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PDBsum entry 1agy

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protein links
Serine esterase PDB id
1agy
Jmol
Contents
Protein chain
197 a.a. *
Waters ×813
* Residue conservation analysis
PDB id:
1agy
Name: Serine esterase
Title: The 1.15 angstrom refined structure of fusarium solani pisi cutinase
Structure: Cutinase. Chain: a. Engineered: yes
Source: Nectria haematococca mpvi. Organism_taxid: 70791. Strain: mpvi. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.15Å     R-factor:   0.175     R-free:   0.197
Authors: A.Nicolas,C.Martinez,C.Cambillau
Key ref:
S.Longhi et al. (1997). Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis. J Mol Biol, 268, 779-799. PubMed id: 9175860 DOI: 10.1006/jmbi.1997.1000
Date:
26-Mar-97     Release date:   01-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00590  (CUTI1_FUSSO) -  Cutinase 1
Seq:
Struc:
230 a.a.
197 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.1.74  - Cutinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cutin + H2O = cutin monomers
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     2 terms  

 

 
DOI no: 10.1006/jmbi.1997.1000 J Mol Biol 268:779-799 (1997)
PubMed id: 9175860  
 
 
Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis.
S.Longhi, M.Czjzek, V.Lamzin, A.Nicolas, C.Cambillau.
 
  ABSTRACT  
 
X-ray data have been recorded to 1.0 A resolution from a crystal of Fusarium solani cutinase using synchrotron radiation and an imaging-plate scanner. The anisotropic treatment of thermal motion led to a fivefold increase in accuracy and to a considerable quality improvement in the electron density maps with respect to an intermediate isotropic model. The final model has an R-factor of 9.4%, with a mean coordinate error of 0.021 A, as estimated from inversion of the least-squares matrix. The availability of an accurate structure at atomic resolution and of meaningful estimates of the errors in its atomic parameters, allowed an extensive analysis of several stereochemical parameters, such as peptide planarity, main-chain and some side-chain bond distances. The hydrogen atoms could be clearly identified in the electron density, thus providing unambiguous evidence on the protonation state of the catalytic histidine residue. The atomic resolution revealed an appreciable extent of flexibility in the cutinase active site, which might be correlated with a possible adaptation to different substrates. The anisotropic treatment of thermal factors provided insights into the anisotropic nature of motions. The analysis of these motions in the two loops delimiting the catalytic crevice pointed out a "breath-like" movement in the substrate binding region of cutinase.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Starting model. Stereo view of the 3Fo - 2Fc electron den- sity map (contoured at 1g) around: a, Met98; b, Pro87 and c, His188. The most anisotropic atoms are highlighted.
Figure 8.
Figure 8. Final model. Stereo view of the 3Fo - 2Fc (1g) around a, the catalytic triad and b, the oxyanion hole. The less occupied conformations of the split positions are shown with thin lines. The solvent site in double conformation coupled to Ser120 O g is also shown.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 268, 779-799) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21333648 M.Lazniewski, K.Steczkiewicz, L.Knizewski, I.Wawer, and K.Ginalski (2011).
Novel transmembrane lipases of alpha/beta hydrolase fold.
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20306187 K.Koschorreck, D.Liu, C.Kazenwadel, R.D.Schmid, and B.Hauer (2010).
Heterologous expression, characterization and site-directed mutagenesis of cutinase CUTAB1 from Alternaria brassicicola.
  Appl Microbiol Biotechnol, 87, 991-997.  
20122196 P.Sundaramurthy, K.Shameer, R.Sreenivasan, S.Gakkhar, and R.Sowdhamini (2010).
HORI: a web server to compute Higher Order Residue Interactions in protein structures.
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18654989 I.T.Sousa, L.Ruiu, C.R.Lowe, and M.A.Taipa (2009).
Synthetic affinity ligands as a novel tool to improve protein stability.
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19810726 Z.Liu, Y.Gosser, P.J.Baker, Y.Ravee, Z.Lu, G.Alemu, H.Li, G.L.Butterfoss, X.P.Kong, R.Gross, and J.K.Montclare (2009).
Structural and functional studies of Aspergillus oryzae cutinase: enhanced thermostability and hydrolytic activity of synthetic ester and polyester degradation.
