Inorganic nitrogen metabolism in bacteria

Current Opinion in Chemical Biology

Volumn 3, Issue 2, 1999, Pages 207-219

  Richardson, David J ^a   Watmough, Nicholas J ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; HYDROXYLAMINE; INORGANIC COMPOUND; NITRATE REDUCTASE; NITRIC OXIDE REDUCTASE; NITRITE; NITROGEN; NITROGEN OXIDE;

BACTERIAL METABOLISM; ELECTRON TRANSPORT; ENZYME ACTIVITY; ENZYME MECHANISM; ENZYME STRUCTURE; NITRIFICATION; NITROGEN FIXATION; NITROGEN METABOLISM; NONHUMAN; OXIDATION REDUCTION REACTION; REVIEW;

BACTERIA (MICROORGANISMS);

EID: 0033120932     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(99)80034-9     Document Type: Article

References (49)

1. Zumft WG: Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 1997, 61:533-616.
2. Ferguson SJ: Nitrogen cycle enzymology. Curr Opin Chem Biol 1998, 2:182-193.
3. Richardson DJ, Wehrfritz JM, Keech A, Crossman LC, Roldan MD, Sears HJ, Butler, CS, Reilly A, Moir JW, Berks BC et al.: The diversity of redox proteins involved in bacterial heterotrophic nitrification and aerobic denitrification. Biochem Soc Trans 1998, 26:401-408.
4. 15N studies in a fluidized bed reactor. Microbiology 1998, 143:2415-2421. The enzymology and bioenergetics of anaerobic ammonia oxidation remains to be elucidated; however, this work suggests an intriguing set of reactions in which hydrazine is a key intermediate.
5. Wu Q, Storrier GD, Pariente F, Wang Y, Shapleigh JP, Abruna HD: A nitrite biosensor based on a maltose binding protein nitrite reductase fusion immobilized on an electropolymerized film of a pyrrole- derived bipyridinium. Anal Chem 1997, 69:4856-4863.
6. Aylott JW, Richardson DJ, Russell DA: Optical biosensing of nitrate ions using a sol-gel immobilized nitrate reductase. Analyst 1997, 122:77-80.
7. Sears HJ, Spiro S, Richardson DJ: Effect of carbon substrate and aeration on nitrate reduction and expression of the periplasmic and membrane-bound nitrate reductases in carbon limited cultures of Paracoccus denitrficans Pd1222. Microbiology 1997, 143:3767-3774.
8. Lin JT, Stewart V: Nitrate assimilation by bacteria. Adv Microb Physiol 1998, 39:1-30.
9. Blasco R, Castillo F, Martinez-Luque M: The assimilatory nitrate reductase from the phototrophic bacterium, Rhodobacter capsulatus E1F1, is a flavoprotein. FEBS Lett 1997, 414:45-49. Genetic studies on bacterial assimilatory nitrate reductases are currently far more advanced than biochemical studies. This is in part because of the poor stability of the enzyme and the low level of expression. This study reports the first characterisation of a two-subunit flavin adenine dinucleotide binding form of the enzyme that is likely to resemble the model shown in Figure 1 that is based on the analysis of gene-derived primary structures of the K. oxytoca system [3].
10. Dias JM, Than ME, Humm A, Huber R, Bourenkov GP, Bartunik HD,Bursakov S, Calvete J, Caldeira J, Carniero C et al.: Crystal strtucture of the first dissimilatory nitrate reductase at 1.9 Ȧ solved by MAD methods. Structure 1999, 7:65-79. This crystal structure of a single subunit form of the periplasmic nitrate reductase (NapA), that lacks the di-haem cytochrome c subunit (NapB), is the first structure of a nitrate reductase. The overall fold of the enzyme and the molydenum coordination is very similar to formate dehydrogenase H. The structure suggests that NAP cycles between mono-oxo Mo(IV) and des-oxo Mo(IV) states during turnover. This would make it different from the di-oxo/mono-oxo cycle predicted from solution studies on the P. dentrificans dimeric NapAB complex [12].
11. 4 cluster. Science 1997, 275:1305-1308. Formate dehydrogenase H will have a very similar fold and spatial location of redox centres to periplasmic nitrate reductase and bacterial assimilatory nitrate reductase. The structure of a form in which nitrite is bound to molybdenum is also presented, which may inform on nitrate binding to molydenum in the related nitrate reductases.
12. Bennet B, Charnock JM, Sears HJ, Berks BC, Thomson AJ, Ferguson SJ, Garner CD, Richardson DJ: Structural investigation of the molybdenum site of the periplasmic nitrate reductase from Thioisphaera pantotropha by X-ray absorption spectroscopy. Biochem J 1996, 317:557-563.
