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PDBsum entry 1tah

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protein metals Protein-protein interface(s) links
Hydrolase(carboxylic esterase) PDB id
1tah
Jmol
Contents
Protein chains
318 a.a. *
Metals
_CA ×4
* Residue conservation analysis
PDB id:
1tah
Name: Hydrolase(carboxylic esterase)
Title: The crystal structure of triacylglycerol lipase from pseudomonas glumae reveals a partially redundant catalytic aspartate
Structure: Lipase. Chain: b, a, c, d. Engineered: yes
Source: Burkholderia glumae. Organism_taxid: 337
Resolution:
3.00Å     R-factor:   0.159     R-free:   0.226
Authors: M.E.M.Noble,A.Cleasby,L.N.Johnson,M.Egmond,L.G.J.Frenken
Key ref: M.E.Noble et al. (1993). The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate. FEBS Lett, 331, 123-128. PubMed id: 8405390 DOI: 10.1016/0014-5793(93)80310-Q
Date:
21-Dec-93     Release date:   31-May-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q05489  (LIP_BURGL) -  Lipase
Seq:
Struc:
358 a.a.
318 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.1.3  - Triacylglycerol lipase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Triacylglycerol + H2O = diacylglycerol + a carboxylate
Triacylglycerol
+ H(2)O
= diacylglycerol
+ carboxylate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     lipid metabolic process   2 terms 
  Biochemical function     protein binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/0014-5793(93)80310-Q FEBS Lett 331:123-128 (1993)
PubMed id: 8405390  
 
 
The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate.
M.E.Noble, A.Cleasby, L.N.Johnson, M.R.Egmond, L.G.Frenken.
 
  ABSTRACT  
 
The family of lipases (triacylglycerol-acyl-hydrolases EC 3.1.1.3) constitutes an interesting class of enzymes because of their ability to interact with lipid-water interfaces, their wide range of substrate specificities, and their potential industrial applications. Here we report the first crystal structure of a bacterial lipase, from Pseudomonas glumae. The structure is formed from three domains, the largest of which contains a subset of the alpha/beta hydrolase fold and a calcium site. Asp263, the acidic residue in the catalytic triad, has previously been mutated into an alanine with only a modest reduction in activity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21074554 J.A.Shayman, R.Kelly, J.Kollmeyer, Y.He, and A.Abe (2011).
Group XV phospholipase A₂, a lysosomal phospholipase A₂.
  Prog Lipid Res, 50, 1.  
21333648 M.Lazniewski, K.Steczkiewicz, L.Knizewski, I.Wawer, and K.Ginalski (2011).
Novel transmembrane lipases of alpha/beta hydrolase fold.
  FEBS Lett, 585, 870-874.  
20658340 S.Patameswaran, A.A.Throat, and S.Patra (2010).
Deciphering role of amino acids for the stability of Staphylococcus aureus lipase (SAL3).
  Interdiscip Sci, 2, 271-279.  
18987131 K.Kuwahara, C.Angkawidjaja, H.Matsumura, Y.Koga, K.Takano, and S.Kanaya (2008).
Importance of the Ca2+-binding sites in the N-catalytic domain of a family I.3 lipase for activity and stability.
  Protein Eng Des Sel, 21, 737-744.
PDB codes: 2zj6 2zj7
17657406 H.Ogino, Y.Katou, R.Akagi, T.Mimitsuka, S.Hiroshima, Y.Gemba, N.Doukyu, M.Yasuda, K.Ishimi, and H.Ishikawa (2007).
Cloning and expression of gene, and activation of an organic solvent-stable lipase from Pseudomonas aeruginosa LST-03.
  Extremophiles, 11, 809-817.  
17586771 J.J.Petkowski, M.Chruszcz, M.D.Zimmerman, H.Zheng, T.Skarina, O.Onopriyenko, M.T.Cymborowski, K.D.Koclega, A.Savchenko, A.Edwards, and W.Minor (2007).
Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit.
  Protein Sci, 16, 1360-1367.
PDB codes: 2fgc 2pc6
17933930 M.A.Salameh, and J.Wiegel (2007).
Purification and characterization of two highly thermophilic alkaline lipases from Thermosyntropha lipolytica.
  Appl Environ Microbiol, 73, 7725-7731.  
17106678 S.Kakugawa, S.Fushinobu, T.Wakagi, and H.Shoun (2007).
Characterization of a thermostable carboxylesterase from the hyperthermophilic bacterium Thermotoga maritima.
  Appl Microbiol Biotechnol, 74, 585-591.  
17645523 T.Sakinç, B.Kleine, and S.G.Gatermann (2007).
Biochemical characterization of the surface-associated lipase of Staphylococcus saprophyticus.
  FEMS Microbiol Lett, 274, 335-341.  
16518399 K.Pauwels, A.Lustig, L.Wyns, J.Tommassen, S.N.Savvides, and P.Van Gelder (2006).
Structure of a membrane-based steric chaperone in complex with its lipase substrate.
  Nat Struct Mol Biol, 13, 374-375.
PDB code: 2es4
  16511160 K.Pauwels, R.Loris, G.Vandenbussche, J.M.Ruysschaert, L.Wyns, and P.Van Gelder (2005).
Crystallization and crystal manipulation of a steric chaperone in complex with its lipase substrate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 791-795.  
15378387 E.A.Snellman, and R.R.Colwell (2004).
Acinetobacter lipases: molecular biology, biochemical properties and biotechnological potential.
  J Ind Microbiol Biotechnol, 31, 391-400.  
12855696 G.Calero, P.Gupta, M.C.Nonato, S.Tandel, E.R.Biehl, S.L.Hofmann, and J.Clardy (2003).
The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2.
  J Biol Chem, 278, 37957-37964.
PDB code: 1pja
  16233516 Y.Kojima, M.Kobayashi, and S.Shimizu (2003).
A novel lipase from Pseudomonas fluorescens HU380: gene cloning, overproduction, renaturation-activation, two-step purification, and characterization.
  J Biosci Bioeng, 96, 242-249.  
12084074 C.Alquati, L.De Gioia, G.Santarossa, L.Alberghina, P.Fantucci, and M.Lotti (2002).
The cold-active lipase of Pseudomonas fragi. Heterologous expression, biochemical characterization and molecular modeling.
  Eur J Biochem, 269, 3321-3328.  
12444965 E.A.Snellman, E.R.Sullivan, and R.R.Colwell (2002).
Purification and properties of the extracellular lipase, LipA, of Acinetobacter sp. RAG-1.
  Eur J Biochem, 269, 5771-5779.  
12216836 H.Chahinian, L.Nini, E.Boitard, J.P.Dubès, L.C.Comeau, and L.Sarda (2002).
Distinction between esterases and lipases: a kinetic study with vinyl esters and TAG.
  Lipids, 37, 653-662.  
11859083 S.T.Jeong, H.K.Kim, S.J.Kim, S.W.Chi, J.G.Pan, T.K.Oh, and S.E.Ryu (2002).
Novel zinc-binding center and a temperature switch in the Bacillus stearothermophilus L1 lipase.
  J Biol Chem, 277, 17041-17047.
PDB code: 1ku0
11566993 E.K.Kim, W.H.Jang, J.H.Ko, J.S.Kang, M.J.Noh, and O.J.Yoo (2001).
Lipase and its modulator from Pseudomonas sp. strain KFCC 10818: proline-to-glutamine substitution at position 112 induces formation of enzymatically active lipase in the absence of the modulator.
  J Bacteriol, 183, 5937-5941.  
11258933 H.González-Navarro, M.C.Bañó, and C.Abad (2001).
The closed/open model for lipase activation. Addressing intermediate active forms of fungal enzymes by trapping of conformers in water-restricted environments.
  Biochemistry, 40, 3174-3183.  
