Crystal structure of a ternary complex of D-2-hydroxy-isocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 Å resolution

Journal of Molecular Biology

Volumn 267, Issue 3, 1997, Pages 640-660

  Dengler, Uwe ^a   Niefind, Karsten ^a,b   Kieß, Michael ^a   Schomburg, Dietmar ^a,b  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b UNIVERSITY OF COLOGNE   (Germany)

Author keywords

D 2 hydroxyisocaproate dehydrogenase; NAD+ dependent D 2 hydroxycarboxylate dehydrogenases; Structural comparison; Substrate specificity; X ray crystallography

Indexed keywords

2 OXOISOCAPROIC ACID; AMMONIUM SULFATE; ARGININE; NICOTINAMIDE ADENINE DINUCLEOTIDE; OXIDOREDUCTASE; RECOMBINANT PROTEIN; SULFATE;

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME MECHANISM; ENZYME SPECIFICITY; LACTOBACILLUS CASEI; MOLECULAR MODEL; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

EID: 0031552374     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0864     Document Type: Article

References (58)

1. Agraz A., Paulsen J., Börner B., Hustedt H. Renaturation, purification, and characterization of recombinant D -2-hydroxyisocaproate dehydrogenase from Escherichia coli. Enzyme Microb. Technol. 17:1995;558-563.
2. Almarsson Ö., Bruice T. C. Evaluation of the factors influencing reactivity and stereospecificity in NAD(P)H dependent dehydrogenase enzymes. J. Am. Chem. Soc. 115:1993;2125-2138.
3. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank. Nucl. Acids Res. 20:1992;2019-2022.
4. +-dependent D -2-hydroxyisocaproate dehydrogenase of Lactobacillus delbrueckii subsp. bulgaricus. Gene cloning and enzyme characterization. Eur. J. Biochem. 224:1994;439-446.
5. Bernstein F. C., Noetzle T. F., Williams G. J. B., Meyer E. F. Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
6. Bork P. Mobile Modules and Motifs. Curr. Opin. Struct. Biol. 2:1992;413-421.
7. Branden C., Tooze J. Enzymes that bind nucleotides. Introduction to Protein Structure. 1991;Garland Publishing, New York.
8. Brünger A. T. Extension of molecular replacement: a new search strategy based on patterson correlation refinement. Acta Crystallog sect. A. A46:1990;46-57.
9. Brünger A. T. X-PLOR. A System for Crystallography and NMR. Manual, Version 3.1. 1992a;Yale University Press, New Haven.
10. Brünger A. T. The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 335:1992b;472-474.
11. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R -factor refinement by molecular dynamics. Science. 235:1987;458-460.
12. Brünger A. T., Krukowski A., Erickson J. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallog sect. A. A46:1990;585-593.
13. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystal-lography. Acta Crystallog sect. D. 50:1994;760-763.
14. Cowtan K. D., Main P. Improvement of macromolecular electron-density maps by the simultaneous application of real and reciprocal space constraints. Acta Crystallog sect. D. 49:1993;148-157.
15. Eklund H., Bränden C.-I. Crystal structure, coenzyme conformations and protein interactions. Pyridine Nucleotide Coenzymes. 1987;Wiley, New York.
16. Engh R. A., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallog sect. A. 47:1991;392-400.
17. Feil I., Lerch H.-P., Schomburg D. Deletion variants of L-hydroxyisocaproate dehydrogenase. Probing substrate specificity. Eur. J. Biochem. 223:1994;857-863.
18. Gilliland G. L., Quiocho F. A. Structure of the L -arabinose-binding protein from Escherichia coli at 2.4 Å resolution. J. Mol. Biol. 146:1981;341-362.
19. Goldberg J. D., Yoshida T., Brick P. Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 Å resolution. J. Mol. Biol. 236:1994;1123-1140.
20. Grau U. M. Structural interactions with enzymes. Everse J., Anderson B., You K. The Pyridine Nucleotide Coenzymes. 1982;Academic Press, New York.
21. Hodel A., Kim S.-H., Brünger A. T. Model bias in macromolecular crystal structures. Acta Crystallog sect. A. 48:1992;851-858.
22. Hummel W., Kula M.-R. Dehydrogenases for the synthesis of chiral compounds. Eur. J. Biochem. 184:1989;1-13.
23. Hummel W., Schütte H., Kula M.-R. D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei. A new enzyme suitable for stereospecific reduction of 2-ketocarboxylic acids. Appl. Microbiol. Biotechnol. 21:1985;7-15.
24. Janin J., Chothia C. Packing of α-helices onto β-pleated sheets and the anatomy of α/β-proteins. J. Mol. Biol. 143:1980;95-128.
25. 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.
26. Kallwass, H. K. W. 1988, Proteinchemische und enzymatische Charakterisierung der D -2-Hydroxyisocaproat-Dehydrogenase aus Lactobacillus casei. PhD thesis, Technische Universität Braunschweig, Germany.
27. Kallwass H. K. W. Potential of R-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei for stereospecific reductions. Enzyme Microb. Technol. 14:1992;28-35.
28. +-dependent D -lactate dehydrogenase. J. Biol. Chem. 267:1992a;20298-20301.
