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PDBsum entry 1auo

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protein Protein-protein interface(s) links
Hydrolase PDB id
1auo
Jmol
Contents
Protein chains
218 a.a. *
Waters ×235
* Residue conservation analysis
PDB id:
1auo
Name: Hydrolase
Title: Carboxylesterase from pseudomonas fluorescens
Structure: Carboxylesterase. Chain: a, b. Engineered: yes
Source: Pseudomonas fluorescens. Organism_taxid: 294. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
1.80Å     R-factor:   0.208     R-free:   0.273
Authors: K.K.Kim,H.K.Song,S.W.Suh
Key ref:
K.K.Kim et al. (1997). Crystal structure of carboxylesterase from Pseudomonas fluorescens, an alpha/beta hydrolase with broad substrate specificity. Structure, 5, 1571-1584. PubMed id: 9438866
Date:
01-Sep-97     Release date:   04-Mar-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q53547  (EST2_PSEFL) -  Carboxylesterase 2
Seq:
Struc:
218 a.a.
218 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.1.1  - Carboxylesterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A carboxylic ester + H2O = an alcohol + a carboxylate
carboxylic ester
+ H(2)O
= alcohol
+ carboxylate
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     carboxylic ester hydrolase activity     2 terms  

 

 
    reference    
 
 
Structure 5:1571-1584 (1997)
PubMed id: 9438866  
 
 
Crystal structure of carboxylesterase from Pseudomonas fluorescens, an alpha/beta hydrolase with broad substrate specificity.
K.K.Kim, H.K.Song, D.H.Shin, K.Y.Hwang, S.Choe, O.J.Yoo, S.W.Suh.
 
