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PDBsum entry 1j00

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Hydrolase PDB id
1j00
Jmol
Contents
Protein chain
178 a.a. *
Ligands
SO4
Waters ×91
* Residue conservation analysis
PDB id:
1j00
Name: Hydrolase
Title: E. Coli thioesterase i/protease i/lysophospholipase l1 in co with diethyl phosphono moiety
Structure: Thioesterase i. Chain: a. Synonym: acyl-coa thioesterase i, protease i, lysophospholi engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: tesa/apea/pldc. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
2.00Å     R-factor:   0.239     R-free:   0.267
Authors: Y.-C.Lo,J.-F.Shaw,Y.-C.Liaw
Key ref:
Y.C.Lo et al. (2003). Crystal structure of Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network. J Mol Biol, 330, 539-551. PubMed id: 12842470 DOI: 10.1016/S0022-2836(03)00637-5
Date:
18-Oct-02     Release date:   08-Jul-03    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0ADA1  (TESA_ECOLI) -  Acyl-CoA thioesterase I
Seq:
Struc:
208 a.a.
178 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.1.1.5  - Lysophospholipase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-lysophosphatidylcholine + H2O = glycerophosphocholine + a carboxylate
2-lysophosphatidylcholine
+ H(2)O
= glycerophosphocholine
+ carboxylate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   2 terms 
  Biological process     lipid metabolic process   2 terms 
  Biochemical function     hydrolase activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(03)00637-5 J Mol Biol 330:539-551 (2003)
PubMed id: 12842470  
 
 
Crystal structure of Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network.
Y.C.Lo, S.C.Lin, J.F.Shaw, Y.C.Liaw.
 
