The crystal structure of 8-amino-7-oxononanoate synthase: A bacterial PLP-dependent, Acyl-CoA-condensing enzyme

Journal of Molecular Biology

Volumn 284, Issue 2, 1998, Pages 401-419

  Alexeev, Dmitriy ^a   Alexeeva, Marina ^a   Baxter, Robert L ^a   Campopiano, Dominic J ^a   Webster, Scott P ^a   Sawyer, Lindsay ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

5 aminolevulinate synthase; 8 amino 7 oxononanoate synthase; Biotin biosynthesis; Pyridoxal 5' phosphate; X ray crystal structure

Indexed keywords

5 AMINOLEVULINATE SYNTHASE; ACYL COENZYME A; ALANINE; BACTERIAL ENZYME; BIOTIN; CITRATE SYNTHASE; PYROPHOSPHATE; SYNTHETASE;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DECARBOXYLATION; ENZYME PURIFICATION; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL;

EID: 0032573591     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2086     Document Type: Article

References (66)

1. Alexander F.W., Sandmeier E., Mehta P., Christen P. Evolutionary relationships among pyridoxal-5′-phosphate-dependent enzymes. Regio-specific α, β and γ families. Eur. J. Biochem. 219:1994;953-960
2. Alexeev D., Baxter R.L., Sawyer L. Mechanistic implications and family relationships from the structure of dethiobiotin synthetase. Structure. 2:1994;1061-1107
3. Antson A.A., Demidkina T.V., Gollnick P., Dauter Z., von Tersch R.L., Long J., Berezhnoy S.N., Phillips R.S., Harutyunyan E.H., Wilson K.S. Three-dimensional structure of tyrosine phenol-lyase. Biochemistry. 32:1993;4195-4206
4. Amone A., Rogers P.H., Hyde C.C., Briley P.D., Metzler C.M., Metzler D.E. Pig cytosolic aspartate aminotransferase the structures of internal aldimine, external aldimine and ketimine and of the β subform. Christen P., Metzler D.E. Transaminases. 1985;138-155 Wiley, New York
5. Bailey G.B., Dempsey W.B. Purification and properties of an α-dialkyl amino acid transaminase. Biochemistry. 6:1967;1526-1533
6. Barton G.J. ALSCRIPT - A tool to format multiple sequence alignments. Protein Eng. 6:1993;37-40
7. Birch O.M., Fuhrmann M., Shaw N.M. Biotin synthase from Escherichia coli, an investigation of the low molecular weight and protein components required for activity in vitro. J. Biol. Chem. 270:1995;19158-19165
8. Bower S., Perkins J.B., Yocum R.R., Howitt C.L., Rahaim P., Pero J. Cloning, sequencing, and characterization of the Bacillus subtilis biotin biosynthetic operon. J. Bacteriol. 178:1996;4122-4130
9. Brunger A.T., Krukowski A. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallog. sect. A. 46:1990;585-593
10. Chothia C., Lesk A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:1986;823-826
11. Christen P., Kasper P., Gehring H., Sterk M. Stereochemical constraint in the evolution of pyridoxal-5′-phosphate-dependent enzymes - a hypothesis. FEBS Letters. 389:1996;12-14
12. Clausen T., Huber R., Laber B., Pohlenz H., Messerschmidt A. Crystal structure of the pyridoxal-5′-phosphate dependent cystathionine β-lyase from Escherichia coli at 1.83 Å J. Mol. Biol. 262:1996;202-224
13. The CCP4 suite programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763
14. Coulson A.F.W., Collins J.F., Lyall A. Protein and nucleic acid sequence database searching a suitable case for parallel processing. Comput. J. 30:1987;420-424
15. Dunathan H.C. Conformation and reaction specificity in pyridoxal phosphate enzymes. Proc. Natl. Acad. Sci. USA. 55:1966;712-716
16. 452 to histidine substitution in the erythroid 5-aminolevulinate synthetase gene in a large pedigree with X-linked hereditary sideroblastic anaemia. Eur. J. Haematol. 58:1997;1-4
17. Eisenberg M.A., Star C. Synthesis of 7-oxo-8-aminopelargonic acid, a biotin vitamer, in cell-free extracts of Escherichia coli biotin auxotrophs. J. Bacteriol. 96:1968;1291-1297
18. Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., Bult C.J., Tomb J.F., Dougherty B.A., Merrick J.M., McKenney K., Sutton G., Fitzhugh W., Fields C., Gocayne J.D., et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269:1995;496-512
19. Ford G.C., Eichele G., Jansonius J.N. Three-dimensional structure of a pyridoxal phosphate dependent enzyme, mitochondrial aspartate aminotransferase. Proc. Natl Acad. Sci. USA. 77:1980;2559-2563
