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Hydrolase (serine esterase) PDB id
1esc
Jmol
Contents
Protein chain
302 a.a. *
Waters ×223
* Residue conservation analysis
PDB id:
1esc
Name: Hydrolase (serine esterase)
Title: The molecular mechanism of enantiorecognition by esterases
Structure: Esterase. Chain: a
Source: Streptomyces scabiei. Organism_taxid: 1930
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.166    
Authors: Y.Wei,J.L.Schottel,U.Derewenda,L.Swenson,S.Patkar, Z.S.Derewenda
Key ref: Y.Wei et al. (1995). A novel variant of the catalytic triad in the Streptomyces scabies esterase. Nat Struct Biol, 2, 218-223. PubMed id: 7773790 DOI: 10.1038/nsb0395-218
Date:
07-Oct-94     Release date:   15-Oct-95    
PROCHECK
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 Headers
 References

Protein chain
Pfam  
P22266  (ESTA_STRSC) -  Esterase
Seq:
Struc: 		345 a.a.
302 a.a.
Key:    Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biochemical function     hydrolase activity     2 terms  

 

 
DOI no: 10.1038/nsb0395-218 Nat Struct Biol 2:218-223 (1995)
PubMed id: 7773790  
 
 
A novel variant of the catalytic triad in the Streptomyces scabies esterase.
Y.Wei, J.L.Schottel, U.Derewenda, L.Swenson, S.Patkar, Z.S.Derewenda.
 