  J Am Chem Soc, 131, 15711-15716.
PDB code: 3gbs
  18540061 M.P.Nyon, D.W.Rice, J.M.Berrisford, H.Huang, A.J.Moir, C.J.Craven, S.Nathan, N.M.Mahadi, and F.D.Abu Bakar (2008).
Crystallization and preliminary X-ray analysis of recombinant Glomerella cingulata cutinase.
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18808119 P.A.Sigala, D.A.Kraut, J.M.Caaveiro, B.Pybus, E.A.Ruben, D.Ringe, G.A.Petsko, and D.Herschlag (2008).
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  J Am Chem Soc, 130, 13696-13708.
PDB codes: 2inx 3cpo
17292835 D.A.Kondrashov, A.W.Van Wynsberghe, R.M.Bannen, Q.Cui, and G.N.Phillips (2007).
Protein structural variation in computational models and crystallographic data.
  Structure, 15, 169-177.  
17419728 N.M.Micaêlo, and C.M.Soares (2007).
Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents.
  FEBS J, 274, 2424-2436.  
18157840 Z.Zheng, W.Qiang, and D.P.Weliky (2007).
Investigation of finite-pulse radiofrequency-driven recoupling methods for measurement of intercarbonyl distances in polycrystalline and membrane-associated HIV fusion peptide samples.
  Magn Reson Chem, 45, S247-S260.  
16604066 A.Y.Lyubimov, P.I.Lario, I.Moustafa, and A.Vrielink (2006).
Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment.
  Nat Chem Biol, 2, 259-264.
PDB codes: 1n4u 1n4v 1n4w 2gew
16779873 L.Ruiu, A.C.Roque, M.A.Taipa, and C.R.Lowe (2006).
De novo design, synthesis and screening of a combinatorial library of complementary ligands directed towards the surface of cutinase from Fusarium solani pisi.
  J Mol Recognit, 19, 372-378.  
17059213 Z.Zheng, R.Yang, M.L.Bodner, and D.P.Weliky (2006).
Conformational flexibility and strand arrangements of the membrane-associated HIV fusion peptide trimer probed by solid-state NMR spectroscopy.
  Biochemistry, 45, 12960-12975.  
16128806 C.B.Faulds, R.Molina, R.Gonzalez, F.Husband, N.Juge, J.Sanz-Aparicio, and J.A.Hermoso (2005).
Probing the determinants of substrate specificity of a feruloyl esterase, AnFaeA, from Aspergillus niger.
  FEBS J, 272, 4362-4371.
PDB code: 2bjh
15968570 H.Maeda, Y.Yamagata, K.Abe, F.Hasegawa, M.Machida, R.Ishioka, K.Gomi, and T.Nakajima (2005).
Purification and characterization of a biodegradable plastic-degrading enzyme from Aspergillus oryzae.
  Appl Microbiol Biotechnol, 67, 778-788.  
15923226 N.M.Micaelo, V.H.Teixeira, A.M.Baptista, and C.M.Soares (2005).
Water dependent properties of cutinase in nonaqueous solvents: a computational study of enantioselectivity.
  Biophys J, 89, 999.  
15281117 A.Barzilai, S.Kumar, H.Wolfson, and R.Nussinov (2004).
Potential folding-function interrelationship in proteins.
  Proteins, 56, 635-649.  
15103133 K.E.McAuley, A.Svendsen, S.A.Patkar, and K.S.Wilson (2004).
Structure of a feruloyl esterase from Aspergillus niger.
  Acta Crystallogr D Biol Crystallogr, 60, 878-887.
PDB codes: 1uwc 1uza
14675549 A.Vrielink, and N.Sampson (2003).
Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?
  Curr Opin Struct Biol, 13, 709-715.  
12609866 C.M.Soares, V.H.Teixeira, and A.M.Baptista (2003).
Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies.
  Biophys J, 84, 1628-1641.  
12929743 J.M.Martinho, A.M.Santos, A.Fedorov, R.P.Baptista, M.A.Taipa, and J.M.Cabral (2003).
Fluorescence of the single tryptophan of cutinase: temperature and pH effect on protein conformation and dynamics.
