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PDBsum entry 1ci9

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1ci9
Jmol
Contents
Protein chains
377 a.a. *
Ligands
DFP ×2
Waters ×571
* Residue conservation analysis
PDB id:
1ci9
Name: Hydrolase
Title: Dfp-inhibited esterase estb from burkholderia gladioli
Structure: Protein (carboxylesterase). Chain: a, b. Synonym: estb. Engineered: yes
Source: Burkholderia gladioli. Organism_taxid: 28095. Atcc: ncppb1891, atcc1028. Collection: ncppb1891, atcc1028. Cellular_location: intracellular. Gene: estb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.176     R-free:   0.235
Authors: U.G.Wagner,E.I.Petersen,H.Schwab,C.Kratky
Key ref:
U.G.Wagner et al. (2002). EstB from Burkholderia gladioli: a novel esterase with a beta-lactamase fold reveals steric factors to discriminate between esterolytic and beta-lactam cleaving activity. Protein Sci, 11, 467-478. PubMed id: 11847270 DOI: 10.1110/ps.33002
Date:
08-Apr-99     Release date:   12-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9KX40  (ESTB_BURGA) -  Esterase EstB
Seq:
Struc:
392 a.a.
377 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     1 term  

 

 
DOI no: 10.1110/ps.33002 Protein Sci 11:467-478 (2002)
PubMed id: 11847270  
 
 
EstB from Burkholderia gladioli: a novel esterase with a beta-lactamase fold reveals steric factors to discriminate between esterolytic and beta-lactam cleaving activity.
U.G.Wagner, E.I.Petersen, H.Schwab, C.Kratky.
 
  ABSTRACT  
 
Esterases form a diverse class of enzymes of largely unknown physiological role. Because many drugs and pesticides carry ester functions, the hydrolysis of such compounds forms at least one potential biological function. Carboxylesterases catalyze the hydrolysis of short chain aliphatic and aromatic carboxylic ester compounds. Esterases, D-alanyl-D-alanine-peptidases (DD-peptidases) and beta-lactamases can be grouped into two distinct classes of hydrolases with different folds and topologically unrelated catalytic residues, the one class comprising of esterases, the other one of beta-lactamases and DD-peptidases. The chemical reactivities of esters and beta-lactams towards hydrolysis are quite similar, which raises the question of which factors prevent esterases from displaying beta-lactamase activity and vice versa. Here we describe the crystal structure of EstB, an esterase isolated from Burkholderia gladioli. It shows the protein to belong to a novel class of esterases with homology to Penicillin binding proteins, notably DD-peptidase and class C beta-lactamases. Site-directed mutagenesis and the crystal structure of the complex with diisopropyl-fluorophosphate suggest Ser75 within the "beta-lactamase" Ser-x-x-Lys motif to act as catalytic nucleophile. Despite its structural homology to beta-lactamases, EstB shows no beta-lactamase activity. Although the nature and arrangement of active-site residues is very similar between EstB and homologous beta-lactamases, there are considerable differences in the shape of the active site tunnel. Modeling studies suggest steric factors to account for the enzyme's selectivity for ester hydrolysis versus beta-lactam cleavage.
 
  Selected figure(s)  
 
