spacer
spacer

PDBsum entry 1a7u

Go to PDB code: 
protein Protein-protein interface(s) links
Haloperoxidase PDB id
1a7u
Jmol
Contents
Protein chains
277 a.a. *
Waters ×399
* Residue conservation analysis
PDB id:
1a7u
Name: Haloperoxidase
Title: Chloroperoxidase t
Structure: Chloroperoxidase t. Chain: a, b. Synonym: haloperoxidase t. Engineered: yes
Source: Streptomyces aureofaciens. Organism_taxid: 1894. Strain: tue24. Gene: cpot. Expressed in: streptomyces lividans. Expression_system_taxid: 1916.
Biol. unit: Trimer (from PQS)
Resolution:
1.75Å     R-factor:   0.149     R-free:   0.176
Authors: B.Hofmann,S.Toelzer,I.Pelletier,J.Altenbuchner,K.-H.Van Pee, H.-J.Hecht
Key ref:
B.Hofmann et al. (1998). Structural investigation of the cofactor-free chloroperoxidases. J Mol Biol, 279, 889-900. PubMed id: 9642069 DOI: 10.1006/jmbi.1998.1802
Date:
17-Mar-98     Release date:   17-Jun-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O31168  (PRXC_STRAU) -  Non-heme chloroperoxidase
Seq:
Struc:
278 a.a.
277 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.10  - Chloride peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RH + Cl- + H2O2 = RCl + 2 H2O
RH
+ Cl(-)
+ H(2)O(2)
= RCl
+ 2 × H(2)O
      Cofactor: Heme
Heme
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1998.1802 J Mol Biol 279:889-900 (1998)
PubMed id: 9642069  
 
 
Structural investigation of the cofactor-free chloroperoxidases.
B.Hofmann, S.Tölzer, I.Pelletier, J.Altenbuchner, K.H.van Pée, H.J.Hecht.
 
  ABSTRACT  
 
The structures of cofactor-free haloperoxidases from Streptomyces aureofaciens, Streptomyces lividans, and Pseudomonas fluorescens have been determined at resolutions between 1.9 A and 1.5 A. The structures of two enzymes complexed with benzoate or propionate identify the binding site for the organic acids which are required for the haloperoxidase activity. Based on these complexes and on the structure of an inactive variant, a reaction mechanism is proposed for the halogenation reaction with peroxoacid and hypohalous acid as reaction intermediates. Comparison of the structures suggests that a specific halide binding site is absent in the enzymes but that hydrophobic organic compounds may fit into the active site pocket for halogenation at preferential sites.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo picture of the electron density of the substrate complexes. The coordinates of the substrate molecules benzoic acid and propionic acid were left out of the entire refinement and all map calculations in order to reduce model bias. The density of the (2F[obs]−F[calc]) map is contoured at the 1.0 σ level and colored green, the density of the (F[obs]–F[calc]) difference map is contoured at the 4.0 σ level and colored blue. (a) Stereo picture of the electron density for the complex of CPO-T with benzoate. Residual electron density at Ser98 indicates the alternative, lower occupancy, side-chain conformation. (b) Stereo picture of the electron density for the complex of CPO-F with propionate.
Figure 4.
Figure 4. Stereo picture of the active site of the Met99Thr variant of CPO-A2. (a) Stereo picture of the electron density showing the bound chloride ion and the side-chain conformation of Thr99 in the variant. The density of the (2F[obs]–F[calc]) map is contoured at the 1.0 σ level. (b) Stereo picture of a superimposition of wild-type CPO-L (C^α trace and carbon atoms colored dark gray) on the variant (C^α trace colored red and carbon atoms colored yellow). The chloride ion is colored magenta. The chloride ion is colored magenta.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 279, 889-900) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19957260 G.Labar, C.Bauvois, F.Borel, J.L.Ferrer, J.Wouters, and D.M.Lambert (2010).
Crystal structure of the human monoacylglycerol lipase, a key actor in endocannabinoid signaling.
  Chembiochem, 11, 218-227.
