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PDBsum entry 1din

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protein links
Hydrolytic enzyme PDB id
1din
Jmol
Contents
Protein chain
234 a.a. *
Waters ×279
* Residue conservation analysis
PDB id:
1din
Name: Hydrolytic enzyme
Title: Dienelactone hydrolase at 2.8 angstroms
Structure: Dienelactone hydrolase. Chain: a. Synonym: dlh. Engineered: yes
Source: Pseudomonas knackmussii. Organism_taxid: 65741. Strain: b13. Gene: clc d. Expressed in: pseudomonas sp.. Expression_system_taxid: 306.
Resolution:
1.80Å     R-factor:   0.150    
Authors: D.L.Ollis,D.Pathak
Key ref: D.Pathak and D.Ollis (1990). Refined structure of dienelactone hydrolase at 1.8 A. J Mol Biol, 214, 497-525. PubMed id: 2380986
Date:
14-Mar-96     Release date:   17-Aug-96    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A115  (CLCD_PSESB) -  Carboxymethylenebutenolidase
Seq:
Struc:
236 a.a.
234 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.1.1.45  - Carboxymethylenebutenolidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4-carboxymethylenebut-2-en-4-olide + H2O = 4-oxohex-2-enedioate
4-carboxymethylenebut-2-en-4-olide
+ H(2)O
= 4-oxohex-2-enedioate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     aromatic compound catabolic process   1 term 
  Biochemical function     carboxylic ester hydrolase activity     3 terms  

 

 
    Added reference    
 
 
J Mol Biol 214:497-525 (1990)
PubMed id: 2380986  
 
 
Refined structure of dienelactone hydrolase at 1.8 A.
D.Pathak, D.Ollis.
 