20. Gallagher D.T., Gilliland G.L., Xiao G., Zondlo J., Fisher K.E., Chinchilla D., Eisenstein E. Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Structure. 6:1998;465-475
21. Gloeckler R., Ohsawa I., Speck D., Ledoux C., Bernard S., Zinsius M., Villeval D., Kisou T., Kamogawa K., Lemoine Y. Cloning and characterization of the Bacillus sphaericus genes controlling the bioconversion of pimelate into dethiobiotin. Gene. 87:1990;63-70
22. Gong J., Ferreira G.C. 5-Aminolevulinate synthase functionally important residues at a glycine loop putative, a pyridoxal phosphate cofactor-binding site. Biochemistry. 34:1995;1678-1685
23. Hayashi H. Pyridoxal enzymes mechanistic diversity and uniformity. J. Biochem. 118:1995;463-473
24. Hayes J.D., Kerr L.A., Cronshaw A.D. Evidence that gluthathione S-transferases B1B1 and B2B2 are the products of separate genes. Biochem. J. 264:1989;437-445
25. 6-dependent enzyme with asymmetry in structure and active site reactivity. Proc. Natl Acad. Sci. USA. 94:1997;4866-4871
26. Higgins D., Bleasby A.J., Fuchs R. CLUSTAL-V-improved software for multiple sequence alignment. Scientist. 8:1994;17-21
27. Hunter G.A., Ferreira G.C. A continuous spectrophotometric assay for 5-aminolevulinate synthase that utilizes substrate cycling. Anal. Biochem. 226:1995;221-224
28. Hyde C.C., Ahmed S.A., Padlan E.A., Miles E.W., Davies D.R. Three-dimensional structure of the tryptophan synthetase α2β2 multienzyme complex from Salmonella typhimurium. J. Biol. Chem. 263:1988;17857-17871
29. Isupov M.N., Anston A.A., Dodson E.J., Dodson G.G., Dementieva I.S., Zakomirdina L.N., Wilson K.S., Dauter Z., Lebedev A.A., Harutyunyan E.H. Crystal structure of tryptophanase. J. Mol. Biol. 276:1998;603-623
30. John R.A. Pyridoxal phosphate-dependent enzymes. Biochim. Biophys. Acta. 1248:1995;81-96
31. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. Sect A. 47:1991;110-119
32. Jordan P.M. The biosynthesis of 5-aminolaevulinic acid and its transformation into uroporphyrinogen III. Jordan P.M. Biosynthesis of Tetrapyrroles. 1991;1-66 Elsevier, Amsterdam
33. Kabsch W., Sander C. Dictionary of protein secondary structure - pattern recognition of hydrogen bonded and geometrical features. Biopolymers. 22:1983;2577-2637
34. Kamitori S., Hirotsu K., Higuchi T., Kondo K., Inoue K., Kuramitsu S., Kagamiyama H., Higuchi Y., Yasuoka N., Kusunoki M., Matsuura Y. Three-dimensional structure of aspartate aminotransferase from Escherichia coli at 2.8 Å resolution. J. Biochem. 104:1988;317-318
35. Kaneko T., Tabata S. Complete genome structure of the unicellular cyanobacterium Synechocystis sp. PCC6803. Plant Cell Physiol. 38:1997;1171-1176
36. Kleywegt G.J., Jones T.A. Phi/psi-chology Ramachandran revisited. Structure. 4:1996;1395-1400
37. Kraulis P.J. MOLSCRIPT a program to produce both detailed and schematic plots of protein structure. J. Appl. Crystallog. 24:1991;946-950
38. Malashkevich V., Strokopytov B.V., Borisov V.V., Dauter Z., Wilson K.S., Torchinsky Yu.M. Crystal structure of the closed form of chicken cytosolic aspartate aminotransferase at 1.9 Å J. Mol. Biol. 247:1995;111-124
39. McPhalen C.A., Vincent M.G., Jansonius J.N. X-ray structure refinement and comparison of three forms of mitochondrial aspartate aminotransferase. J. Mol. Biol. 225:1992;495-517
40. Mehta P.K., Christen P. Homology of 1-aminocyclopropane-1-carboxylate synthase, 8-amino-7-oxonanoate synthase, 2-amino-6-caprolactam racemase, 2,2-dialkyglycone decarboxylase, glutamate-1-semialdehyde 2,1-aminomutase and isopenicillin-N-epimerase with aminotransferases. Biochem. Biophys. Res. Commun. 198:1994;138-143
41. Mehta P.K., Hale T.I., Christen P. Aminotransferases demonstration of homology and division into evolutionary subgroups. Eur. J. Biochem. 214:1993;549-561
42. Merrill A.H.J., Jones D.D. An update of the enzymology and regulation of sphingomyelin metabolism. Biochim. Biophys. Acta. 1037:1990;24-29
43. Momany C., Ernst S., Ghosh R., Chang N.-L., Hackert M.L. Crystallographic structure of a PLP-dependent ornithine decarboxylase from Lactobacillus 30a to 3.0 Å resolution. J. Mol. Biol. 252:1995;643-655
