
11170459 M.Chen-Goodspeed, M.A.Sogorb, F.Wu, S.B.Hong, and F.M.Raushel (2001).
Structural determinants of the substrate and stereochemical specificity of phosphotriesterase.
  Biochemistry, 40, 1325-1331.  
11258882 M.M.Benning, H.Shim, F.M.Raushel, and H.M.Holden (2001).
High resolution X-ray structures of different metal-substituted forms of phosphotriesterase from Pseudomonas diminuta.
  Biochemistry, 40, 2712-2722.
PDB codes: 1hzy 1i03 1i0b 1i0d 1jgm
11599021 Y.P.Pang (2001).
Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method.
  Proteins, 45, 183-189.  
10858282 H.Shim, and F.M.Raushel (2000).
Self-assembly of the binuclear metal center of phosphotriesterase.
  Biochemistry, 39, 7357-7364.  
10074338 B.diSioudi, J.K.Grimsley, K.Lai, and J.R.Wild (1999).
Modification of near active site residues in organophosphorus hydrolase reduces metal stoichiometry and alters substrate specificity.
  Biochemistry, 38, 2866-2872.  
10074353 E.Meyer, T.J.Kappock, C.Osuji, and J.Stubbe (1999).
Evidence for the direct transfer of the carboxylate of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to generate 4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase.
  Biochemistry, 38, 3012-3018.  
9930975 S.B.Hong, and F.M.Raushel (1999).
Stereochemical constraints on the substrate specificity of phosphotriesterase.
  Biochemistry, 38, 1159-1165.  
10368287 S.Benini, W.R.Rypniewski, K.S.Wilson, S.Miletti, S.Ciurli, and S.Mangani (1999).
A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels.
  Structure, 7, 205-216.
PDB codes: 2ubp 3ubp
9651332 H.Shim, S.B.Hong, and F.M.Raushel (1998).
Hydrolysis of phosphodiesters through transformation of the bacterial phosphotriesterase.
  J Biol Chem, 273, 17445-17450.  
9667912 R.J.Kazlauskas, and H.K.Weber (1998).
Improving hydrolases for organic synthesis.
  Curr Opin Chem Biol, 2, 121-126.  
9730812 S.M.Fabiane, M.K.Sohi, T.Wan, D.J.Payne, J.H.Bateson, T.Mitchell, and B.J.Sutton (1998).
Crystal structure of the zinc-dependent beta-lactamase from Bacillus cereus at 1.9 A resolution: binuclear active site with features of a mononuclear enzyme.
  Biochemistry, 37, 12404-12411.
PDB code: 1bc2
9914255 U.Ermler, W.Grabarse, S.Shima, M.Goubeaud, and R.K.Thauer (1998).
Active sites of transition-metal enzymes with a focus on nickel.
  Curr Opin Struct Biol, 8, 749-758.  
9047295 J.M.Kuo, M.Y.Chae, and F.M.Raushel (1997).
Perturbations to the active site of phosphotriesterase.
  Biochemistry, 36, 1982-1988.  
9325279 L.M.Watkins, H.J.Mahoney, J.K.McCulloch, and F.M.Raushel (1997).
Augmented hydrolysis of diisopropyl fluorophosphate in engineered mutants of phosphotriesterase.
  J Biol Chem, 272, 25596-25601.  
9220990 S.B.Hong, L.S.Mullins, H.Shim, and F.M.Raushel (1997).
Mechanism-based inhibitors for the inactivation of the bacterial phosphotriesterase.
  Biochemistry, 36, 9022-9028.  
18576121 S.Ohuchi, H.Nakamura, H.Sligiura, M.Narita, and K.Sode (1997).
An optical resolution of racemic organophosphorous esters by phosphotriesterase-catalyzing hydrolysis.
  Appl Biochem Biotechnol, 63, 659-665.  
  8931134 J.B.Thoden, P.A.Frey, and H.M.Holden (1996).
High-resolution X-ray structure of UDP-galactose 4-epimerase complexed with UDP-phenol.
  Protein Sci, 5, 2149-2161.
PDB code: 2udp
8718883 S.B.Hong, and F.M.Raushel (1996).
Metal-substrate interactions facilitate the catalytic activity of the bacterial phosphotriesterase.
  Biochemistry, 35, 10904-10912.  
8939754 S.J.Cooper, G.A.Leonard, S.M.McSweeney, A.W.Thompson, J.H.Naismith, S.Qamar, A.Plater, A.Berry, and W.N.Hunter (1996).
The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold.
  Structure, 4, 1303-1315.
PDB code: 1zen
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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