PDB code: 3hju
20099871 K.M.McCulloch, T.Mukherjee, T.P.Begley, and S.E.Ealick (2010).
Structure determination and characterization of the vitamin B6 degradative enzyme (E)-2-(acetamidomethylene)succinate hydrolase.
  Biochemistry, 49, 1226-1235.
PDB code: 3kxp
20080731 R.A.Steiner, H.J.Janssen, P.Roversi, A.J.Oakley, and S.Fetzner (2010).
Structural basis for cofactor-independent dioxygenation of N-heteroaromatic compounds at the alpha/beta-hydrolase fold.
  Proc Natl Acad Sci U S A, 107, 657-662.
PDB codes: 2wj3 2wj4 2wj6 2wm2 3ibt
19998400 S.Mulyani, E.Egel, C.Kittel, S.Turkanovic, W.Wohlleben, R.D.Süssmuth, and K.H.van Pée (2010).
The thioesterase Bhp is involved in the formation of beta-hydroxytyrosine during balhimycin biosynthesis in Amycolatopsis balhimycina.
  Chembiochem, 11, 266-271.  
20112920 d.e. .L.T.Yin, P.Bernhardt, K.L.Morley, Y.Jiang, J.D.Cheeseman, V.Purpero, J.D.Schrag, and R.J.Kazlauskas (2010).
Switching catalysis from hydrolysis to perhydrolysis in Pseudomonas fluorescens esterase.
  Biochemistry, 49, 1931-1942.
PDB codes: 3hea 3hi4
19486005 A.R.King, A.Lodola, C.Carmi, J.Fu, M.Mor, and D.Piomelli (2009).
A critical cysteine residue in monoacylglycerol lipase is targeted by a new class of isothiazolinone-based enzyme inhibitors.
  Br J Pharmacol, 157, 974-983.  
18359859 A.Smeets, E.Loumaye, A.Clippe, J.F.Rees, B.Knoops, and J.P.Declercq (2008).
The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers.
  Protein Sci, 17, 700-710.
PDB codes: 2v2g 2v32 2v41
18058773 C.Li, M.Hassler, and T.D.Bugg (2008).
Catalytic promiscuity in the alpha/beta-hydrolase superfamily: hydroxamic acid formation, C--C bond formation, ester and thioester hydrolysis in the C--C hydrolase family.
  Chembiochem, 9, 71-76.  
18175319 M.Okai, Y.Miyauchi, A.Ebihara, W.C.Lee, K.Nagata, and M.Tanokura (2008).
Crystal structure of the proline iminopeptidase-related protein TTHA1809 from Thermus thermophilus HB8.
  Proteins, 70, 1646-1649.
PDB code: 2yys
18595691 S.Bhattacharya, J.N.Labutti, D.R.Seiner, and K.S.Gates (2008).
Oxidative inactivation of protein tyrosine phosphatase 1B by organic hydroperoxides.
  Bioorg Med Chem Lett, 18, 5856-5859.  
17333168 M.Kataoka, K.Honda, K.Sakamoto, and S.Shimizu (2007).
Microbial enzymes involved in lactone compound metabolism and their biotechnological applications.
  Appl Microbiol Biotechnol, 75, 257-266.  
17486317 R.De Mot, G.Schoofs, and I.Nagy (2007).
Proteome analysis of Streptomyces coelicolor mutants affected in the proteasome system reveals changes in stress-responsive proteins.
  Arch Microbiol, 188, 257-271.  
16786268 J.K.Song, H.J.Ahn, H.S.Kim, and B.K.Song (2006).
Molecular cloning and expression of perhydrolase genes from Pseudomonas aeruginosa and Burkholderia cepacia in Escherichia coli.
  Biotechnol Lett, 28, 849-856.  
16195462 C.Dong, S.Flecks, S.Unversucht, C.Haupt, K.H.van Pée, and J.H.Naismith (2005).
Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination.
  Science, 309, 2216-2219.
