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PDBsum entry 1jji

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1jji
Jmol
Contents
Protein chains
311 a.a. *
Ligands
EPE ×4
Waters ×561
* Residue conservation analysis
PDB id:
1jji
Name: Hydrolase
Title: The crystal structure of a hyper-thermophilic carboxylestera the archaeon archaeoglobus fulgidus
Structure: Carboxylesterase. Chain: a, b, c, d. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.20Å     R-factor:   0.203     R-free:   0.235
Authors: G.De Simone,V.Menchise,G.Manco,L.Mandrich,N.Sorrentino,D.Lan M.Rossi,C.Pedone
Key ref:
G.De Simone et al. (2001). The crystal structure of a hyper-thermophilic carboxylesterase from the archaeon Archaeoglobus fulgidus. J Mol Biol, 314, 507-518. PubMed id: 11846563 DOI: 10.1006/jmbi.2001.5152
Date:
06-Jul-01     Release date:   05-Dec-01    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
O28558  (O28558_ARCFU) -  Carboxylesterase (EstA)
Seq:
Struc:
311 a.a.
311 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1006/jmbi.2001.5152 J Mol Biol 314:507-518 (2001)
PubMed id: 11846563  
 
 
The crystal structure of a hyper-thermophilic carboxylesterase from the archaeon Archaeoglobus fulgidus.
G.De Simone, V.Menchise, G.Manco, L.Mandrich, N.Sorrentino, D.Lang, M.Rossi, C.Pedone.
 