44. Mukherjee J.J., Dekker E.E. Purification, properties and N-terminal amino acid sequence of homogeneous Escherichia coli 2-amino-3-ketobutyrate CoA ligase, a pyridoxal phosphate-dependent enzyme. J. Biol. Chem. 262:1987;14441-14447
45. Nicholls A., Bharadwaj R., Honig B. GRASP graphical representation and analysis of surface properties. Biophys. J. 64:1993;166-170
46. Okamoto A., Higuchi T., Hirotsu K., Kuramitsu S., Kagamiyama H. X-ray crystallographic study of pyridoxal 5′-phosphate aspartate aminotransferases from Escherichia coli in open and closed form. J. Biochem. 116:1994;95-107
47. Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson C., Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J. The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of thebio operon. J. Biol. Chem. 263:1988;19577-19585
48. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326
49. Pearson W.R., Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA. 85:1988;2444-2448
50. Ploux O., Marquet A. The 8-amino-7-oxopelargonate synthase from Bacillus sphaericus - purification and preliminary characterization of the cloned enzyme overproduced in Escherichia coli. Biochem. J. 283:1992;327-331
51. Ploux O., Marquet A. Mechanistic studies on the 8-amino-7-oxopelargonate synthase, a pyridoxal-5′-phosphate-dependent enzyme involved in biotin biosynthesis. Eur. J. Biochem. 236:1996;301-308
52. Read R. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallog. sect. A. 42:1986;140-149
53. Sambrook J., Fritsch E.F., Maniatis F. Molecular Cloning: A Laboratory Manual. 2nd edit.:1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
54. Sakurai N., Akatsuka H., Kawai E., Imai Y., Komatsubara S. Complete sequence and organisation of the Serratia marcescens biotin operon. Microbiology. 142:1996;3295-3303
55. Shaw J.P., Petsko G.A., Ringe D. Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9 Å resolution. Biochemistry. 36:1997;1329-1342
56. Sheldrick G.M., Schneider T.R. SHELX-97. High resolution refinement. Methods Enzymol. 277:1997;319-343
57. Shen B.W., Henning M., Hohenester E., Jansonius J.N., Schirmer T. Crystal structure of human recombinant ornithine aminotransferase. J. Mol Biol. 277:1998;81-102
58. Spinelli S., Ploux O., Marquet A., Anguille C., Jelsch C., Cambillau C., Martinez C. Crystallization and preliminary X-ray study of the 8-amino-7-oxopelargonate synthase from Bacillus sphaericus. Acta Crystallog. sect D. 62:1996;866-868
59. Studier F.W., Rosenberg A.H., Dunn J.J., Dubendorff J.W. Use of T7 RNA polymerase to direct selective high-level expression of cloned genes. Methods Enzymol. 185:1990;60-89
60. Sturrock S.S., Dryden D.T.F. A prediction of the amino acids and structures involved in DNA recognition by type I restriction and modification enzymes. Nucl. Acids Res. 25:1997;3408-3414
61. Sugio S., Petsko G.A., Manning J.M., Soda K., Ringe D. Crystal structure of a D-amino acid aminotransferase how the protein controls stereoselectivity. Biochemistry. 34:1995;9661-9669
62. Toney M.D., Kirsch J.F. Kinetics and equilibria for the reactions of coenzymes with wild type and the Y70F mutant of Escherichia coli aspartate aminotransferase. Biochemistry. 30:1991;7461-7466
63. Toney M.D., Hohenester E., Cowan S.W., Jansonius J.N. Dialkylglycine decarboxylase structure bifunctional active site and alkali metal sites. Science. 261:1993;756-759
64. Toney M.D., Hohenester E., Keller J.W., Jansonius J.N. Structural and mechanistic analysis of two refined crystal structures of the pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase. J. Mol. Biol. 245:1995;151-179
65. Watanabe N., Sakabe K., Sakabe N., Higashi T., Sasaki K., Aibara S., Morita Y., Yonaha K., Toyama S., Fukutani H. Crystal structure analysis of ω-amino acid pyruvate aminotransferase with a newly developed Weissenberg camera and an imaging plate using synchrotron radiation. J. Biochem. 105:1989;1-3
66. Wu C.H., Bao Y.Y., Shao C.P., Shiuan D. Molecular cloning and nucleic acid sequencing of the bioF (7-keto-8-amino pelargonic acid synthase), bioC and bioD (dethiobiotin synthase) genes of Erwinia herbicola. Mol. Biol. Int. 41:1997;311-315