The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans

Structure

Volumn 8, Issue 4, 2000, Pages 349-362

  Britton, K L ^a   Langridge, S J ^a   Baker, P J ^a   Weeradechapon, K ^a   Sedelnikova, S E ^a   De Lucas, J R ^b   Rice, D W ^a   Turner, G ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UNIVERSITY OF ALCALÁ   (Spain)

Author keywords

Enolase superfamily; Glyoxylate cycle; Isocitrate lyase; PEP mutase; TIM barrel protein

Indexed keywords

ENOLASE; FUNGAL ENZYME; GLYOXYLIC ACID; ISOCITRATE LYASE; MUTASE;

AMINO ACID SEQUENCE; ARTICLE; ASPERGILLUS NIDULANS; BINDING SITE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ESCHERICHIA COLI; FUNGUS; NONHUMAN; PRIORITY JOURNAL; X RAY DIFFRACTION;

ASPERGILLUS; EMERICELLA NIDULANS; ESCHERICHIA COLI; FUNGI; MYCOBACTERIUM LEPRAE;

EID: 0034656088     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(00)00117-9     Document Type: Article

References (59)

1. Campbell J.J.R., Smith R.A., Eagles B.A. A deviation from the conventional tricarboxylic acid cycle in Pseudomonas aeruginosa. Biochim. Biophys. Acta. 11:1953;594.
2. Vanni P., Giachetti E., Pinzauti G., McFadden B.A. Comparative structure, function and regulation of isocitrate lyase, an important assimilatory enzyme. Comp. Biochem. Physiol. B95:1990;431-458.
3. 2-units by a modified tricarboxylic acid cycle. Nature. 179:1957;988-991.
4. Garnak M., Reeves H.C. Purification and properties of phosphorylated isocitrate dehydrogenase of Escherichia coli. J. Biol. Chem. 254:1979;7915-7920.
5. Robertson E.F., Hoyt J.C., Reeves H.C. In vitro phosphorylation of Escherichia coli isocitrate lyase. Curr. Microbiol. 15:1987;103-105.
6. Robertson E.F., Hoyt J.C., Reeves H.C. Evidence for histidine phosphorylation in Escherichia coli isocitrate lyase. J. Biol. Chem. 253:1987;2477-2488.
7. Nimmo H.G., Borthwick A.C., El-Mansi E.M.T., Holms W.H., Mackintosh C., Nimmo G.A. Regulation of the enzymes at the branchpoint between the citric-acid cycle and the glyoxylate bypass in Escherichia coli. Biochem. Soc. Symp. 54:1987;93-101.
8. Hoyt J.C., Reeves H.C. In vitro phosphorylation of isocitrate lyase from Escherichia coli. Biochem. Biophys. Res. Comm. 153:1988;875-880.
9. Kornberg H.L., Elsden S.R. The metabolism of 2-carbon compounds by microorganisms. Adv. Enzymol. 13:1961;402-470.
10. Shimamoto G., Berk R.S. Taurine catabolism. III. Evidence for participation of the glyoxylate cycle. Biochim. Biophys. Acta. 632:1980;399-407.
11. Simon M.W., Martin E., Mukkada A.J. Evidence for a functional glyoxylate cycle in the Leishmaniae. J. Bacteriol. 135:1978;895-899.
12. Schloss J.V., Cleland W.W. Inhibition of isocitrate lyase by 3-nitroproprionate, a reaction-intermediate analogue. Biochemistry. 21:1982;4420-4427.
13. McFadden B.A., Purohit S. Itaconate, an isocitrate lyase-directed inhibitor in Pseudomonas indigofera. J. Bacteriol. 131:1977;136-144.
14. Rice D.W. The use of phase combination in the refinement of phosphoglycerate kinase at 2.5 Å resolution. Acta Crystallogr. A. 37:1981;491-500.
15. Kabsch W., Sander C. Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
16. Banner D.W., Waley S.G.et al. Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 Å resolution using amino acid sequence data. Nature. 255:1975;609-614.
17. Chothia C. The 14th barrel rolls out. Nature. 333:1988;598-599.
18. Farber G.K., Petsko G.A. The evolution of α/β barrel enzymes. Trends Biol. Sci. 15:1990;228-234.
19. De Lucas J.R., Amor C., Diaz M., Turner G., Laborda F. Purification and properties of isocitrate lyase from Aspergillus nidulans, a model enzyme to study catabolite inactivation in filamentous fungi. Microbiol. Res. 101:1997;410-414.
20. Lee B., Richards F.M. The interpretation of protein structures; estimation of static accessibility. J. Mol. Biol. 55:1971;379-400.
21. Attwood T.K., Payne A.W.R., Michie A.D., Parry-Smith D.J. A Colour Interactive Editor for Multiple Alignments - CINEMA. EMBnet. News. 3:1997;3.
22. Matsuoka M., McFadden B.A. Isolation, hyperexpression, and sequencing of the aceA gene encoding isocitrate lyase in Escherichia coli. J. Bacteriol. 170:1988;4528-4536.
23. Ko Y.H., McFadden B.A. Alkylation of isocitrate lyase from Escherichia coli by 3-bromopyruvate. Arch. Biochem. Biophys. 278:1990;373-380.
24. Ko Y.H., Cremo C.R., McFadden B.A. Vanadate-dependent photomodification of serine 319 and 321 in the active site of isocitrate lyase from Escherichia coli. J. Biol. Chem. 267:1992;91-95.
25. Rehman A., McFadden B.A. Serine 319 and 321 are functional in isocitrate lyase from E. coli. Curr. Microbiol. 34:1997;205-211.
26. Diehl P., McFadden B.A. Site-directed mutagenesis of lysine 193 in Escherichia coli isocitrate lyase by use of unique restriction enzyme site elimination. J. Bacteriol. 175:1993;2263-2270.