29. +-dependent D -lactate dehydrogenase. Evidence for the presence of Arg-235, His-303, Tyr-101, and Trp-19 at or near the active site. J. Biol. Chem. 267:1992b;8499-8513.
30. +-dependent D -lactate dehydrogenase: comparison of primary structure of 2-hydroxy acid dehydrogenases. Biochem. Biophys. Res. Commun. 184:1992c;60-66.
31. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
32. Lamzin V. S., Aleshin A. E., Strokopytov B. V., Yukhnevich M. G., Popov V. O., Harutyunyan E. H., Wilson K. S. Crystal structure of NAD-dependent formate dehydrogenase. Eur. J. Biochem. 206:1992;441-452.
33. Lamzin V. S., Dauter Z., Popov V. O., Harutyunyan E. H, Wilson K. S. High resolution structures of holo and apo formate dehydrogenase. J. Mol. Biol. 236:1994a;759-785.
34. Lamzin V. S., Dauter Z., Wilson K. S. Dehydrogenation through the looking-glass. Nature Struct. Biol. 1:1994b;281-282.
35. Laskowski R. A, MacArthur M. W., Moss D. S., Thornton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26:1992;283-291.
36. Lerch H.-P., Blöcker H., Kallwass H., Hoppe J., Tsai H., Collins J. Cloning, sequencing and expression in Escherichia coli of the D -2-hydroxyisocaproate dehydrogenase gene of Lactobacillus casei. Gene. 78:1989;47-57.
37. Leslie A. G. W., Brick P., Wonacott A. J. An improved program package for the measurement of oscillation photographs. CCP4 News. 18:1986;33-39.
38. Lessel U., Schomburg D. Similarities between protein 3-D structures. Protein Eng. 7:1994;1175-1187.
39. Li H., Goldstein B. M. Carboxamide group conformation in the nicotinamide and thiazole-4-carboxamide rings: implications for enzyme binding. J. Med. Chem. 35:1992;3560-3567.
40. Matthews B. W. Solvent content of protein crystals. J. Mol. Biol. 33:1968;491-497.
41. Niefind, K. 1993, Röntgenkristallographische Untersuchungen an drei mikrobiellen Enzymen: D -2-Hydroxyisocaproat-Dehydrogenase aus Lactobacillus casei, L -2-Hydroxyisocaproat-Dehydrogenase aus Lactobacillus confusus, Alkalische Protease aus Bacillus alcalophilus/Variante Q59R. PhD thesis, Technische Universität Braunschweig.
42. Niefind K., Hecht H.-J., Schomburg D. Crystallization and preliminary characterization of crystals of D -2-hydroxyisocaproate dehydrogenase from Lactobacillus casei. J. Mol. Biol. 229:1994;400-402.
43. Niefind K., Hecht H.-J., Schomburg D. Crystal structure of L -2-hydroxyisocaproate dehydrogenase from Lactobacillus confusus at 2.2 Å resolution. An example of strong asymmetry between subunits. J. Mol. Biol. 251:1995;256-281.
44. Oppenheimer N. J., Handlon A. L. Mechanism of NAD-dependent enzymes. Sigman D. S. The Enzymes. 1992;Academic Press, Inc. San Diego.
45. Quiocho F. A., Vyas N. K. Novel stereospecificity of the L -arabinose-binding protein. Nature. 310:1984;381-386.
46. Rao S. T., Rossmann M. G. Comparison of super-secondary structure in proteins. J. Mol. Biol. 76:1973;241-256.
47. Read R. J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallog sect. A. 42:1986;140-149.
48. Schomburg D., Reichelt J. BRAGI: a comprehensive protein modeling program system. J. Mol. Graph. 6:1988;161-165.
49. max-type cooperative enzyme phosphoglycerate dehydrogenase. Nature Struct. Biol. 2:1995;69-76.
50. Schütte H., Hummel W., Kula M.-R. L-2-hydroxyisocaproate dehydrogenase: a new enzyme from Lactobacillus confusus for the stereospecific reduction of 2-ketocarboxylic acids. Appl. Microbiol. Biotechnol. 19:1984;167-176.
51. Siddiqui A. S., Barton G. J. Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Sci. 4:1995;872-884.
52. Stoll V. S., Kimber M. S., Pai E. Insights into substrate binding by D -2-ketoacid dehydrogenases from the structure of Lactobacillus pentosusD -lactate dehydrogenase. Structure. 4:1996;437-447.
53. Stone K. L., LoPresti M. B., Crawford J. M., DeAngelis R., Wiliams K. R. Enzymatic digestion of proteins and HPLC peptide isolation. P. T. Matsudaira. A Practical Guide to Protein and Peptide Purification for Microsequencing. 1989;Academic Press, San Diego.
54. Taguchi H., Ohta T. Histidine 296 is essential for the catalysis in Lactobacillus plantarumD -lactate dehydrogenase. J. Biol. Chem. 268:1993;18030-18034.
55. Taguchi H., Ohta T. Essential role of arginine 235 in the substrate-binding of Lactobacillus plantarumD -lactate dehydrogenase. J. Biochem. 115:1994;930-936.
56. Vinals C., Depiereux E., Feytmans E. Prediction of structurally conserved regions of D -specific hydroxy acid dehydrogenases by multiple alignment with formate dehydrogenase. Biochem. Biophys. Res. Commun. 192:1993;182-188.
57. Vinals C., De Bolle X., Depiereux E., Feytmans E. Knowledge-based modeling of the D -lactate dehydrogenase three-dimensional structure. Proteins: Struct. Funct. Genet. 21:1995;307-318.
58. Wisconsin Sequence Analysis Package. Program Manual. 1994;Genetics Computer Group, Inc. University Research Park, 575 Science Drive, Madison.