  Photochem Photobiol, 78, 15-22.  
12937341 N.Engler, A.Ostermann, N.Niimura, and F.G.Parak (2003).
Hydrogen atoms in proteins: positions and dynamics.
  Proc Natl Acad Sci U S A, 100, 10243-10248.  
12077437 K.Kawasaki, H.Kondo, M.Suzuki, S.Ohgiya, and S.Tsuda (2002).
Alternate conformations observed in catalytic serine of Bacillus subtilis lipase determined at 1.3 A resolution.
  Acta Crystallogr D Biol Crystallogr, 58, 1168-1174.
PDB code: 1isp
11375495 A.González, G.Larsson, R.Persson, and E.Cedergren-Zeppezauer (2001).
Atomic resolution structure of Escherichia coli dUTPase determined ab initio.
  Acta Crystallogr D Biol Crystallogr, 57, 767-774.
PDB codes: 1eu5 1euw
11258922 C.Betzel, S.Gourinath, P.Kumar, P.Kaur, M.Perbandt, S.Eschenburg, and T.P.Singh (2001).
Structure of a serine protease proteinase K from Tritirachium album limber at 0.98 A resolution.
  Biochemistry, 40, 3080-3088.
PDB code: 1ic6
11170208 E.P.Melo, T.Q.Faria, L.O.Martins, A.M.Gonçalves, and J.M.Cabral (2001).
Cutinase unfolding and stabilization by trehalose and mannosylglycerate.
  Proteins, 42, 542-552.  
11340663 G.M.Langdon, M.A.Jiménez, C.G.Genzor, S.Maldonado, J.Sancho, and M.Rico (2001).
Anabaena apoflavodoxin hydrogen exchange: on the stable exchange core of the alpha/beta(21345) flavodoxin-like family.
  Proteins, 43, 476-488.  
11264580 R.A.Steiner, H.J.Rozeboom, A.de Vries, K.H.Kalk, G.N.Murshudov, K.S.Wilson, and B.W.Dijkstra (2001).
X-ray structure of bovine pancreatic phospholipase A2 at atomic resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 516-526.
PDB code: 1g4i
10673441 A.Dessen (2000).
Phospholipase A(2) enzymes: structural diversity in lipid messenger metabolism.
  Structure, 8, R15-R22.  
10873862 I.Leiros, F.Secundo, C.Zambonelli, S.Servi, and E.Hough (2000).
The first crystal structure of a phospholipase D.
  Structure, 8, 655-667.
PDB code: 1f0i
11018723 K.Berggren, M.R.Egmond, and F.Tjerneld (2000).
Substitutions of surface amino acid residues of cutinase probed by aqueous two-phase partitioning.
  Biochim Biophys Acta, 1481, 317-327.  
11099798 M.R.Egmond, and J.de Vlieg (2000).
Fusarium solani pisi cutinase.
  Biochimie, 82, 1015-1021.  
10739939 M.Würtele, M.Hahn, K.Hilpert, and W.Höhne (2000).
Atomic resolution structure of native porcine pancreatic elastase at 1.1 A.
  Acta Crystallogr D Biol Crystallogr, 56, 520-523.
PDB code: 1qnj
11063575 X.Chen, D.E.Wolfgang, and N.S.Sampson (2000).
Use of the parallax-quench method to determine the position of the active-site loop of cholesterol oxidase in lipid bilayers.
  Biochemistry, 39, 13383-13389.  
10387068 C.G.Schipke, D.B.Goodin, D.E.McRee, and C.D.Stout (1999).
Oxidized and reduced Azotobacter vinelandii ferredoxin I at 1.4 A resolution: conformational change of surface residues without significant change in the [3Fe-4S]+/0 cluster.
  Biochemistry, 38, 8228-8239.
PDB codes: 6fdr 7fd1 7fdr
10556791 C.M.Carvalho, M.R.Aires-Barros, and J.M.Cabral (1999).
Cutinase: from molecular level to bioprocess development.
  Biotechnol Bioeng, 66, 17-34.  
10089308 D.Ghosh, M.Erman, M.Sawicki, P.Lala, D.R.Weeks, N.Li, W.Pangborn, D.J.Thiel, H.Jörnvall, R.Gutierrez, and J.Eyzaguirre (1999).
