Refined crystal structure of methylamine dehydrogenase from Paracoccus denitrificans at 1.75 Å resolution

Journal of Molecular Biology

Volumn 276, Issue 1, 1998, Pages 131-149

  Chen, Longyin ^a   Doi, Mitsunobu ^a   Durley, Rosemary C E ^a   Chistoserdov, Andrei Y ^b   Lidstrom, Mary E ^b   Davidson, Victor L ^c   Mathews, F Scott ^a  

^a Dept Biochem Molec Biophys W ^*  (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c UNIVERSITY OF MISSISSIPPI   (United States)

Author keywords

Amino acid derived cofactor; Crystal structure; Methylamine dehydrogenase; Quinoprotein; Tryptophan tryptophylquinone

Indexed keywords

AMINE DEHYDROGENASE; ASPARTIC ACID; CARBONYL DERIVATIVE; MONOVALENT CATION; QUINONE DERIVATIVE; THREONINE; TRYPTOPHAN; TRYPTOPHAN TRYPTOPHYLQUINONE; TYROSINE; UNCLASSIFIED DRUG; WATER;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; COVALENT BOND; CROSS LINKING; CRYSTAL STRUCTURE; DISULFIDE BOND; DNA SEQUENCE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBUNIT; NONHUMAN; OXIDATION REDUCTION REACTION; PARACOCCUS DENITRIFICANS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN QUATERNARY STRUCTURE;

BACTERIA (MICROORGANISMS); PARACOCCUS DENITRIFICANS;

EID: 0032512707     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1511     Document Type: Article

References (52)