13. McAlpine AS, McEwan AG, Bailey S: The high resolution crystal structure of DMSO reductase in complex DMSO. J Mol Biol 1998, 275:613-623 Research into the dimethylsulfoxide reductase over the past four years has led to a debate over whether or not the enzymes cycles through a di-oxo/mono-oxo or mono-oxo/des-oxo catalytic cycle. This argument now seems likely to be played out with respect to the periplasmic nitrate reductase. This paper favours the di-oxo/mono-oxo cycle and gives evidence for this that includes the structure of a substrate-bound species.
14. Luykx DMAM, Duine JA, deVries S: Molybdopterin radical in bacterial aldehyde dehydrogenases. Biochemistry 1998, 37:11366-11375. The first detection of a molybdopterin radical in a molybdoenzyme is reported. This important observation could have far reaching implications for both electron and proton transfer in molybdoenzymes including nitrate reductases.
15. Rousset M, Montet Y, Guigliarelli B, Forget N, Asso M, Bertrand P, Fontacilla-Camps JC, Hatchikian EC: [3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis. Proc Natl Acad Sci USA 1998, 95:11625-11630.
16. Magalon A, Asso M, Guigliarelli B, Rothery RA, Bertrand P, Giordano G, Blasco F: Molybdenum cofactor properties and [Fe-S] cluster coordination in Escherichia coli nitrate reductase A: Investigation by site-directed mutagenesis of the conserved His-50 residue in the NarG subunit. Biochemistry 1998, 37:7363-7370.
17. Magalon AM, Rothery R, Lemesle-Meunier D, Frixon C, Weiner JH and Blasco F: Heme axial ligation by the highly conserved his resifues in helix II of cytochrome b (Narl) of the Escherichia coli nitrate reductase A (NarGHI). J Biol Chem 1997, 272:25652-25658.
18. NR) of the Escherichia coli nitrate reductase A. J Biol Chem 1998, 273:10851-10856.
19. 1-independent electron transfer to periplasmic oxidoreductases including periplasmic nitrate reductase and trimethylanine oxidase reductase.
20. Lu G, Campbell WH, Schneider G, Lindqvist Y: Crystal structure of the FAD-containing fragment of corn nitrate reductase at 2.5 Å resolution: Relationship to other flavoprotein reductases. Structure 1994, 2:809-821.
21. Shiraishi N, CRoy C, Kaur J, Campbell WH: Engineering of pyridine nucleotide specificity of nitrate reductase: Mutagenesis of recombinant cytochrome b reductase fragment of Neurospora crassa NADPH : Nitrate reductase. Arch Biochem Biophys 1998, 358:104-115.
22. Kisker C, Schindelin H, Pacheco A, Wehbi W, Garrett RM, Rajagopalan KV, Enemark JH, Rees JH: Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase. Cell 1997, 91:973-983. The structure of sulfite oxidase (SO) with sulfate bound in the catalytic pocket will provide a structural framework for understanding the mechanism of the closely related eukaryotic nitrate reductases (NRs). In this paper, the structure is discussed in the context of both SO and NR.
23. Garton SD, Garrett RM, Rajagopalan KV, Johnson MK: Resonance Raman characterisation of the molybdenum centre in sulfite oxidase - Identification of Mo=O stretching modes. J Am Chem Soc 1997, 119:2590-2591.
24. 1 nitrite reductase does not exhibit the same ligand rearrangement around haem c upon reduction [26].
25. 3 electronic configuration. This 'inverted' ground state represents a relocation of unpaired spin density from orbitals extending above and below the haem plane to an orbital lying in that plane and this will have important consequences for the binding of π-unsaturated ligands such as nitric oxide, of in this case the product molecule.
26. Nurizzo D, Silvestrini MC, Mathieu M, Cutruzzola F, Bourgeois D, Fülop V, Hajdu J, Brunori M, Tegoni M, Cambillau C: N-terminal arm exchange is observed in the 2.15 Å crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa. Structure 1997, 5:1157-1171.
27. 1 nitrite reductase are shown to be very similar to those of the P denitrificans enzyme, despite significant differences in the oxidised forms of the enzymes, it is suggested that this paper be read in conjunction with [24•,25••,28].
28. Dodd FE, Van Beeumen J, Eady RR, Hasnain SS: X-ray structure of a blue-copper nitrite reductase in two crystal forms. The nature of the copper sites, mode of substrate binding and recognition by redox partner. J Mol Biol 1998, 282:369-382.