  ABSTRACT  
 
The structure of dienelactone hydrolase (DLH) from Pseudomonus sp. B13, after stereochemically restrained least-squares refinement at 1.8 A resolution, is described. The final molecular model of DLH has a conventional R value of 0.150 and includes all but the carboxyl-terminal three residues that are crystallographically disordered. The positions of 279 water molecules are included in the final model. The root-mean-square deviation from ideal bond distances for the model is 0.014 A and the error in atomic co-ordinates is estimated to be 0.15 A. DLH is a monomeric enzyme containing 236 amino acid residues and is a member of the beta-ketoadipate pathway found in bacteria and fungi. DLH is an alpha/beta protein containing seven helices and eight strands of beta-pleated sheet. A single 4-turn 3(10)-helix is seen. The active-site Cys123 residues at the N-terminal end of an alpha-helix that is peculiar in its consisting entirely of hydrophobic residues (except for a C-terminal lysine). The beta-sheet is composed of parallel strands except for strand 2, which gives rise to a short antiparallel region at the N-terminal end of the central beta-sheet. The active-site cysteine residue is part of a triad of residues consisting of Cys123, His202 and Asp171, and is reminiscent of the serine/cysteine proteases. As in papain and actinidin, the active thiol is partially oxidized during X-ray data collection. The positions of both the reduced and the oxidized sulphur are described. The active site geometry suggests that a change in the conformation of the native thiol occurs upon diffusion of substrate into the active site cleft of DLH. This enables nucleophilic attack by the gamma-sulphur to occur on the cyclic ester substrate through a ring-opening reaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20177059 T.Ishizuka, I.Fujimori, M.Kato, C.Noji-Sakikawa, M.Saito, Y.Yoshigae, K.Kubota, A.Kurihara, T.Izumi, T.Ikeda, and O.Okazaki (2010).
Human carboxymethylenebutenolidase as a bioactivating hydrolase of olmesartan medoxomil in liver and intestine.
  J Biol Chem, 285, 11892-11902.  
17957779 I.Martínez-Martínez, J.Navarro-Fernández, J.Daniel Lozada-Ramírez, F.García-Carmona, and A.Sánchez-Ferrer (2008).
YesT: a new rhamnogalacturonan acetyl esterase from Bacillus subtilis.
  Proteins, 71, 379-388.  
17170116 L.I.de Eugenio, P.García, J.M.Luengo, J.M.Sanz, J.S.Román, J.L.García, and M.A.Prieto (2007).
Biochemical evidence that phaZ gene encodes a specific intracellular medium chain length polyhydroxyalkanoate depolymerase in Pseudomonas putida KT2442: characterization of a paradigmatic enzyme.
  J Biol Chem, 282, 4951-4962.  
17106678 S.Kakugawa, S.Fushinobu, T.Wakagi, and H.Shoun (2007).
Characterization of a thermostable carboxylesterase from the hyperthermophilic bacterium Thermotoga maritima.
  Appl Microbiol Biotechnol, 74, 585-591.  
16964968 G.P.Horsman, J.Ke, S.Dai, S.Y.Seah, J.T.Bolin, and L.D.Eltis (2006).
Kinetic and structural insight into the mechanism of BphD, a C-C bond hydrolase from the biphenyl degradation pathway.
  Biochemistry, 45, 11071-11086.
PDB code: 2og1
16551354 G.Schneider, G.Neuberger, M.Wildpaner, S.Tian, I.Berezovsky, and F.Eisenhaber (2006).
Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases.
  BMC Bioinformatics, 7, 164.  
16294303 H.Yano, and M.Kuroda (2006).
Disulfide proteome yields a detailed understanding of redox regulations: a model study of thioredoxin-linked reactions in seed germination.
  Proteomics, 6, 294-300.  
16162494 H.J.Korza, and M.Bochtler (2005).
Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow.
  J Biol Chem, 280, 40802-40812.
PDB codes: 1zrs 2aum 2aun
15983415 H.K.Kim, J.W.Liu, P.D.Carr, and D.L.Ollis (2005).
Following directed evolution with crystallography: structural changes observed in changing the substrate specificity of dienelactone hydrolase.
  Acta Crystallogr D Biol Crystallogr, 61, 920-931.
PDB codes: 1zi6 1zi8 1zi9 1zic 1zix 1ziy 1zj4 1zj5
12147492 Y.Hotta, S.Ezaki, H.Atomi, and T.Imanaka (2002).
Extremely stable and versatile carboxylesterase from a hyperthermophilic archaeon.
  Appl Environ Microbiol, 68, 3925-3931.  
10801485 A.Mølgaard, S.Kauppinen, and S.Larsen (2000).
Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases.
  Structure, 8, 373-383.
PDB codes: 1deo 1dex
11053834 A.Robinson, K.J.Edwards, P.D.Carr, J.D.Barton, G.D.Ewart, and D.L.Ollis (2000).
Structure of the C123S mutant of dienelactone hydrolase (DLH) bound with the PMS moiety of the protease inhibitor phenylmethylsulfonyl fluoride (PMSF).
  Acta Crystallogr D Biol Crystallogr, 56, 1376-1384.
PDB code: 1ggv
10747780 Y.Jia, T.J.Kappock, T.Frick, A.J.Sinskey, and J.Stubbe (2000).
Lipases provide a new mechanistic model for polyhydroxybutyrate (PHB) synthases: characterization of the functional residues in Chromatium vinosum PHB synthase.
  Biochemistry, 39, 3927-3936.  
  9864312 E.Masai, S.Shinohara, H.Hara, S.Nishikawa, Y.Katayama, and M.Fukuda (1999).
Genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of Sphingomonas paucimobilis SYK-6.
  J Bacteriol, 181, 55-62.  