11084600 N.A.Turner, E.C.Needs, J.A.Khan, and E.N.Vulfson (2001).
Analysis of conformational states of Candida rugosa lipase in solution: implications for mechanism of interfacial activation and separation of open and closed forms.
  Biotechnol Bioeng, 72, 108-118.  
11150608 A.Svendsen (2000).
Lipase protein engineering.
  Biochim Biophys Acta, 1543, 223-238.  
10629173 J.Yang, K.Kobayashi, Y.Iwasaki, H.Nakano, and T.Yamane (2000).
In vitro analysis of roles of a disulfide bridge and a calcium binding site in activation of Pseudomonas sp. strain KWI-56 lipase.
  J Bacteriol, 182, 295-302.  
11099797 R.Rosenstein, and F.Götz (2000).
Staphylococcal lipases: biochemical and molecular characterization.
  Biochimie, 82, 1005-1014.  
11099802 Y.Cajal, A.Svendsen, J.De Bolós, S.A.Patkar, and M.A.Alsina (2000).
Effect of the lipid interface on the catalytic activity and spectroscopic properties of a fungal lipase.
  Biochimie, 82, 1053-1061.  
10747780 Y.Jia, T.J.Kappock, T.Frick, A.J.Sinskey, and J.Stubbe (2000).
Lipases provide a new mechanistic model for polyhydroxybutyrate (PHB) synthases: characterization of the functional residues in Chromatium vinosum PHB synthase.
  Biochemistry, 39, 3927-3936.  
10216267 E.R.Sullivan, J.G.Leahy, and R.R.Colwell (1999).
Cloning and sequence analysis of the lipase and lipase chaperone-encoding genes from Acinetobacter calcoaceticus RAG-1, and redefinition of a proteobacterial lipase family and an analogous lipase chaperone family.
  Gene, 230, 277-286.  
9890877 J.W.Simons, M.D.van Kampen, I.Ubarretxena-Belandia, R.C.Cox, C.M.Alves dos Santos, M.R.Egmond, and H.M.Verheij (1999).
Identification of a calcium binding site in Staphylococcus hyicus lipase: generation of calcium-independent variants.
  Biochemistry, 38, 2.  
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.  
10388774 M.Graupner, L.Haalck, F.Spener, H.Lindner, O.Glatter, F.Paltauf, and A.Hermetter (1999).
Molecular dynamics of microbial lipases as determined from their intrinsic tryptophan fluorescence.
  Biophys J, 77, 493-504.  
10329649 M.Nardini, I.S.Ridder, H.J.Rozeboom, K.H.Kalk, R.Rink, D.B.Janssen, and B.W.Dijkstra (1999).
The x-ray structure of epoxide hydrolase from Agrobacterium radiobacter AD1. An enzyme to detoxify harmful epoxides.
  J Biol Chem, 274, 14579-14586.
PDB code: 1ehy
9915834 Y.Bourne, P.Taylor, P.E.Bougis, and P.Marchot (1999).
Crystal structure of mouse acetylcholinesterase. A peripheral site-occluding loop in a tetrameric assembly.
  J Biol Chem, 274, 2963-2970.
PDB code: 1maa
  9647843 G.Gerritse, R.W.Hommes, and W.J.Quax (1998).
Development of a lipase fermentation process that uses a recombinant Pseudomonas alcaligenes strain.
  Appl Environ Microbiol, 64, 2644-2651.  
9485442 H.F.Tzeng, L.T.Laughlin, and R.N.Armstrong (1998).
Semifunctional site-specific mutants affecting the hydrolytic half-reaction of microsomal epoxide hydrolase.
  Biochemistry, 37, 2905-2911.  
9501519 H.K.Kim, S.Y.Park, J.K.Lee, and T.K.Oh (1998).
Gene cloning and characterization of thermostable lipase from Bacillus stearothermophilus L1.
  Biosci Biotechnol Biochem, 62, 66-71.  