29. Veselov A, Olesen K, Sienkiewicz A, Shapleigh JP, Scholes CP: Electronic structural information from Q-band ENDOR on the type 1 and type 2 copper liganding environment in wild-type and mutant forms of copper-containing nitrite reductase. Biochemistry 1998, 37:6095-6105. This details the heterologous expression and purification of copper-containing nitrite reductase fused to a 36 amino acid fragment of the maltose binding protein. The wild type fusion protein was characterised by a combination of rapid reaction kinetics, electrochemistry and electron-nuclear double resonance and the effects of mutations to Met182 (a ligand to the type 1 copper centre) and His287 (a residue close to the type II copper centre which does not function as a ligand) documented.
30. Watmough NJ, Butland G, Cheesman MR, Moir JWB, Richardson DJ, Spiro S: Nitric oxide in bacteria: Synthesis and consumption. Biochim Biophys Acta 1999: in press.
31. 552 contains five rather than four covalently bound c-type haems and that one of these is associated with a CXXCK-binding motif instead of the coventional CXXCH. Moreover, this c-type cytochrome with an axial lysine ligand appears to be required for nitrite reductase activity and hence may represent the first example of a novel catalytic haem.
32. B dinuclear centre of bacterial nitric oxide reductase.
33. 1 nitrite reductases).
34. B(II)-NO.
35. 3 from Escherichia coli. J Bioenerg Biomemb 1998, 30:55-62.
36. Moënne-Loccoz P, de Vries S: Structural characterization of the catalytic high-spin heme b of nitric oxide reductase: A resonance Raman study. J Am Chem Soc 1998, 120:5147-5152.
37. Girsch P, de Vries S: Purification and initial kinetic and spectroscopic characterization of NO reductase from Paracoccus denitrificans. Biochim Biophys Acta 1997, 1318:20-216.
38. Brucker EA, Olson JS, Ikeda-Saito M, Phillips GN Jr: Nitric oxide myoglobin: Crystal structure and analysis of ligand geometry. Proteins 1998, 30:352-356.
39. B. Biochemistry 1997, 36:16259-16266.
40. Cramm R, Siddiqui RA, Friedrich B: Two isofunctional nitric oxide reductases in Alcaligenes eutrophus H16. J Bacteriol 1997, 179:6769-6777.
41. Z centres are variants of the same dinuclear centre and that catalysis takes place via a distinct histidine-coordinated polynuclear Cu centre. One reason for arguing this is the absence of sufficient conserved cysteine residues in nitric oxide synthase (NOS) to coordinate more than one bis-thiolate centre. There are, however, a number of highly conserved histidine residues in NOS, including an HHXH motif. This has led to the suggestion that the catalytic site of NOS may be an electron paramagnetic resonance and optically silent type III dinuclear copper centre perhaps similar to that found in multicopper oxidases.
42. Hooper AB, Vannelli T, Bergmann DJ, Arciero DM: Enzymology of the oxidation of ammonia to nitrite by bacteria. Antonie Van Leeuwenhoek 1997, 71:59-67.
43. Nyugen HH, Elliott SJ, Tip JH, Chan S: The particulate methane monooxygenase from methylococcus capsulatus (Bath) is a novel copper-containing three-subunit enzyme. Isolation and characterization. J Biol Chem 1998, 273:7957-7966. The purification of a stable three subunit form of the particulate methane monooxygenase (pMMO) is a significant achievement. There is considerable amino acid sequence identity and overlap in substrate specificity between pMMO and ammonia monooxygenase AMO, and the spectroscopic studies on pMMO will almost certainly provide insight into the properties of AMO.
44. Igarashi N, Moriyama H, Fujiwara T, Fukumori Y, Tanaka N: The 2.8 Å structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea. Nat Struct Biol 1997, 4:276-284.
45. Arciero DM, Golombek A, Hendrich MP, Hooper AB: Correlation of optical and EPR signals with the P460 heme of hydroxylamine oxidoreductase from Nitrosomonas europaea. Biochemistry 1998, 37:523-529. This careful study provides and detailed optical and electron paramagnetic resonance study on the haems of the hydroxylamine oxidase (HAO) and interprets the data with reference to the HAO structure.
46. 554 from Nitrosomonas europaea. Nat Struct Biol 1998, 5:1005-1012.
47. Arciero DM, Hooper AB: Consideration of a pritorin structure for haem P-460 of hydroxylamine oxidoreductase and its implications regarding reaction mechanism. Biochem Soc Trans 1998, 26:385-389.
48. Schalk J, Outstad H, Kuenen JG, Jetten MS: The anaerobic oxidation of hydrazine: A novel reaction in microbial nitrogen metabolism. FEMS Microbiol Lett 1998, 158:61-67.
49. F Cutruzzola, M Arese, S Grasso, A Bellelli, M Brunori: Mutagenesis of nitrite reductase from Pseudomonas aeruginosa: Tyrosine-10 in the c heme domain is not invloved in catalysis. FEBS Lett 1997, 412:365-369.