PDBsum entry 1u4n

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Hydrolase PDB id
Protein chain
308 a.a. *
Waters ×252
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure analysis of the m211s/r215l est2 mutant
Structure: Carboxylesterase est2. Chain: a. Engineered: yes. Mutation: yes
Source: Alicyclobacillus acidocaldarius. Organism_taxid: 405212. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.10Å     R-factor:   0.179     R-free:   0.233
Authors: G.De Simone,V.Menchise,V.Alterio,L.Mandrich,M.Rossi,G.Manco,
Key ref:
G.De Simone et al. (2004). The crystal structure of an EST2 mutant unveils structural insights on the H group of the carboxylesterase/lipase family. J Mol Biol, 343, 137-146. PubMed id: 15381425 DOI: 10.1016/j.jmb.2004.08.014
26-Jul-04     Release date:   05-Oct-04    
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Protein chain
Pfam   ArchSchema ?
Q7SIG1  (Q7SIG1_ALIAC) -  Hydrolase
310 a.a.
308 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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


DOI no: 10.1016/j.jmb.2004.08.014 J Mol Biol 343:137-146 (2004)
PubMed id: 15381425  
The crystal structure of an EST2 mutant unveils structural insights on the H group of the carboxylesterase/lipase family.
G.De Simone, V.Menchise, V.Alterio, L.Mandrich, M.Rossi, G.Manco, C.Pedone.
Esterase 2 (EST2) from the thermophilic eubacterium Alicyclobacillus acidocaldarius is a thermostable serine hydrolase belonging to the H group of the esterase/lipase family. This enzyme hydrolyzes monoacylesters of different acyl-chain length and various compounds with industrial interest. EST2 displays an optimal temperature at 70 degrees C and maximal activity with pNP-esters having acyl-chain bearing from six to eight carbon atoms. EST2 mutants with different substrate specificity were also designed, generated by site-directed mutagenesis, and biochemically characterized. To better define at structural level the enzyme reaction mechanism, a crystallographic analysis of one of these mutants, namely M211S/R215L, was undertaken. Here we report its three-dimensional structure at 2.10A resolution. Structural analysis of the enzyme revealed an unexpected dimer formation as a consequence of a domain-swapping event involving its N-terminal region. This phenomenon was absent in the case of the enzyme bound to an irreversible inhibitor having optimal substrate structural features. A detailed comparison of the enzyme structures before and following binding to this molecule showed a movement of the N-terminal helices resulting from a trans-cis isomerization of the F37-P38 peptide bond. These findings suggest that this carboxylesterase presents two distinct structural arrangements reminiscent of the open and closed forms already reported for lipases. Potential biological implications associated with the observed quaternary reorganization are here discussed in light of the biochemical properties of other lipolytic members of the H group.
  Selected figure(s)  
Figure 1.
Figure 1. (a) Overall fold of M211S/R215L EST2 mutant. b-Strands and helices belonging to the canonical a/b hydrolase fold are shown in yellow and red, respectively. Helices belonging to the 62 residues insertion between b6 and b7 are shown in cyan while helices belonging to the N-terminal region are shown in blue. Catalytic triad residues are shown in ball-and-stick representation. (b) Schematic representation of the M211S/R215L EST2 mutant fold. The color scheme corresponds to that used in (a). b-Strands are shown as arrows (b1, 47-55; b2, 58-66; b3, 74-80; b4, 107-111; b5, 144-153; b6, 178-182; b7, 244-251; b8, 272-281), a-helices as cylinders (a1, 4-16; a2, 26-34; a3, 93-105; a4, 122-137; a5, 156-172; a6, 194-200; a7, 207-219; a8, 254-268; a9, 291-310) and 3[10] helices as cubes (G1, 21-25; G2, 138-142; G3, 221-227; G4, 231-235; G5, 283-288). (c) Overall fold of M211S/R215L in M211S/R215L-HDSC complex structure.13 The color scheme corresponds to that used in (a). (d) Schematic representation of the fold of M211S/R215L in M211S/R215L-HDSC.
Figure 8.
Figure 8. Molecular surface of the M211S/R215L molecule in its closed form, viewed from the direction above the active site. The surface corresponding to the movable region (L3-F37) is shown in yellow. The catalytic serine is shown in red.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 343, 137-146) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20386955 Y.S.Shang, X.E.Zhang, X.D.Wang, Y.C.Guo, Z.P.Zhang, and Y.F.Zhou (2010).
Biochemical characterization and mutational improvement of a thermophilic esterase from Sulfolobus solfataricus P2.
  Biotechnol Lett, 32, 1151-1157.  
18076040 L.Mandrich, V.Menchise, V.Alterio, G.De Simone, C.Pedone, M.Rossi, and G.Manco (2008).
Functional and structural features of the oxyanion hole in a thermophilic esterase from Alicyclobacillus acidocaldarius.
  Proteins, 71, 1721-1731.
PDB code: 2hm7
16978018 D.K.Nomura, K.A.Durkin, K.P.Chiang, G.B.Quistad, B.F.Cravatt, and J.E.Casida (2006).
Serine hydrolase KIAA1363: toxicological and structural features with emphasis on organophosphate interactions.
  Chem Res Toxicol, 19, 1142-1150.  
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