Determination of a protein structure by iodination: the structure of iodinated acetylxylan esterase.
  Acta Crystallogr D Biol Crystallogr, 55, 779-784.
PDB codes: 1bs9 2axe
10329772 E.A.Merritt (1999).
Expanding the model: anisotropic displacement parameters in protein structure refinement.
  Acta Crystallogr D Biol Crystallogr, 55, 1109-1117.  
10388742 E.Y.Lau, and T.C.Bruice (1999).
Consequences of breaking the Asp-His hydrogen bond of the catalytic triad: effects on the structure and dynamics of the serine esterase cutinase.
  Biophys J, 77, 85-98.  
10220318 J.J.Prompers, A.Groenewegen, C.W.Hilbers, and H.A.Pepermans (1999).
Backbone dynamics of Fusarium solani pisi cutinase probed by nuclear magnetic resonance: the lack of interfacial activation revisited.
  Biochemistry, 38, 5315-5327.  
10320324 J.J.Prompers, B.van Noorloos, M.L.Mannesse, A.Groenewegen, M.R.Egmond, H.M.Verheij, C.W.Hilbers, and H.A.Pepermans (1999).
NMR studies of Fusarium solani pisi cutinase in complex with phosphonate inhibitors.
  Biochemistry, 38, 5982-5994.  
10494852 K.Gruber, M.Gugganig, U.G.Wagner, and C.Kratky (1999).
Atomic resolution crystal structure of hydroxynitrile lyase from Hevea brasiliensis.
  Biol Chem, 380, 993.
PDB code: 1qj4
10607665 M.Nardini, and B.W.Dijkstra (1999).
Alpha/beta hydrolase fold enzymes: the family keeps growing.
  Curr Opin Struct Biol, 9, 732-737.  
10089358 O.Carugo, and P.Argos (1999).
Reliability of atomic displacement parameters in protein crystal structures.
  Acta Crystallogr D Biol Crystallogr, 55, 473-478.  
10404588 P.Heikinheimo, A.Goldman, C.Jeffries, and D.L.Ollis (1999).
Of barn owls and bankers: a lush variety of alpha/beta hydrolases.
  Structure, 7, R141-R146.  
10570246 S.Longhi, and C.Cambillau (1999).
Structure-activity of cutinase, a small lipolytic enzyme.
  Biochim Biophys Acta, 1441, 185-196.  
10089457 T.Sandalova, G.Schneider, H.Käck, and Y.Lindqvist (1999).
Structure of dethiobiotin synthetase at 0.97 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 610-624.
PDB code: 1byi
10089487 E.Dodson (1998).
The role of validation in macromolecular crystallography.
  Acta Crystallogr D Biol Crystallogr, 54, 1109-1118.  
9753430 P.Kuhn, M.Knapp, S.M.Soltis, G.Ganshaw, M.Thoene, and R.Bott (1998).
The 0.78 A structure of a serine protease: Bacillus lentus subtilisin.
  Biochemistry, 37, 13446-13452.
PDB code: 1gci
9818269 R.A.Laskowski, M.W.MacArthur, and J.M.Thornton (1998).
Validation of protein models derived from experiment.
  Curr Opin Struct Biol, 8, 631-639.  
9914254 S.Longhi, M.Czjzek, and C.Cambillau (1998).
Messages from ultrahigh resolution crystal structures.
  Curr Opin Struct Biol, 8, 730-737.  
9562561 Y.Wei, L.Swenson, C.Castro, U.Derewenda, W.Minor, H.Arai, J.Aoki, K.Inoue, L.Servin-Gonzalez, and Z.S.Derewenda (1998).
Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 A resolution.
  Structure, 6, 511-519.
PDB code: 1jfr
9345628 K.Moffat, and Z.Ren (1997).
Synchrotron radiation applications to macromolecular crystallography.
  Curr Opin Struct Biol, 7, 689-696.  
9345627 Z.Dauter, V.S.Lamzin, and K.S.Wilson (1997).
The benefits of atomic resolution.
  Curr Opin Struct Biol, 7, 681-688.  
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.