PDB codes: 2apg 2aqj 2ar8 2ard
16321951 F.Elmi, H.T.Lee, J.Y.Huang, Y.C.Hsieh, Y.L.Wang, Y.J.Chen, S.Y.Shaw, and C.J.Chen (2005).
Stereoselective esterase from Pseudomonas putida IFO12996 reveals alpha/beta hydrolase folds for D-beta-acetylthioisobutyric acid synthesis.
  J Bacteriol, 187, 8470-8476.
PDB code: 1zoi
15803517 P.Bernhardt, K.Hult, and R.J.Kazlauskas (2005).
Molecular basis of perhydrolase activity in serine hydrolases.
  Angew Chem Int Ed Engl, 44, 2742-2746.  
15975510 S.M.Saario, O.M.Salo, T.Nevalainen, A.Poso, J.T.Laitinen, T.Järvinen, and R.Niemi (2005).
Characterization of the sulfhydryl-sensitive site in the enzyme responsible for hydrolysis of 2-arachidonoyl-glycerol in rat cerebellar membranes.
  Chem Biol, 12, 649-656.  
15632289 T.Kaneko, N.Tanaka, and T.Kumasaka (2005).
Crystal structures of RsbQ, a stress-response regulator in Bacillus subtilis.
  Protein Sci, 14, 558-565.
PDB codes: 1wom 1wpr
14672934 B.Padmanabhan, T.Kuzuhara, N.Adachi, and M.Horikoshi (2004).
The crystal structure of CCG1/TAF(II)250-interacting factor B (CIB).
  J Biol Chem, 279, 9615-9624.
PDB code: 1imj
15139923 C.H.Kim, J.H.Lee, J.H.Heo, O.S.Kwon, H.A.Kang, and S.K.Rhee (2004).
Cloning and expression of a novel esterase gene cpoA from Burkholderia cepacia.
  J Appl Microbiol, 96, 1306-1316.  
15159570 I.Janda, Y.Devedjiev, D.Cooper, M.Chruszcz, U.Derewenda, A.Gabrys, W.Minor, A.Joachimiak, and Z.S.Derewenda (2004).
Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 angstroms resolution.
  Acta Crystallogr D Biol Crystallogr, 60, 1101-1107.
PDB code: 1uxo
15213385 J.D.Cheeseman, A.Tocilj, S.Park, J.D.Schrag, and R.J.Kazlauskas (2004).
Structure of an aryl esterase from Pseudomonas fluorescens.
  Acta Crystallogr D Biol Crystallogr, 60, 1237-1243.
PDB code: 1va4
14998991 K.Gruber, G.Gartler, B.Krammer, H.Schwab, and C.Kratky (2004).
Reaction mechanism of hydroxynitrile lyases of the alpha/beta-hydrolase superfamily: the three-dimensional structure of the transient enzyme-substrate complex certifies the crucial role of LYS236.
  J Biol Chem, 279, 20501-20510.
PDB codes: 1sc9 1sci 1sck 1scq
  15215448 T.A.Binkowski, P.Freeman, and J.Liang (2004).
pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins.
  Nucleic Acids Res, 32, W555-W558.  
15523680 U.T.Bornscheuer, and R.J.Kazlauskas (2004).
Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways.
  Angew Chem Int Ed Engl, 43, 6032-6040.  
12878604 A.Jansson, J.Niemi, P.Mäntsälä, and G.Schneider (2003).
Crystal structure of aclacinomycin methylesterase with bound product analogues: implications for anthracycline recognition and mechanism.
  J Biol Chem, 278, 39006-39013.
PDB codes: 1q0r 1q0z
12542698 K.Honda, M.Kataoka, E.Sakuradani, and S.Shimizu (2003).
Role of Acinetobacter calcoaceticus 3,4-dihydrocoumarin hydrolase in oxidative stress defence against peroxoacids.
  Eur J Biochem, 270, 486-494.  
12892883 R.De Mot, A.De Schrijver, G.Schoofs, and A.H.Parret (2003).
The thiocarbamate-inducible Rhodococcus enzyme ThcF as a member of the family of alpha/beta hydrolases with haloperoxidative side activity.