  ABSTRACT  
 
Escherichia coli thioesterase I (TAP) is a multifunctional enzyme possessing activities of thioesterase, esterase, arylesterase, protease, and lysophospholipase. In particular, TAP has stereoselectivity for amino acid derivative substrates, hence it is useful for the kinetic resolution of racemic mixtures of industrial chemicals. In the present work, the crystal structure of native TAP was determined at 1.9A, revealing a minimal SGNH-hydrolase fold. The structure of TAP in complex with a diethyl phosphono moiety (DEP) identified its catalytic triad, Ser10-Asp154-His157, and oxyanion hole, Ser10-Gly44-Asn73. The oxyanion hole of TAP consists of three residues each separated from the other by more than 3.5A, implying that all of them are highly polarized when substrate bound. The catalytic (His)C(epsilon1)-H...O=C hydrogen bond usually plays a role in the catalytic mechanisms of most serine hydrolases, however, there were none present in SGNH-hydrolases. We propose that the existence of the highly polarized tri-residue-constituted oxyanion hole compensates for the lack of a (His)C(epsilon1)-H...O=C hydrogen bond. This suggests that members of the SGNH-hydrolase family may employ a unique catalytic mechanism. In addition, most SGNH-hydrolases have low sequence identities and presently there is no clear criterion to define consensus sequence blocks. Through comparison of TAP and the three SGNH-hydrolase structures currently known, we have identified a unique hydrogen bond network which stabilizes the catalytic center: a newly discovered structural feature of SGNH-hydrolases. We have defined these consensus sequence blocks providing a basis for the sub-classification of SGNH-hydrolases.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo diagrams of the oxyanion hole in the TAP-DEP structure. The oxyanion hole residues Ser10, Gly44 and Asn73, catalytic triad and DEP modified Ser10, are represented as ball-and-sticks. The green broken-line indicates the hydrogen bonds between the oxyanion oxygen atom and the hydrogen-donating residues. The cyan broken-line indicates that the N epsilon 2 of His157 is hydrogen bonded to the O2 of the leaving group of DEP. The 2F[o] -F[c] electron density of DEP is countered at the 1s level.
Figure 7.
Figure 7. Superimposition of the conserved hydrogen bond network in the SGNH-hydrolase family. (a) Stereo view of the hydrogen bond network of consensus regions in the TAP structure. The 2F[o] -F[c] electron density of water molecules is countered at the 2.5s level. (b) Stereo view of superimposition of the hydrogen bond network of TAP and PAF-AH(Ib)a1 structures. The transparent and green sticks indicate TAP and PAF-AH(Ib)a1, respectively. (c) The transparent and yellow sticks indicate TAP and RGAH, respectively. (d) The transparent and red sticks indicate TAP and SsEst, respectively.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 539-551) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20882276 B.E.Alber (2011).
Biotechnological potential of the ethylmalonyl-CoA pathway.
  Appl Microbiol Biotechnol, 89, 17-25.  
21069734 J.Ma, Q.Lu, Y.Yuan, H.Ge, K.Li, W.Zhao, Y.Gao, L.Niu, and M.Teng (2011).
Crystal structure of isoamyl acetate-hydrolyzing esterase from Saccharomyces cerevisiae reveals a novel active site architecture and the basis of substrate specificity.
  Proteins, 79, 662-668.
PDB code: 3mil
20057119 A.Masayama, S.Kato, T.Terashima, A.Mølgaard, H.Hemmi, T.Yoshimura, and R.Moriyama (2010).
Bacillus subtilis spore coat protein LipC is a phospholipase B.
  Biosci Biotechnol Biochem, 74, 24-30.  
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.  
20931591 I.Leščić Ašler, N.Ivić, F.Kovačić, S.Schell, J.Knorr, U.Krauss, S.Wilhelm, B.Kojić-Prodić, and K.E.Jaeger (2010).
Probing enzyme promiscuity of SGNH hydrolases.
  Chembiochem, 11, 2158-2167.  
  20445266 J.T.Weadge, P.P.Yip, H.Robinson, K.Arnett, P.A.Tipton, and P.L.Howell (2010).
Expression, purification, crystallization and preliminary X-ray analysis of Pseudomonas aeruginosa AlgX.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 588-591.  
20383468 S.Yu, B.Zheng, X.Zhao, and Y.Feng (2010).
Gene cloning and characterization of a novel thermophilic esterase from Fervidobacterium nodosum Rt17-B1.
  Acta Biochim Biophys Sin (Shanghai), 42, 288-295.  
19789923 Y.Okamura, T.Kimura, H.Yokouchi, M.Meneses-Osorio, M.Katoh, T.Matsunaga, and H.Takeyama (2010).
Isolation and characterization of a GDSL esterase from the metagenome of a marine sponge-associated bacteria.
  Mar Biotechnol (NY), 12, 395-402.  
  19724118 A.Brzuszkiewicz, E.Nowak, Z.Dauter, M.Dauter, H.Cieśliński, A.Długołecka, and J.Kur (2009).
Structure of EstA esterase from psychrotrophic Pseudoalteromonas sp. 643A covalently inhibited by monoethylphosphonate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 862-865.
PDB code: 3hp4
18224318 C.Peña-Montes, A.González, D.Castro-Ochoa, and A.Farrés (2008).
Purification and biochemical characterization of a broad substrate specificity thermostable alkaline protease from Aspergillus nidulans.
  Appl Microbiol Biotechnol, 78, 603-612.  
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.  
18174153 O.Onder, S.Turkarslan, D.Sun, and F.Daldal (2008).
Overproduction or absence of the periplasmic protease DegP severely compromises bacterial growth in the absence of the dithiol: disulfide oxidoreductase DsbA.
  Mol Cell Proteomics, 7, 875-890.  
17646166 A.L.Lewis, H.Cao, S.K.Patel, S.Diaz, W.Ryan, A.F.Carlin, V.Thon, W.G.Lewis, A.Varki, X.Chen, and V.Nizet (2007).
NeuA sialic acid O-acetylesterase activity modulates O-acetylation of capsular polysaccharide in group B Streptococcus.
  J Biol Chem, 282, 27562-27571.  
17220231 B.Sun, X.H.Zhang, X.Tang, S.Wang, Y.Zhong, J.Chen, and B.Austin (2007).
A single residue change in Vibrio harveyi hemolysin results in the loss of phospholipase and hemolytic activities and pathogenicity for turbot (Scophthalmus maximus).
  J Bacteriol, 189, 2575-2579.  
17516048 H.Cieśliński, A.M.Białkowska, A.Długołecka, M.Daroch, K.L.Tkaczuk, H.Kalinowska, J.Kur, and M.Turkiewicz (2007).
A cold-adapted esterase from psychrotrophic Pseudoalteromas sp. strain 643A.
  Arch Microbiol, 188, 27-36.  
16972310 W.J.Wu, S.I.Tyukhtenko, and T.H.Huang (2006).
Direct NMR resonance assignments of the active site histidine residue in Escherichia coli thioesterase I/protease I/lysophospholipase L1.
  Magn Reson Chem, 44, 1037-1040.  
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
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.  
15043875 H.S.Ro, H.P.Hong, B.H.Kho, S.Kim, and B.H.Chung (2004).
Genome-wide cloning and characterization of microbial esterases.
  FEMS Microbiol Lett, 233, 97.  
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.