Figure 6.
Fig. 6. Section through surface representations of the esterase EstB from B. gladioli (a) and the -lactamase P99 from E. cloacae (b). Both enzymes are in corresponding orientations, and the surface is cut approximately at the height of the active site, the approximate location of which is indicated by an arrow. Outer surfaces are drawn in shades of light gray, inner surfaces in dark blue. Figure produced with GRASP (Nicholls 1993).
Figure 7.
Fig. 7. Modeling the tetrahedral intermediate formed by the attack of the nucleophile Ser75 of EstB on the carbonyl functions of the ester (a) and -lactam (b) of 7-ACA. In generating these complexes, the constraint was imposed that the oxygen atom of the tetrahedral intermediate should remain within hydrogen-bonding distance from the putative oxyanion hole. The figure illustrates that the tetrahedral intermediate for ester cleavage (a) fits the active site well, whereas the corresponding intermediate for hydrolysis of the -lactam (b) leads to steric clashes between protein and substrate. Figure produced with Sybyl, Vers. 6.4 (Tripos).
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2002, 11, 467-478) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21318360 E.Y.Yu, M.A.Kwon, M.Lee, J.Y.Oh, J.E.Choi, J.Y.Lee, B.K.Song, D.H.Hahm, and J.K.Song (2011).
Isolation and characterization of cold-active family VIII esterases from an arctic soil metagenome.
  Appl Microbiol Biotechnol, 90, 573-581.  
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
19889645 K.Yasuhira, N.Shibata, G.Mongami, Y.Uedo, Y.Atsumi, Y.Kawashima, A.Hibino, Y.Tanaka, Y.H.Lee, D.Kato, M.Takeo, Y.Higuchi, and S.Negoro (2010).
X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation.
  J Biol Chem, 285, 1239-1248.
PDB codes: 3a2p 3a2q
19190902 K.Rashamuse, V.Magomani, T.Ronneburg, and D.Brady (2009).
A novel family VIII carboxylesterase derived from a leachate metagenome library exhibits promiscuous beta-lactamase activity on nitrocefin.
  Appl Microbiol Biotechnol, 83, 491-500.  
  19255492 S.Kim, S.Joo, S.Yoon, S.Kim, J.Moon, Y.Ryu, K.K.Kim, and T.D.Kim (2009).
Purification, crystallization and preliminary crystallographic analysis of Est-Y29: a novel oligomeric beta-lactamase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 310-312.  
19521995 T.Ohki, N.Shibata, Y.Higuchi, Y.Kawashima, M.Takeo, D.Kato, and S.Negoro (2009).
Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase.
  Protein Sci, 18, 1662-1673.
PDB codes: 2zly 2zm2 2zm8 2zm9
19875080 X.Gao, X.Xie, I.Pashkov, M.R.Sawaya, J.Laidman, W.Zhang, R.Cacho, T.O.Yeates, and Y.Tang (2009).
Directed evolution and structural characterization of a simvastatin synthase.
  Chem Biol, 16, 1064-1074.
PDB codes: 3hl9 3hlb 3hlc 3hld 3hle 3hlf 3hlg
18988191 X.Xie, I.Pashkov, X.Gao, J.L.Guerrero, T.O.Yeates, and Y.Tang (2009).
Rational improvement of simvastatin synthase solubility in Escherichia coli leads to higher whole-cell biocatalytic activity.
  Biotechnol Bioeng, 102, 20-28.  
18226203 N.Peitsaro, Z.Polianskyte, J.Tuimala, I.Pörn-Ares, J.Liobikas, O.Speer, D.Lindholm, J.Thompson, and O.Eriksson (2008).
Evolution of a family of metazoan active-site-serine enzymes from penicillin-binding proteins: a novel facet of the bacterial legacy.
  BMC Evol Biol, 8, 26.  
18232040 R.Kourist, P.Domínguez de María, and U.T.Bornscheuer (2008).
Enzymatic synthesis of optically active tertiary alcohols: expanding the biocatalysis toolbox.
  Chembiochem, 9, 491-498.  
18421151 S.Okazaki, A.Suzuki, H.Komeda, Y.Asano, and T.Yamane (2008).
Deduced catalytic mechanism of D-amino acid amidase from Ochrobactrum anthropi SV3.
  J Synchrotron Radiat, 15, 250-253.  
18005425 H.Jiang, and C.Blouin (2007).
Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions.
  BMC Bioinformatics, 8, 444.  
17294326 M.Schütte, and S.Fetzner (2007).
EstA from Arthrobacter nitroguajacolicus Rü61a, a thermo- and solvent-tolerant carboxylesterase related to class C beta-lactamases.
  Curr Microbiol, 54, 230-236.  
17712554 S.Y.Park, J.T.Kim, S.G.Kang, J.H.Woo, J.H.Lee, H.T.Choi, and S.J.Kim (2007).
A new esterase showing similarity to putative dienelactone hydrolase from a strict marine bacterium, Vibrio sp. GMD509.
  Appl Microbiol Biotechnol, 77, 107-115.  
16632249 C.Dürr, H.J.Schnell, A.Luzhetskyy, R.Murillo, M.Weber, K.Welzel, A.Vente, and A.Bechthold (2006).
Biosynthesis of the terpene phenalinolactone in Streptomyces sp. Tü6071: analysis of the gene cluster and generation of derivatives.
  Chem Biol, 13, 365-377.  
16672512 C.Elend, C.Schmeisser, C.Leggewie, P.Babiak, J.D.Carballeira, H.L.Steele, J.L.Reymond, K.E.Jaeger, and W.R.Streit (2006).
Isolation and biochemical characterization of two novel metagenome-derived esterases.
  Appl Environ Microbiol, 72, 3637-3645.  
16131658 M.Delmarcelle, M.C.Boursoit, P.Filée, S.L.Baurin, J.M.Frère, and B.Joris (2005).
Specificity inversion of Ochrobactrum anthropi D-aminopeptidase to a D,D-carboxypeptidase with new penicillin binding activity by directed mutagenesis.
  Protein Sci, 14, 2296-2303.  
15388939 M.N.Isupov, A.A.Brindley, E.J.Hollingsworth, G.N.Murshudov, A.A.Vagin, and J.A.Littlechild (2004).
Crystallization and preliminary X-ray diffraction studies of a fungal hydrolase from Ophiostoma novo-ulmi.
  Acta Crystallogr D Biol Crystallogr, 60, 1879-1882.  
14579323 L.N.Kinch, Y.Qi, T.J.Hubbard, and N.V.Grishin (2003).
CASP5 target classification.
  Proteins, 53, 340-351.  
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.