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PDBsum entry 1nww

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1nww
Jmol
Contents
Protein chains
145 a.a. *
Ligands
HPN ×2
MES
Waters ×378
* Residue conservation analysis
PDB id:
1nww
Name: Hydrolase
Title: Limonene-1,2-epoxide hydrolase
Structure: Limonene-1,2-epoxide hydrolase. Chain: a, b. Ec: 3.3.2.8
Source: Rhodococcus erythropolis. Organism_taxid: 1833. Strain: dcl14
Biol. unit: Dimer (from PQS)
Resolution:
1.20Å     R-factor:   0.148     R-free:   0.175
Authors: M.Arand,B.M.Hallberg,J.Zou,T.Bergfors,F.Oesch,M.J.Van Der Werf,J.A.M.De Bont,T.A.Jones,S.L.Mowbray
Key ref:
M.Arand et al. (2003). Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site. EMBO J, 22, 2583-2592. PubMed id: 12773375 DOI: 10.1093/emboj/cdg275
Date:
07-Feb-03     Release date:   10-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9ZAG3  (LIMA_RHOER) -  Limonene-1,2-epoxide hydrolase
Seq:
Struc:
149 a.a.
145 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.3.2.8  - Limonene-1,2-epoxide hydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 1,2-epoxymenth-8-ene + H2O = menth-8-ene-1,2-diol
1,2-epoxymenth-8-ene
Bound ligand (Het Group name = HPN)
matches with 66.00% similarity
+ H(2)O
= menth-8-ene-1,2-diol
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     2 terms  

 

 
    Key reference    
 
 
DOI no: 10.1093/emboj/cdg275 EMBO J 22:2583-2592 (2003)
PubMed id: 12773375  
 
 
Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site.
M.Arand, B.M.Hallberg, J.Zou, T.Bergfors, F.Oesch, M.J.van der Werf, J.A.de Bont, T.A.Jones, S.L.Mowbray.
 