27. Diehl P., McFadden B.A. The importance of four histidine residues in isocitrate lyase. J. Bacteriol. 176:1994;927-931.
28. Fersht. A. (1985). Enzyme structure and mechanism (2nd edn) pp. 413-416, W.H. Freeman, New York.
29. Rehman A., McFadden B.A. The consequence of replacing histidine 356 in isocitrate lyase from Escherichia coli. Arch. Biochem. Biophys. 336:1996;309-315.
30. Grindley H.M., Artymiuk P.J., Rice D.W., Willett P. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J. Mol. Biol. 229:1993;707-721.
31. Bernstein F.C., Tasumi M.et al. The protein data bank: a computer-based archival file for molecular structures. J. Mol. Biol. 112:1977;535-542.
32. 2+-oxalate. Structure. 7:1999;539-548.
33. Farber G.K. An α/β barrel full of evolutionary trouble. Curr. Opin. Struct. Biol. 3:1993;409-412.
34. Reardon D., Farber G.K. Protein motifs .4. The structure and evolution of α/β barrel proteins. FASEB J. 9:1995;497-503.
35. Helin S., Kahn P.C., Guha Bh.L., Mallows D.G., Goldman A. The refined X-ray structure of muconate lactonizing enzyme from Pseudomonas putida PRS2000 at 1.85 Å resolution. J. Mol. Biol. 254:1995;918-941.
36. Neidhart D.J., Gerlt J.A.et al. Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5 Å resolution: identification of the active site and possible catalytic residues. Biochemistry. 30:1991;9264-9273.
37. Babbitt P.C., Gerlt J.A. The enolase superfamily: a general strategy for enzyme-catalysed abstraction of the α-protons of carboxylic acids. Biochemistry. 35:1996;16489-16501.
38. Langridge S.J., Baker P.J., De Lucas J.R., Sedelnikova S.E., Turner G., Rice D.W. Isocitrate lyase from Aspergillus nidulans: crystallisation and X-ray analysis of a glyoxylate cycle enzyme. Acta Crystallogr. D. 53:1997;488-490.
39. Hamlin R. Multiwire area X-ray diffractometers. Methods Enzymol. 114:1985;416-452.
40. Xuong N.H., Nielsen C., Hamlin R., Anderson D. Strategy for data collection from protein crystals using a multiwire counter area detector diffractometer. J. Appl. Crystallogr. 18:1985;342-350.
41. Howard A.J., Nielsen C., Young N.H. Software for a diffractometer with multiwire area detector. Methods Enzymol. 114:1985;452-472.
42. Leslie A.G.W. Recent changes to the MOSFLM package for processing film and image data. Wolf W.M., Wilson K.S. Joint CCP4 and ESF-EADBM Newsletter on Protein Crystallography, no. 26. 1992;SERC Daresbury Laboratory, Warrington, UK.
43. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D. 50:1994;760-763.
44. Otwinowski Z. Maximum likelihood refinement of heavy atom parameters in isomorphous replacement and anomalous scattering. Wolf W., Evans P.R., Leslie A.G.W. Proceedings of the CCP4 Study Weekend. 1991;80-86 SERC Daresbury Laboratory, Warrington, UK.
45. Cowtan K. DM an automated procedure for phase improvement by density modification. Bailey S., Wilson K. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography no. 31. 1994;34-38 SERC Daresbury Laboratory, Warrington, UK.
46. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119.
47. Jones T.A. Interactive computer graphics: FRODO. Methods Enzymol. 115:1985;157-171.
48. Tronrud D.E., Ten Eyck L.F., Matthews B.W. An efficient general-purpose least squares refinement program for macromolecular structures. Acta Crystallogr. A. 43:1987;489-501.
49. Tronrud D.E. Conjugate-direction minimisation: an improved method for the refinement macromolecules. Acta Crystallogr. A. 48:1992;912-916.
50. Moews P.C., Kretsinger R.H. Refinement of the structure of carp muscle calcium-binding parvalbumin by model building and difference Fourier analysis. J. Mol. Biol. 91:1975;201-228.
51. Gainey L.D.S., Connerton I.F., Lewis E.H., Turner G., Ballance D.J. Characterisation of the glyoxysomal isocitrate lyase genes of Aspergillus nidulans (ACUD) and Neurospora crassa (ACU-3). Curr. Genet. 21:1992;43-47.
52. Mitchell E.M., Artymiuk P.J., Rice D.W., Willett P. Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J. Mol. Biol. 212:1990;151-166.
53. Bron C., Kerbosch J. Algorithm 457 - finding all cliques of an undirected graph. Commun. ACM. 16:1973;575-577.
54. Barton G.J. ALSCRIPT - a tool to format multiple sequence alignments. Protein Eng. 6:1993;37-40.
55. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:1991;946-950.
56. Ferrin T.E., Huang C.C., Jarvis L.E., Langridge R. The MIDAS display system. J. Mol. Graph. 6:1988;13-27.
57. Bacon D.J., Anderson W.F. A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph. 6:1988;219-220.
58. Merritt E.A., Murphy M.E.P. Raster3D version 2.0 - a program for photorealistic molecular graphics. Acta Crystallogr. D. 50:1994;869-873.
59. Nichols A., Sharp K.A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struc. Funct. Genet. 11:1991;281-296.