  FEMS Microbiol Lett, 224, 197-203.  
11933065 B.Reva, A.Finkelstein, and S.Topiol (2002).
Threading with chemostructural restrictions method for predicting fold and functionally significant residues: application to dipeptidylpeptidase IV (DPP-IV).
  Proteins, 47, 180-193.  
11933063 E.Shaw, L.A.McCue, C.E.Lawrence, and J.S.Dordick (2002).
Identification of a novel class in the alpha/beta hydrolase fold superfamily: the N-myc differentiation-related proteins.
  Proteins, 47, 163-168.  
12011065 J.J.Polderman-Tijmes, P.A.Jekel, C.M.Jeronimus-Stratingh, A.P.Bruins, J.M.Van Der Laan, T.Sonke, and D.B.Janssen (2002).
Identification of the catalytic residues of alpha-amino acid ester hydrolase from Acetobacter turbidans by labeling and site-directed mutagenesis.
  J Biol Chem, 277, 28474-28482.  
12454479 M.M.Mehanni, A.P.Turnbull, S.E.Sedelnikova, P.J.Baker, S.Foster, and D.W.Rice (2002).
Crystallization and preliminary X-ray analysis of the ytxM gene product from Bacillus subtilis.
  Acta Crystallogr D Biol Crystallogr, 58, 2138-2140.  
11880037 O.Puk, P.Huber, D.Bischoff, J.Recktenwald, G.Jung, R.D.Süssmuth, K.H.van Pée, W.Wohlleben, and S.Pelzer (2002).
Glycopeptide biosynthesis in Amycolatopsis mediterranei DSM5908: function of a halogenase and a haloperoxidase/perhydrolase.
  Chem Biol, 9, 225-235.  
11958814 V.M.Dembitsky, and M.Srebnik (2002).
Natural halogenated fatty acids: their analogues and derivatives.
  Prog Lipid Res, 41, 315-367.  
11571150 M.G.Mason, A.S.Ball, B.J.Reeder, G.Silkstone, P.Nicholls, and M.T.Wilson (2001).
Extracellular heme peroxidases in actinomycetes: a case of mistaken identity.
  Appl Environ Microbiol, 67, 4512-4519.  
10673439 J.Zou, B.M.Hallberg, T.Bergfors, F.Oesch, M.Arand, S.L.Mowbray, and T.A.Jones (2000).
Structure of Aspergillus niger epoxide hydrolase at 1.8 A resolution: implications for the structure and function of the mammalian microsomal class of epoxide hydrolases.
  Structure, 8, 111-122.
PDB code: 1qo7
10722044 K.H.van Pée, S.Keller, T.Wage, I.Wynands, H.Schnerr, and S.Zehner (2000).
Enzymatic halogenation catalyzed via a catalytic triad and by oxidoreductases.
  Biol Chem, 381, 1-5.  
10601844 M.Kataoka, K.Honda, and S.Shimizu (2000).
3,4-Dihydrocoumarin hydrolase with haloperoxidase activity from Acinetobacter calcoaceticus F46.
  Eur J Biochem, 267, 3.  
10684634 S.M.Fleming, T.A.Robertson, G.J.Langley, and T.D.Bugg (2000).
Catalytic mechanism of a C-C hydrolase enzyme: evidence for a gem-diol intermediate, not an acyl enzyme.
  Biochemistry, 39, 1522-1531.  
  10482514 F.Fischer, S.Künne, and S.Fetzner (1999).
Bacterial 2,4-dioxygenases: new members of the alpha/beta hydrolase-fold superfamily of enzymes functionally related to serine hydrolases.
  J Bacteriol, 181, 5725-5733.  
10021409 J.Littlechild (1999).
Haloperoxidases and their role in biotransformation reactions.
  Curr Opin Chem Biol, 3, 28-34.  
10607665 M.Nardini, and B.W.Dijkstra (1999).
Alpha/beta hydrolase fold enzymes: the family keeps growing.
  Curr Opin Struct Biol, 9, 732-737.  
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 code is shown on the right.