9032074 J.D.Schrag, Y.Li, M.Cygler, D.Lang, T.Burgdorf, H.J.Hecht, R.Schmid, D.Schomburg, T.J.Rydel, J.D.Oliver, L.C.Strickland, C.M.Dunaway, S.B.Larson, J.Day, and A.McPherson (1997).
The open conformation of a Pseudomonas lipase.
  Structure, 5, 187-202.
PDB codes: 2lip 3lip
9032073 K.K.Kim, H.K.Song, D.H.Shin, K.Y.Hwang, and S.W.Suh (1997).
The crystal structure of a triacylglycerol lipase from Pseudomonas cepacia reveals a highly open conformation in the absence of a bound inhibitor.
  Structure, 5, 173-185.
PDB code: 1oil
  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
  8762132 A.C.Wallace, R.A.Laskowski, and J.M.Thornton (1996).
Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases.
  Protein Sci, 5, 1001-1013.  
18626893 A.Louwrier, G.J.Drtina, and A.M.Klibanov (1996).
On the issue of interfacial activation of lipase in nonaqueous media.
  Biotechnol Bioeng, 50, 1-5.  
8598267 H.K.Kim, J.K.Lee, H.Kim, and T.K.Oh (1996).
Characterization of an alkaline lipase from Proteus vulgaris K80 and the DNA sequence of the encoding gene.
  FEMS Microbiol Lett, 135, 117-121.  
8756458 J.Li, R.Szittner, Z.S.Derewenda, and E.A.Meighen (1996).
Conversion of serine-114 to cysteine-114 and the role of the active site nucleophile in acyl transfer by myristoyl-ACP thioesterase from Vibrio harveyi.
  Biochemistry, 35, 9967-9973.  
9022707 J.W.Simons, H.Adams, R.C.Cox, N.Dekker, F.Götz, A.J.Slotboom, and H.M.Verheij (1996).
The lipase from Staphylococcus aureus. Expression in Escherichia coli, large-scale purification and comparison of substrate specificity to Staphylococcus hyicus lipase.
  Eur J Biochem, 242, 760-769.  
8743049 K.Gulomova, E.Ziomek, J.D.Schrag, K.Davranov, and M.Cygler (1996).
Purification and characterization of a Penicillium sp. lipase which discriminates against diglycerides.
  Lipids, 31, 379-384.  
  8606184 M.J.Brumlik, and J.T.Buckley (1996).
Identification of the catalytic triad of the lipase/acyltransferase from Aeromonas hydrophila.
  J Bacteriol, 178, 2060-2064.  
8702766 T.Hisano, Y.Hata, T.Fujii, J.Q.Liu, T.Kurihara, N.Esaki, and K.Soda (1996).
Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold.
  J Biol Chem, 271, 20322-20330.
PDB code: 1jud
  7606661 A.Schirmer, C.Matz, and D.Jendrossek (1995).
Substrate specificities of poly(hydroxyalkanoate)-degrading bacteria and active site studies on the extracellular poly(3-hydroxyoctanoic acid) depolymerase of Pseudomonas fluorescens GK13.
  Can J Microbiol, 41, 170-179.  
7492621 A.Svendsen, K.Borch, M.Barfoed, T.B.Nielsen, E.Gormsen, and S.A.Patkar (1995).
Biochemical properties of cloned lipases from the Pseudomonas family.
  Biochim Biophys Acta, 1259, 9.  
8591035 G.Rudenko, E.Bonten, A.d'Azzo, and W.G.Hol (1995).
Three-dimensional structure of the human 'protective protein': structure of the precursor form suggests a complex activation mechanism.
  Structure, 3, 1249-1259.
PDB code: 1ivy
7737171 K.Nikoleit, R.Rosenstein, H.M.Verheij, and F.Götz (1995).
Comparative biochemical and molecular analysis of the Staphylococcus hyicus, Staphylococcus aureus and a hybrid lipase. Indication for a C-terminal phospholipase domain.