  ABSTRACT  
 
Epoxide hydrolases are essential for the processing of epoxide-containing compounds in detoxification or metabolism. The classic epoxide hydrolases have an alpha/beta hydrolase fold and act via a two-step reaction mechanism including an enzyme-substrate intermediate. We report here the structure of the limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis, solved using single-wavelength anomalous dispersion from a selenomethionine-substituted protein and refined at 1.2 A resolution. This enzyme represents a completely different structure and a novel one-step mechanism. The fold features a highly curved six-stranded mixed beta-sheet, with four alpha-helices packed onto it to create a deep pocket. Although most residues lining this pocket are hydrophobic, a cluster of polar groups, including an Asp-Arg-Asp triad, interact at its deepest point. Site-directed mutagenesis supports the conclusion that this is the active site. Further, a 1.7 A resolution structure shows the inhibitor valpromide bound at this position, with its polar atoms interacting directly with the residues of the triad. We suggest that several bacterial proteins of currently unknown function will share this structure and, in some cases, catalytic properties.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 The active site. (A) Catalytic residues, showing their relationship to each other and supporting side-chains, as well as to the water molecule and endogenous ligand found in the LEH active site. Hydrogen-bonding interactions are shown by dotted lines. Colouring of the ribbon portions follows the rainbow scheme defined in Figure 2. The electron density of the endogenous ligand (modelled as heptanamide) in the final 2F[o] - Fc[o] map is contoured at a level of 1 . (B) Hydrogen-bonding interactions between active-site groups and the endogenous ligand. The figure shows Asp132 acting as the base and Asp101 as the acid. Where the donor–acceptor relationship is not clear from the available data, hydrogen bonds are indicated by double-headed arrows. (C) Complex with valpromide. The electron density of the final 2F[o] - Fc[o] map is contoured at a level of 1 .
Figure 5.
Figure 5 Mechanisms of epoxide hydrolases. (A) The mechanism of LEH indicated by the experimental results, using styrene oxide as an example. The catalytic water molecule is held in place and activated by hydrogen bonding to residues Asp132, Asn55 and Tyr53. The activated water molecule forces epoxide ring opening by nucleophilic attack at one of the ring carbons. At the same time, Asp101 activates the epoxide ring by donation of a proton to the epoxide oxygen (acid catalysis). Thus the formation of the diol from the epoxide proceeds in a single step by a push–pull mechanism. After this step, Asp132 should be in the protonated state and Asp101 should be charged, which can be rapidly reversed with the aid of Arg99 as a proton shuttle. The hydrogen bond donor/acceptor atoms for Tyr53 and Asp55 cannot be proved using current information, and only one of the two possibilities is drawn. (B) Reaction mechanism of / fold EHs. In these enzymes, two tyrosines position the epoxide oxygen by hydrogen bonding and activate the epoxide for nucleophilic attack by an aspartic acid residue. This first step leads to the formation of an enzyme–substrate ester intermediate. Subsequent hydrolysis of the intermediate is achieved by a water molecule activated by a His-Asp/Glu charge relay system. The hydrolysis leads to product formation and reconstitution of the active enzyme. The tyrosines and charge relay system are only shown in the present scheme where they contribute to the mechanism.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 2583-2592) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20372740 D.O'Hagan, and J.W.Schmidberger (2010).
Enzymes that catalyse SN2 reaction mechanisms.
  Nat Prod Rep, 27, 900-918.  
20179877 P.Domínguez de María, R.W.van Gemert, A.J.Straathof, and U.Hanefeld (2010).
Biosynthesis of ethers: unusual or common natural events?
  Nat Prod Rep, 27, 370-392.  
19496106 B.T.Ueberbacher, G.Oberdorfer, K.Gruber, and K.Faber (2009).
Epoxide-hydrolase-initiated hydrolysis/rearrangement cascade of a methylene-interrupted bis-epoxide yields chiral THF moieties without involvement of a "cyclase".
  Chembiochem, 10, 1697-1704.  
19301315 C.Li, K.E.Roege, and W.L.Kelly (2009).
Analysis of the indanomycin biosynthetic gene cluster from Streptomyces antibioticus NRRL 8167.
  Chembiochem, 10, 1064-1072.  
19340413 M.Decker, M.Arand, and A.Cronin (2009).
Mammalian epoxide hydrolases in xenobiotic metabolism and signalling.
  Arch Toxicol, 83, 297-318.  
19500970 M.J.Sippl (2009).
Fold space unlimited.
  Curr Opin Struct Biol, 19, 312-320.  
18585390 B.K.Biswal, C.Morisseau, G.Garen, M.M.Cherney, C.Garen, C.Niu, B.D.Hammock, and M.N.James (2008).
The molecular structure of epoxide hydrolase B from Mycobacterium tuberculosis and its complex with a urea-based inhibitor.
  J Mol Biol, 381, 897-912.
PDB codes: 2e3j 2zjf
18383502 C.Morisseau, B.D.Hammock, and G.Brookes (2008).
Gerry Brooks and epoxide hydrolases: four decades to a pharmaceutical.
  Pest Manag Sci, 64, 594-609.  
18675376 H.Deng, and D.O'Hagan (2008).
The fluorinase, the chlorinase and the duf-62 enzymes.
  Curr Opin Chem Biol, 12, 582-592.  
19025863 L.Smith, H.Hong, J.B.Spencer, and P.F.Leadlay (2008).
Analysis of specific mutants in the lasalocid gene cluster: evidence for enzymatic catalysis of a disfavoured polyether ring closure.
  Chembiochem, 9, 2967-2975.  
17405175 E.Y.Lee, and M.L.Shuler (2007).
Molecular engineering of epoxide hydrolase and its application to asymmetric and enantioconvergent hydrolysis.
  Biotechnol Bioeng, 98, 318-327.  
16632258 A.R.Gallimore, C.B.Stark, A.Bhatt, B.M.Harvey, Y.Demydchuk, V.Bolanos-Garcia, D.J.Fowler, J.Staunton, P.F.Leadlay, and J.B.Spencer (2006).
Evidence for the role of the monB genes in polyether ring formation during monensin biosynthesis.
  Chem Biol, 13, 453-460.  
16767782 A.R.Gallimore, and J.B.Spencer (2006).
Stereochemical uniformity in marine polyether ladders--implications for the biosynthesis and structure of maitotoxin.
  Angew Chem Int Ed Engl, 45, 4406-4413.  
15822179 C.Morisseau, and B.D.Hammock (2005).
Epoxide hydrolases: mechanisms, inhibitor designs, and biological roles.
  Annu Rev Pharmacol Toxicol, 45, 311-333.  
15748653 J.W.Newman, C.Morisseau, and B.D.Hammock (2005).
Epoxide hydrolases: their roles and interactions with lipid metabolism.
  Prog Lipid Res, 44, 1.  
15071504 A.Sultana, P.Kallio, A.Jansson, J.S.Wang, J.Niemi, P.Mäntsälä, and G.Schneider (2004).
Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation.
  EMBO J, 23, 1911-1921.
PDB code: 1sjw
12943851 E.J.de Vries, and D.B.Janssen (2003).
Biocatalytic conversion of epoxides.
  Curr Opin Biotechnol, 14, 414-420.  
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.