  ABSTRACT  
 
BACKGROUND: A group of esterases, classified as carboxylesterases, hydrolyze carboxylic ester bonds with relatively broad substrate specificity and are useful for stereospecific synthesis and hydrolysis of esters. One such carboxylesterase from Pseudomonas fluorescens is a homodimeric enzyme, consisting of 218-residue subunits. It shows a limited sequence similarity to some members of the alpha/beta hydrolase superfamily. Although crystal structures of a number of serine esterases and lipases have been reported, structural information on carboxylesterases is very limited. This study was undertaken in order to provide such information and to understand a structural basis for the substrate specificity of this carboxylesterase. RESULTS: In this study, the crystal structure of carboxylesterase from P. fluorescens has been determined by the isomorphous replacement method and refined to 1.8 A resolution. Each subunit consists of a central seven-stranded beta sheet flanked by six alpha helices. The structure reveals the catalytic triad as Ser 114-His 199-Asp 168. The structure of the enzyme in complex with the inhibitor phenylmethylsulfonyl fluoride has also been determined and refined to 2.5 . The inhibitor is covalently attached to Ser 114 of both subunits, with the aromatic ring occupying a hydrophobic site defined by the aliphatic sidechains of Leu23, Ile58, Ile70, Met73 and Val170. No large structural changes are observed between the free and inhibitor-bound structures. CONCLUSIONS: Carboxylesterase from P. fluorescens has the alpha/beta hydrolase fold and the Ser-His-Asp catalytic triad. The active-site cleft in each subunit is formed by the six loops covering the catalytic serine residue. Three of the active-site loops in each subunit are involved in a head-to-head subunit interaction to form a dimer; it may be these extra structural elements, not seen in other esterases, that account for the inability of carboxylesterase to hydrolyze long chain fatty acids. As a result of dimerization, the active-site clefts from the two subunits merge to form holes in the dimer. The active-site clefts are relatively open and thus the catalytic residues are exposed to the solvent. An oxyanion hole, formed by nitrogen atoms of Leu23 and Gln115, is present in both the free and inhibitor-bound structures. An open active site, as well as a large binding pocket for the acid part of substrates, in P. fluorescens carboxylesterase may contribute to its relatively broad substrate specificity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21059179 J.Martinez, S.Mancini, E.Tauberger, C.Weise, W.Saenger, and M.Solioz (2011).
Regulation and structure of YahD, a copper-inducible α/β serine hydrolase of Lactococcus lactis IL1403.
  FEMS Microbiol Lett, 314, 57-66.
PDB code: 3og9
21351219 Y.Jiang, K.L.Morley, J.D.Schrag, and R.J.Kazlauskas (2011).
Different active-site loop orientation in serine hydrolases versus acyltransferases.
  Chembiochem, 12, 768-776.
PDB code: 3ia2
20506386 D.C.Cantu, Y.Chen, and P.J.Reilly (2010).
Thioesterases: a new perspective based on their primary and tertiary structures.
  Protein Sci, 19, 1281-1295.  
19274093 D.Y.Little, and L.Chen (2009).
Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.
  PLoS ONE, 4, e4762.  
  16754966 C.Y.Yang, K.H.Chin, C.C.Chou, A.H.Wang, and S.H.Chou (2006).
Structure of XC6422 from Xanthomonas campestris at 1.6 A resolution: a small serine alpha/beta-hydrolase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 498-503.
PDB code: 2fuk
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.  
15717224 A.Pesaresi, G.Devescovi, D.Lamba, V.Venturi, and G.Degrassi (2005).
Isolation, characterization, and heterologous expression of a carboxylesterase of Pseudomonas aeruginosa PAO1.
  Curr Microbiol, 50, 102-109.  
15753098 D.H.Shin, N.Oganesyan, J.Jancarik, H.Yokota, R.Kim, and S.H.Kim (2005).
Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum.
  J Biol Chem, 280, 18326-18335.
PDB codes: 1ytd 1yte 1ytk 2i1o
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
15624212 J.W.Arndt, R.Schwarzenbacher, R.Page, P.Abdubek, E.Ambing, T.Biorac, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, M.Hornsby, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, L.Jaroszewski, S.A.Lesley, I.Levin, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, E.Nigoghossian, J.Ouyang, W.S.Peti, K.Quijano, R.Reyes, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, A.White, G.Wolf, Q.Xu, O.Zagnitko, K.O.Hodgson, J.Wooley, and I.A.Wilson (2005).
Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution.
  Proteins, 58, 755-758.
PDB code: 1vkh
15648092 K.Murayama, M.Shirouzu, T.Terada, S.Kuramitsu, and S.Yokoyama (2005).
Crystal structure of TT1662 from Thermus thermophilus HB8: a member of the alpha/beta hydrolase fold enzymes.
  Proteins, 58, 982-984.
PDB code: 1ufo
15688435 M.Zheng, K.Ginalski, L.Rychlewski, and N.V.Grishin (2005).
Protein domain of unknown function DUF1023 is an alpha/beta hydrolase.
  Proteins, 59, 1-6.  
15802654 S.Quevillon-Cheruel, N.Leulliot, M.Graille, N.Hervouet, F.Coste, H.Bénédetti, C.Zelwer, J.Janin, and H.Van Tilbeurgh (2005).
Crystal structure of yeast YHR049W/FSH1, a member of the serine hydrolase family.
  Protein Sci, 14, 1350-1356.
PDB code: 1ycd
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
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
14579361 R.P.Bahadur, P.Chakrabarti, F.Rodier, and J.Janin (2003).
Dissecting subunit interfaces in homodimeric proteins.
  Proteins, 53, 708-719.  
12577257 U.Schulze-Gahmen, J.Pelaschier, H.Yokota, R.Kim, and S.H.Kim (2003).
Crystal structure of a hypothetical protein, TM841 of Thermotoga maritima, reveals its function as a fatty acid-binding protein.
  Proteins, 50, 526-530.
PDB code: 1mgp
11979432 A.H.Prowse, L.Vanderveer, S.W.Milling, Z.Z.Pan, R.L.Dunbrack, X.X.Xu, and A.K.Godwin (2002).
OVCA2 is downregulated and degraded during retinoid-induced apoptosis.
  Int J Cancer, 99, 185-192.  
12007643 U.T.Bornscheuer (2002).
Microbial carboxyl esterases: classification, properties and application in biocatalysis.
  FEMS Microbiol Rev, 26, 73-81.  
11574472 B.J.Feys, L.J.Moisan, M.A.Newman, and J.E.Parker (2001).
Direct interaction between the Arabidopsis disease resistance signaling proteins, EDS1 and PAD4.
  EMBO J, 20, 5400-5411.  
11248699 E.De Vendittis, T.Ursby, R.Rullo, M.A.Gogliettino, M.Masullo, and V.Bocchini (2001).
Phenylmethanesulfonyl fluoride inactivates an archaeal superoxide dismutase by chemical modification of a specific tyrosine residue. Cloning, sequencing and expression of the gene coding for Sulfolobus solfataricus superoxide dismutase.
  Eur J Biochem, 268, 1794-1801.  
11738044 J.A.Prates, N.Tarbouriech, S.J.Charnock, C.M.Fontes, L.M.Ferreira, and G.J.Davies (2001).
The structure of the feruloyl esterase module of xylanase 10B from Clostridium thermocellum provides insights into substrate recognition.
  Structure, 9, 1183-1190.
PDB codes: 1gkk 1gkl
11226219 J.E.Padilla, C.Colovos, and T.O.Yeates (2001).
Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments.
  Proc Natl Acad Sci U S A, 98, 2217-2221.  
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
10944393 H.Ponstingl, K.Henrick, and J.M.Thornton (2000).
Discriminating between homodimeric and monomeric proteins in the crystalline state.
  Proteins, 41, 47-57.  
10944388 V.Z.Pletnev, T.S.Zamolodchikova, W.A.Pangborn, and W.L.Duax (2000).
Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities.
  Proteins, 41, 8.
PDB code: 1euf
11080636 Y.Devedjiev, Z.Dauter, S.R.Kuznetsov, T.L.Jones, and Z.S.Derewenda (2000).
Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 A.
  Structure, 8, 1137-1146.
PDB code: 1fj2
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.  
10607665 M.Nardini, and B.W.Dijkstra (1999).
Alpha/beta hydrolase fold enzymes: the family keeps growing.
  Curr Opin Struct Biol, 9, 732-737.  
10561608 M.T.Garcia-Conesa, P.A.Kroon, J.Ralph, F.A.Mellon, I.J.Colquhoun, L.Saulnier, J.F.Thibault, and G.Williamson (1999).
A cinnamoyl esterase from Aspergillus niger can break plant cell wall cross-links without release of free diferulic acids.
  Eur J Biochem, 266, 644-652.  
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.  
10064901 T.Toyoda, H.Sugimoto, and S.Yamashita (1999).
Sequence, expression in Escherichia coli, and characterization of lysophospholipase II.
  Biochim Biophys Acta, 1437, 182-193.  
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.