  ABSTRACT  
 
The crystal structure of AFEST, a novel hyper-thermophilic carboxylesterase from the archaeon Archaeoglobus fulgidus, complexed with a sulphonyl derivative, has been determined and refined to 2.2 A resolution. This enzyme, which has recently been classified as a member of the hormone- sensitive-lipase (H) group of the esterase/lipase superfamily, presents a canonical alpha/beta hydrolase core, shielded on the C-terminal side by a cap region composed of five alpha-helices. It contains the catalytic triad Ser160, His285 and Asp255, whereby the nucleophile is covalently modified and the oxyanion hole formed by Gly88, Gly89 and Ala161. A structural comparison of AFEST with its mesophilic and thermophilic homologues, Brefeldin A esterase from Bacillus subtilis (BFAE) and EST2 from Alicyclobacillus acidocaldarius, reveals an increase in the number of intramolecular ion pairs and secondary structure content, as well as a significant reduction in loop extensions and ratio of hydrophobic to charged surface area. The variety of structural differences suggests possible strategies for thermostabilization of lipases and esterases with potential industrial applications.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Overall fold of AFEST: b-strands and helices belonging to the canonical a/b hydrolase fold are shown in yellow and in red, respectively, while helices forming the cap domain are shown in blue. The residues of the catalytic triad are shown in ball-and-stick representation: Ser160 bound to the Hepes molecule (cyan), His285 (magenta) and Asp255 (green). Generated using Molscript[67].
Figure 3.
Figure 3. The AFEST dimer viewed normal to the molecular 2-fold axis. Subunit A is shown in red and subunit B in green. The active site residues are shown as ball-and-stick. This Figure was generated with the program Molscript[67].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 507-518) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21054894 L.JunGang, Z.KeGui, and H.WenJun (2010).
Cloning and biochemical characterization of a novel lipolytic gene from activated sludge metagenome, and its gene product.
  Microb Cell Fact, 9, 83.  
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.  
19544040 M.Levisson, J.van der Oost, and S.W.Kengen (2009).
Carboxylic ester hydrolases from hyperthermophiles.
  Extremophiles, 13, 567-581.  
19247785 P.Del Vecchio, M.Elias, L.Merone, G.Graziano, J.Dupuy, L.Mandrich, P.Carullo, B.Fournier, D.Rochu, M.Rossi, P.Masson, E.Chabriere, and G.Manco (2009).
Structural determinants of the high thermal stability of SsoPox from the hyperthermophilic archaeon Sulfolobus solfataricus.
  Extremophiles, 13, 461-470.  
18096218 F.Naseem, and R.H.Khan (2008).
Structural intermediates of acid unfolded Con-A in different co-solvents: fluoroalcohols and polyethylene glycols.
  Int J Biol Macromol, 42, 158-165.  
18337155 K.Hirano, M.Ueguchi-Tanaka, and M.Matsuoka (2008).
GID1-mediated gibberellin signaling in plants.
  Trends Plant Sci, 13, 192-199.  
18600322 X.Chu, H.He, C.Guo, and B.Sun (2008).
Identification of two novel esterases from a marine metagenomic library derived from South China Sea.
  Appl Microbiol Biotechnol, 80, 615-625.  
17625021 J.S.Byun, J.K.Rhee, N.D.Kim, J.Yoon, D.U.Kim, E.Koh, J.W.Oh, and H.S.Cho (2007).
Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties.
  BMC Struct Biol, 7, 47.
PDB code: 2c7b
  17350931 L.Mandrich, M.Pezzullo, M.Rossi, and G.Manco (2007).
SSoNDelta and SSoNDeltalong: two thermostable esterases from the same ORF in the archaeon Sulfolobus solfataricus?
  Archaea, 2, 109-115.  
  17620715 S.Kim, S.Joo, H.C.Yoon, Y.Ryu, K.K.Kim, and T.D.Kim (2007).
Purification, crystallization and preliminary crystallographic analysis of Est25: a ketoprofen-specific hormone-sensitive lipase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 579-581.  
16354661 C.Deb, J.Daniel, T.D.Sirakova, B.Abomoelak, V.S.Dubey, and P.E.Kolattukudy (2006).
A novel lipase belonging to the hormone-sensitive lipase family induced under starvation to utilize stored triacylglycerol in Mycobacterium tuberculosis.
  J Biol Chem, 281, 3866-3875.  
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.  
16598011 J.K.Rhee, D.Y.Kim, D.G.Ahn, J.H.Yun, S.H.Jang, H.C.Shin, H.S.Cho, J.G.Pan, and J.W.Oh (2006).
Analysis of the thermostability determinants of hyperthermophilic esterase EstE1 based on its predicted three-dimensional structure.
  Appl Environ Microbiol, 72, 3021-3025.  
  16511287 J.S.Byun, J.K.Rhee, D.U.Kim, J.W.Oh, and H.S.Cho (2006).
Crystallization and preliminary X-ray crystallographic analysis of EstE1, a new and thermostable esterase cloned from a metagenomic library.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 145-147.  
16670095 Q.Wang, G.Yang, Y.Liu, and Y.Feng (2006).
Discrimination of esterase and peptidase activities of acylaminoacyl peptidase from hyperthermophilic Aeropyrum pernix K1 by a single mutation.
  J Biol Chem, 281, 18618-18625.  
15837391 B.M.Nair, L.A.Joachimiak, S.Chattopadhyay, I.Montano, and J.L.Burns (2005).
Conservation of a novel protein associated with an antibiotic efflux operon in Burkholderia cenocepacia.
  FEMS Microbiol Lett, 245, 337-344.  
15811801 H.Atomi (2005).
Recent progress towards the application of hyperthermophiles and their enzymes.
  Curr Opin Chem Biol, 9, 166-173.  
16086253 M.Rusnak, J.Nieveler, R.D.Schmid, and R.Petri (2005).
The putative lipase, AF1763, from Archaeoglobus fulgidusis is a carboxylesterase with a very high pH optimum.
  Biotechnol Lett, 27, 743-748.  
14617621 G.De Simone, L.Mandrich, V.Menchise, V.Giordano, F.Febbraio, M.Rossi, C.Pedone, and G.Manco (2004).
A substrate-induced switch in the reaction mechanism of a thermophilic esterase: kinetic evidences and structural basis.
  J Biol Chem, 279, 6815-6823.
PDB code: 1qz3
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.  
  16233734 K.Ejima, J.Liu, Y.Oshima, K.Hirooka, S.Shimanuki, Y.Yokota, H.Hemmi, T.Nakayama, and T.Nishino (2004).
Molecular cloning and characterization of a thermostable carboxylesterase from an archaeon, Sulfolobus shibatae DSM5389: non-linear kinetic behavior of a hormone-sensitive lipase family enzyme.
  J Biosci Bioeng, 98, 445-451.  
14993683 K.Gerber, A.Schiefner, P.Seige, K.Diederichs, W.Boos, and W.Welte (2004).
Crystallization and preliminary X-ray analysis of Aes, an acetyl-esterase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 60, 531-533.  
15373841 S.Canaan, D.Maurin, H.Chahinian, B.Pouilly, C.Durousseau, F.Frassinetti, L.Scappuccini-Calvo, C.Cambillau, and Y.Bourne (2004).
Expression and characterization of the protein Rv1399c from Mycobacterium tuberculosis. A novel carboxyl esterase structurally related to the HSL family.
  Eur J Biochem, 271, 3953-3961.  
12943843 J.K.Yano, and T.L.Poulos (2003).
New understandings of thermostable and peizostable enzymes.
  Curr Opin Biotechnol, 14, 360-365.  
14501134 N.Sorrentino, G.De Simone, V.Menchise, L.Mandrich, M.Rossi, G.Manco, and C.Pedone (2003).
Crystallization and preliminary X-ray diffraction studies of Aes acetyl-esterase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 59, 1846-1848.  
12421810 X.Zhu, N.A.Larsen, A.Basran, N.C.Bruce, and I.A.Wilson (2003).
Observation of an arsenic adduct in an acetyl esterase crystal structure.
  J Biol Chem, 278, 2008-2014.
PDB codes: 1lzk 1lzl
12374803 L.Mandrich, E.Caputo, B.M.Martin, M.Rossi, and G.Manco (2002).
The Aes protein and the monomeric alpha-galactosidase from Escherichia coli form a non-covalent complex. Implications for the regulation of carbohydrate metabolism.
  J Biol Chem, 277, 48241-48247.  
12147492 Y.Hotta, S.Ezaki, H.Atomi, and T.Imanaka (2002).
Extremely stable and versatile carboxylesterase from a hyperthermophilic archaeon.
  Appl Environ Microbiol, 68, 3925-3931.  
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.