  ABSTRACT  
 
The crystal structure of a novel esterase from Streptomyces scabies, a causal agent of the potato scab disease, was solved at 2.1 A resolution. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases. The active site contains a dyad of Ser 14 and His 283, closely resembling two of the three components of typical Ser-His-Asp(Glu) triads from other serine hydrolases. Proper orientation of the active site imidazol is maintained by a hydrogen bond between the N delta-H group and a main chain oxygen. Thus, the enzyme constitutes the first known natural variation of the chymotrypsin-like triad in which a carboxylic acid is replaced by a neutral hydrogen-bond acceptor.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19201950 H.Kontkanen, A.Westerholm-Parvinen, M.Saloheimo, M.Bailey, M.Rättö, I.Mattila, M.Mohsina, N.Kalkkinen, T.Nakari-Setälä, and J.Buchert (2009).
Novel Coprinopsis cinerea polyesterase that hydrolyzes cutin and suberin.
  Appl Environ Microbiol, 75, 2148-2157.  
19116015 G.Li, K.Wang, and Y.H.Liu (2008).
Molecular cloning and characterization of a novel pyrethroid-hydrolyzing esterase originating from the Metagenome.
  Microb Cell Fact, 7, 38.  
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.  
18931117 Y.J.Park, S.J.Yoon, and H.B.Lee (2008).
A novel thermostable arylesterase from the archaeon Sulfolobus solfataricus P1: purification, characterization, and expression.
  J Bacteriol, 190, 8086-8095.  
17190827 A.Ben-Shem, D.Fass, and E.Bibi (2007).
Structural basis for intramembrane proteolysis by rhomboid serine proteases.
  Proc Natl Acad Sci U S A, 104, 462-466.
PDB code: 2irv
16301800 E.Bitto, C.A.Bingman, J.G.McCoy, S.T.Allard, G.E.Wesenberg, and G.N.Phillips (2005).
The structure at 1.6 Angstroms resolution of the protein product of the At4g34215 gene from Arabidopsis thaliana.
  Acta Crystallogr D Biol Crystallogr, 61, 1655-1661.
PDB code: 2apj
15845496 S.Banerji, M.Bewersdorff, B.Hermes, N.P.Cianciotto, and A.Flieger (2005).
Characterization of the major secreted zinc metalloprotease- dependent glycerophospholipid:cholesterol acyltransferase, PlaC, of Legionella pneumophila.
  Infect Immun, 73, 2899-2909.  
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
15522763 C.C.Akoh, G.C.Lee, Y.C.Liaw, T.H.Huang, and J.F.Shaw (2004).
GDSL family of serine esterases/lipases.
  Prog Lipid Res, 43, 534-552.  
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
15653427 I.Lescić, M.Zehl, R.Müller, B.Vukelić, M.Abramić, J.Pigac, G.Allmaier, and B.Kojić-Prodić (2004).
Structural characterization of extracellular lipase from Streptomyces rimosus: assignment of disulfide bridge pattern by mass spectrometry.
  Biol Chem, 385, 1147-1156.  
15317784 J.A.Schmidt, G.F.Browning, and P.F.Markham (2004).
Mycoplasma hyopneumoniae p65 surface lipoprotein is a lipolytic enzyme with a preference for shorter-chain fatty acids.
  J Bacteriol, 186, 5790-5798.  
12007643 U.T.Bornscheuer (2002).
Microbial carboxyl esterases: classification, properties and application in biocatalysis.
  FEMS Microbiol Rev, 26, 73-81.  
11567087 H.J.Snijder, J.H.Van Eerde, R.L.Kingma, K.H.Kalk, N.Dekker, M.R.Egmond, and B.W.Dijkstra (2001).
Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad.
  Protein Sci, 10, 1962-1969.
PDB codes: 1ild 1ilz 1im0
  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
11150608 A.Svendsen (2000).
Lipase protein engineering.
  Biochim Biophys Acta, 1543, 223-238.  
  10673440 P.C.Bourne, M.N.Isupov, and J.A.Littlechild (2000).
The atomic-resolution structure of a novel bacterial esterase.
  Structure, 8, 143-151.
PDB code: 1qlw
10955989 R.L.Kingma, M.Fragiathaki, H.J.Snijder, B.W.Dijkstra, H.M.Verheij, N.Dekker, and M.R.Egmond (2000).
Unusual catalytic triad of Escherichia coli outer membrane phospholipase A.
  Biochemistry, 39, 10017-10022.  
10206957 C.VanValkenburgh, X.Chen, C.Mullins, H.Fang, and N.Green (1999).
The catalytic mechanism of endoplasmic reticulum signal peptidase appears to be distinct from most eubacterial signal peptidases.
  J Biol Chem, 274, 11519-11525.  
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.  
10570246 S.Longhi, and C.Cambillau (1999).
Structure-activity of cutinase, a small lipolytic enzyme.
  Biochim Biophys Acta, 1441, 185-196.  
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.  
9768757 L.Mosyak, D.M.Zaller, and D.C.Wiley (1998).
The structure of HLA-DM, the peptide exchange catalyst that loads antigen onto class II MHC molecules during antigen presentation.
  Immunity, 9, 377-383.
PDB code: 1hdm
  9829953 R.Berger, M.Hoffmann, and U.Keller (1998).
Molecular analysis of a gene encoding a cell-bound esterase from Streptomyces chrysomallus.
  J Bacteriol, 180, 6396-6399.  
  9385633 A.C.Wallace, N.Borkakoti, and J.M.Thornton (1997).
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
  Protein Sci, 6, 2308-2323.  
9020589 M.Paetzel, and R.E.Dalbey (1997).
Catalytic hydroxyl/amine dyads within serine proteases.
  Trends Biochem Sci, 22, 28-31.  
  9293006 P.Sommer, C.Bormann, and F.Götz (1997).
Genetic and biochemical characterization of a new extracellular lipase from Streptomyces cinnamomeus.
  Appl Environ Microbiol, 63, 3553-3560.  
  9041628 S.Longhi, M.Mannesse, H.M.Verheij, G.H.De Haas, M.Egmond, E.Knoops-Mouthuy, and C.Cambillau (1997).
Crystal structure of cutinase covalently inhibited by a triglyceride analogue.
  Protein Sci, 6, 275-286.
PDB code: 1oxm
  8606158 C.Tesch, K.Nikoleit, V.Gnau, F.Götz, and C.Bormann (1996).
Biochemical and molecular characterization of the extracellular esterase from Streptomyces diastatochromogenes.
  J Bacteriol, 178, 1858-1865.  
8548458 J.J.Tesmer, T.J.Klem, M.L.Deras, V.J.Davisson, and J.L.Smith (1996).
The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families.
  Nat Struct Biol, 3, 74-86.
PDB code: 1gpm
7768883 L.Serre, E.C.Verbree, Z.Dauter, A.R.Stuitje, and Z.S.Derewenda (1995).
The Escherichia coli malonyl-CoA:acyl carrier protein transacylase at 1.5-A resolution. Crystal structure of a fatty acid synthase component.
  J Biol Chem, 270, 12961-12964.
PDB code: 1mla
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.