  Eur J Biochem, 228, 732-738.  
7592717 L.W.Tjoelker, C.Eberhardt, J.Unger, H.L.Trong, G.A.Zimmerman, T.M.McIntyre, D.M.Stafforini, S.M.Prescott, and P.W.Gray (1995).
Plasma platelet-activating factor acetylhydrolase is a secreted phospholipase A2 with a catalytic triad.
  J Biol Chem, 270, 25481-25487.  
7786905 M.A.Taipa, K.Liebeton, J.V.Costa, J.M.Cabral, and K.E.Jaeger (1995).
Lipase from Chromobacterium viscosum: biochemical characterization indicating homology to the lipase from Pseudomonas glumae.
  Biochim Biophys Acta, 1256, 396-402.  
7737187 M.C.Bertolini, J.D.Schrag, M.Cygler, E.Ziomek, D.Y.Thomas, and T.Vernet (1995).
Expression and characterization of Geotrichum candidum lipase I gene. Comparison of specificity profile with lipase II.
  Eur J Biochem, 228, 863-869.  
7785849 M.R.Egmond, W.P.Antheunisse, C.M.van Bemmel, P.Ravestein, and L.G.Frenken (1995).
Structural and functional aspects of an industrial lipase.
  Ann N Y Acad Sci, 750, 195-201.  
7851405 P.Stadler, A.Kovac, L.Haalck, F.Spener, and F.Paltauf (1995).
Stereoselectivity of microbial lipases. The substitution at position sn-2 of triacylglycerol analogs influences the stereoselectivity of different microbial lipases.
  Eur J Biochem, 227, 335-343.  
7596283 R.G.Kok, J.J.van Thor, I.M.Nugteren-Roodzant, M.B.Brouwer, M.R.Egmond, C.B.Nudel, B.Vosman, and K.J.Hellingwerf (1995).
Characterization of the extracellular lipase, LipA, of Acinetobacter calcoaceticus BD413 and sequence analysis of the cloned structural gene.
  Mol Microbiol, 15, 803-818.  
7634094 B.Rubin (1994).
Grease pit chemistry exposed.
  Nat Struct Biol, 1, 568-572.  
8087556 J.Uppenberg, M.T.Hansen, S.Patkar, and T.A.Jones (1994).
The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica.
  Structure, 2, 293-308.
PDB codes: 1tca 1tcb 1tcc
7946464 K.E.Jaeger, S.Ransac, B.W.Dijkstra, C.Colson, M.van Heuvel, and O.Misset (1994).
Bacterial lipases.
  FEMS Microbiol Rev, 15, 29-63.  
8202471 L.Swenson, R.Green, R.Joerger, M.Haas, K.Scott, Y.Wei, U.Derewenda, D.M.Lawson, and Z.S.Derewenda (1994).
Crystallization and preliminary crystallographic studies of the precursor and mature forms of a neutral lipase from the fungus Rhizopus delemar.
  Proteins, 18, 301-306.  
8044845 N.P.Walker, R.V.Talanian, K.D.Brady, L.C.Dang, N.J.Bump, C.R.Ferenz, S.Franklin, T.Ghayur, M.C.Hackett, and L.D.Hammill (1994).
Crystal structure of the cysteine protease interleukin-1 beta-converting enzyme: a (p20/p10)2 homodimer.
  Cell, 78, 343-352.  
7765546 R.J.Kazlauskas (1994).
Elucidating structure-mechanism relationships in lipases: prospects for predicting and engineering catalytic properties.
  Trends Biotechnol, 12, 464-472.  
7656005 U.Derewenda, L.Swenson, R.Green, Y.Wei, G.G.Dodson, S.Yamaguchi, M.J.Haas, and Z.S.Derewenda (1994).
An unusual buried polar cluster in a family of fungal lipases.
  Nat Struct Biol, 1, 36-47.
PDB code: 1tia
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 codes are shown on the right.