10388775 G.H.Peters, T.M.Frimurer, J.N.Andersen, and O.H.Olsen (1999).
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  Biophys J, 77, 505-515.  
10547694 K.E.Jaeger, B.W.Dijkstra, and M.T.Reetz (1999).
Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases.
  Annu Rev Microbiol, 53, 315-351.  
10404588 P.Heikinheimo, A.Goldman, C.Jeffries, and D.L.Ollis (1999).
Of barn owls and bankers: a lush variety of alpha/beta hydrolases.
  Structure, 7, R141-R146.  
9922164 D.J.Quirk, C.Park, J.E.Thompson, and R.T.Raines (1998).
His...Asp catalytic dyad of ribonuclease A: conformational stability of the wild-type, D121N, D121A, and H119A enzymes.
  Biochemistry, 37, 17958-17964.  
9720251 J.Pleiss, M.Fischer, and R.D.Schmid (1998).
Anatomy of lipase binding sites: the scissile fatty acid binding site.
  Chem Phys Lipids, 93, 67-80.  
9636030 L.W.Schultz, D.J.Quirk, and R.T.Raines (1998).
His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes.
  Biochemistry, 37, 8886-8898.
PDB codes: 3rsd 4rsd
  9440530 M.Brückmann, R.Blasco, K.N.Timmis, and D.H.Pieper (1998).
Detoxification of protoanemonin by dienelactone hydrolase.
  J Bacteriol, 180, 400-402.  
9695945 V.Fülöp, Z.Böcskei, and L.Polgár (1998).
Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis.
  Cell, 94, 161-170.
PDB codes: 1qfm 1qfs
9562561 Y.Wei, L.Swenson, C.Castro, U.Derewenda, W.Minor, H.Arai, J.Aoki, K.Inoue, L.Servin-Gonzalez, and Z.S.Derewenda (1998).
Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 A resolution.
  Structure, 6, 511-519.
PDB code: 1jfr
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9268342 A.Wang, R.Loo, Z.Chen, and E.A.Dennis (1997).
Regiospecificity and catalytic triad of lysophospholipase I.
  J Biol Chem, 272, 22030-22036.  
9253409 L.Jin, B.A.Seaton, and J.F.Head (1997).
Crystal structure at 2.8 A resolution of anabolic ornithine transcarbamylase from Escherichia coli.
  Nat Struct Biol, 4, 622-625.
PDB code: 1akm
  8819168 A.J.Beveridge (1996).
A theoretical study of the active sites of papain and S195C rat trypsin: implications for the low reactivity of mutant serine proteinases.
  Protein Sci, 5, 1355-1365.  
8702766 T.Hisano, Y.Hata, T.Fujii, J.Q.Liu, T.Kurihara, N.Esaki, and K.Soda (1996).
Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold.
  J Biol Chem, 271, 20322-20330.
PDB code: 1jud
8805565 U.G.Wagner, M.Hasslacher, H.Griengl, H.Schwab, and C.Kratky (1996).
Mechanism of cyanogenesis: the crystal structure of hydroxynitrile lyase from Hevea brasiliensis.
  Structure, 4, 811-822.
PDB code: 1yas
7592717 L.W.Tjoelker, C.Eberhardt, J.Unger, H.L.Trong, G.A.Zimmerman, T.M.McIntyre, D.M.Stafforini, S.M.Prescott, and P.W.Gray (1995).
Plasma platelet-activating factor acetylhydrolase is a secreted phospholipase A2 with a catalytic triad.
  J Biol Chem, 270, 25481-25487.  
7765834 J.Powlowski, and V.Shingler (1994).
Genetics and biochemistry of phenol degradation by Pseudomonas sp. CF600.
  Biodegradation, 5, 219-236.  
7765840 M.Schlömann (1994).
Evolution of chlorocatechol catabolic pathways. Conclusions to be drawn from comparisons of lactone hydrolases.
  Biodegradation, 5, 301-321.  
8110969 S.E.Huston, and G.R.Marshall (1994).
Alpha/3(10)-helix transitions in alpha-methylalanine homopeptides: conformational transition pathway and potential of mean force.
  Biopolymers, 34, 75-90.  
8497485 E.Cheah, G.W.Ashley, J.Gary, and D.Ollis (1993).
Catalysis by dienelactone hydrolase: a variation on the protease mechanism.
  Proteins, 16, 64-78.  
8321908 J.Massoulié, L.Pezzementi, S.Bon, E.Krejci, and F.M.Vallette (1993).
Molecular and cellular biology of cholinesterases.
  Prog Neurobiol, 41, 31-91.  
  7684040 M.Schlömann, K.L.Ngai, L.N.Ornston, and H.J.Knackmuss (1993).
Dienelactone hydrolase from Pseudomonas cepacia.
  J Bacteriol, 175, 2994-3001.  
  8407778 S.R.Kaschabek, and W.Reineke (1993).
Degradation of chloroaromatics: purification and characterization of maleylacetate reductase from Pseudomonas sp. strain B13.
  J Bacteriol, 175, 6075-6081.  
  7691794 Y.Nagata, T.Nariya, R.Ohtomo, M.Fukuda, K.Yano, and M.Takagi (1993).
Cloning and sequencing of a dehalogenase gene encoding an enzyme with hydrolase activity involved in the degradation of gamma-hexachlorocyclohexane in Pseudomonas paucimobilis.
  J Bacteriol, 175, 6403-6410.  
8438232 Z.S.Derewenda, and A.M.Sharp (1993).
News from the interface: the molecular structures of triacylglyceride lipases.
  Trends Biochem Sci, 18, 20-25.  
1785133 A.Maelicke (1991).
Acetylcholine esterase: the structure.
  Trends Biochem Sci, 16, 355-356.  
1949158 C.Toniolo, and E.Benedetti (1991).
The polypeptide 310-helix.
  Trends Biochem Sci, 16, 350-353.  
1866431 D.Pathak, G.Ashley, and D.Ollis (1991).
Thiol protease-like active site found in the enzyme dienelactone hydrolase: localization using biochemical, genetic, and structural tools.
  Proteins, 9, 267-279.  
  2026135 S.M.Franken, H.J.Rozeboom, K.H.Kalk, and B.W.Dijkstra (1991).
Crystal structure of haloalkane dehalogenase: an enzyme to detoxify halogenated alkanes.
  EMBO J, 10, 1297-1302.
PDB code: 2had
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.