1. Anthony C. Quinoproteins in C1-dissimilation by bacteria. Jongejan J.A., Duine J.A. PQQ and Quinoproteins. 1989;1-11 Kluwer Academic Publishers, Dordrecht
2. Barton G.J. Alscript, a tool to format multiple sequence alignments. Protein Eng. 6:1993;37-40
3. Bishop G.R., Davidson V.L. Intermolecular electron transfer from substrate-reduced methylamine dehydrogenase to amicyanin is linked to proton transfer. Biochemistry. 34:1995;12082-12086
4. Bishop G.R., Davidson V.L. Catalytic role of monovalent cations in the mechanism of proton transfer which gates an interprotein electron transfer reaction. Biochemistry. 36:1997;13586-13592
5. Bishop G.R., Brooks H.B., Davidson V.L. Evidence for a tryptophan tryptophylquinone intermediate in the physiologic reaction between methylamine dehydrogenase and amicyanin. Biochemistry. 35:1996;8948-8954
6. 15N-NMR of the tryptophan tryptophylquinone aminoquinol reaction intermediate of methylamine dehydrogenase. J. Am. Chem. Soc. 118:1996;12868-12869
7. Brooks H.B., Jones L.H., Davidson V.L. Deuterium kinetic isotope effect and stopped-flow kinetic studies of quinoprotein methylamine dehydrogenase. Biochemistry. 32:1993;2725-2729
8. Brunger A.T. X-PLOR (version 2.1) Manual of a System for Crystallography and NMR. 1990;Yale University, New Haven
9. Burley S.K., Petsko G.A. Amino-aromatic interactions in proteins. FEBS Letters. 32:1986;139-143
10. Chen L., Lim L.W., Mathews F.S., Davidson V.L., Husain M. Preliminary X-ray crystallographic studies of methylamine dehydrogenase and methylamine dehydrogenase-amicyanin complex from Paracoccus denitrificans. J. Mol. Biol. 203:1988;1137-1138
11. Chen L., Mathews F.S., Davidson V.L., Huizinga E.G., Vellieux F.M.D., Duine J.A., Hol W.J.G. Crystallographic investigations of the tryptophan-derived cofactor in the quinoprotein methylamine dehydrogenase. FEBS Letters. 287:1991;163-166
12. Chen L., Mathews F.S., Davidson V.L., Huizinga E.G., Vellieux F.M.D., Hol W.J.G. Three-dimensional structure of the quinoprotein methylamine dehydrogenase from Paracoccus denitrificans determined by molecular replacement at 2.8 Å resolution. Proteins: Struct. Funct. Genet. 14:1992;288-299
13. Chen L., Durley R., Poliks B.J., Hamada K., Chen Z., Mathews F.S., Davidson L., Satow Y., Huizinga E., Vellieux F.M.D., Hol W.G.J. Crystal structure of an electron-transfer complex between methylamine dehydrogenase and amicyanin. Biochemistry. 31:1992;4959-4964
14. 551i. Science. 264:1994;86-90
15. Chistoserdov A.Y., Boyd J., Mathews F.S., Lidstrom M.E. The genetic organization of the MAU gene cluster of the facultative autotroph Paracoccus denitrificans. Biochem. Biophys. Res. Commun. 184:1992;1181-1189
16. Chistoserdov A.Y., McIntire W.S., Mathews F.S., Lidstrom M.E. The genetic sequence of Bacterium W3A1. J. Bacteriol. 176:1994;4073-4080
17. Connolly M.J. Analytical molecular surface calculation. J. Appl. Crystallog. 24:1983;548-558
18. Davidson V.L. Methylamine dehydrogenase. Davidson V.L. Principles and Applications of Quinoproteins. 1993;73-95 Marcel Dekker, New York
19. Davidson V.L., Graichen M.E., Jones L.H. Mechanism or reaction of allylamine with the quinoprotein methylamine dehydrogenase. Biochem. J. 308:1995;487-492
20. De Beer R., Duine J.A., Frank J., Large P.J. The prosthetic group of methylamine dehydrogenase from Pseudomonas AM1. Biochim. Biophys. Acta. 662:1980;370-374
21. Engh R.A., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallog. sect. A. 47:1991;392-400
22. Farber H.R., Groom C.R., Baker H.M., Morgan W.T., Smith A., Baker E.N. 1.8 Å structure of the C-terminal domain of rabbit serum haemopexin. Structure. 3:1995;551-559
23. 1. Cell. 81:1995;369-377
24. Gorren A.C.F., Duine J.A. The effects of pH and cations on the spectral and kinetic properties of methylamine dehydrogenase from Thiobacillus versutus. Biochemistry. 33:1994;12202-12209
25. Gorren A.C., de Vries S., Duine J.A. Binding of monovalent cations to methylamine dehydrogenase in the semiquinone state and its effect on electron transfer. Biochemistry. 34:1995;9748-9754
26. Howard A.J., Nielsen C., Xuong Ng.H. Software for a diffractometer with multiwire area detector. Methods Enzymol. 114:1985;452-472
27. Huitema F., van Beeumen J., van Driessche G., Duine J.A., Canters G.W. Cloning and sequencing of the gene coding for the large subunit of methylamine dehydrogenase from Thiobacillus versutus. J. Bacteriol. 175:1993;6254-6259
28. Huizinga E.G., Zanten B.A.M., van Duine J.A., Jongejan J.A., Huitema F., Wilson K.S., Hol W.G.J. Active site structure of methylamine dehydrogenase hydrazines identify C6 as the reactive site of the tryptophan-derived quinone cofactor. Biochemistry. 31:1992;9789-9795
29. Husain M., Davidson V.L. An inducible periplasmic blue copper protein from Paracoccus denitrificans. J. Biol. Chem. 260:1985;14626-14629
30. Husain M., Davidson V.L. Characterization of two inducible periplasmic c-type cytochromes from Paracoccus denitrificans. 261:1986;8577-8580
31. Husain M., Davidson V.L. Purification and properties of methylamine dehydrogenase from Paracoccus denitrificans. J. Bacteriol. 169:1987;1712-1717
32. Ito N., Phillips S.E.V., Stevens C., Ogel Z.B., McPherson M.J., Keen J.N., Yadav K.D.S., Knowles P.F. Novel thioether bond revealed by a 1.7 Å crystal structure of galactose oxidase. Nature. 350:1991;87-90
33. Kabsch W., Sander C. Dictionary of protein secondary structure pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637
34. Kraulis P.J. MOLSCRIPT a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950
35. Kumar M.A., Davidson V.L. Chemical cross-linking study of complex formation between methylamine dehydrogenase and amicyanin from Paracoccus denitrificans. Biochemistry. 29:1990;5299-5304
36. Kuusk V., McIntire W.S. Influence of monovalent cations on the ultraviolet-visible spectrum of tryptophan tryptophylquinone-containing methylamine dehydrogenase from bacterium W3A1. J. Biol. Chem. 269:1994;26136-26143
37. Luzzati V. Traitement statistique des erreurs la determination des structures crystallines. Acta Crystallog. 5:1952;801-810
38. McIntire W.S., Wemmer D.E., Chistoserdov A., Lidstrom M.E. A new cofactor in a prokaryotic enzyme tryptophan tryptophylquinone as the redox prosthetic group in methylamine dehydrogenase. Science. 252:1991;817-824
39. Morris A.L., MacArthur M.W., Hutchinson E.G., Thornton J.M. Stereochemical quality of protein structure coordinates. Proteins: Struct. Funct. Genet. 12:1992;345-364
40. Murzin A.G. Structural principles for the propeller assembly of β-sheets the preference for seven-fold symmetry. Proteins: Struct. Funct. Genet. 14:1992;191-201
41. Ramachandran G.N., Sasasekharan V. Conformations of polypeptides and proteins. Advan. Protein Chem. 23:1968;283-437
42. Roussel A., Cambillau C. TURBO-FRODO. Silicon Graphics Geometry Partners Directory 86. 1991;Silicon Graphics, Mountain View, CA, USA
43. Scrutton N.S., Raine A.R. Cation-pi bonding and amino-aromatic interactions in the biomolecular recognition of substituted ammonium ligands. Biochem. J. 319:1996;1-8
44. Shirai S., Matsumoto T., Tobari J. Methylamine dehydrogenase of Pseudomonas AM1, a subunit enzyme. J. Biochem. (Tokyo). 83:1978;1599-1607
45. Tronrud D.E., Ten Eyck L., Matthews B.W. An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallog. sect A. 43:1987;489-501
46. Van Beeumen J., Van Driessche G., Huitema F., Duine J.A., Canters G.W. N-Terminal heterogeneity of methylamine dehydrogenase from Thiobacillus versutus. FEBS Letters. 333:1993;188-192
47. van der Palen C.J., Slotbloom C.J., Jongejan L., Reijnders W.N., Harms N., Duine J.A., van Spanning R.J.M. Mutational analysis of mau genes involved in methylamine metabolism in Paracoccus denitrificans. Eur. J. Biochem. 230:1995;860-871
48. van Spanning R.J.M., Wansell C.W., Reijnders W.N.M., Oltmann L.F., Stouthamer A.H. Mutagenesis of the gene encoding amicyanin of Paracoccus denitrificans and the resultant effect on methylamine dehydrogenase. FEBS Letters. 275:1990;217-220
49. Varghese J.N., Laver W.G., Coleman P.P. Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 Å resolution. Nature. 303:1983;35-40
50. Vellieux F.M.D., Huitema F., Groendijk H., Kalk K.H., Frank J., Jongejan J.A., Duine J.A., Petratos K., Drenth J., Hol W.G.J. Structure of quinoprotein methylamine dehydrogenase at 2.25 Å resolution. EMBO J. 8:1989;2171-2178
51. Vellieux F.M.D., Kalk K.H., Drenth J., Hol W.G.J. Structure determination of quinoprotein methylamine dehydrogenase from Thiobacillus versutus. Acta Crystallog. sect. B. 46:1990;806-823
52. Xia Z.-x., Dai W.-w., Xiong J.-p., Hao Z.-p., Davidson V.L., White S., Mathews F.S. The three-dimensional structures of methanol dehydrogenase from two methylotrophic bacteria at 2.6 Å resolution. J. Biol. Chem. 267:1992;22289-22297