151
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Metzler DE, Metzler CM, Sauke DJ. Electron Transport, Oxidative Phosphorylation, and Hydroxylation. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50021-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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152
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Copper complexes of a new tridentate imidazole-containing ligand: spectroscopy, structures and nitrite reductase reactivity. Inorganica Chim Acta 2000. [DOI: 10.1016/s0020-1693(00)00271-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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153
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Boulanger MJ, Kukimoto M, Nishiyama M, Horinouchi S, Murphy ME. Catalytic roles for two water bridged residues (Asp-98 and His-255) in the active site of copper-containing nitrite reductase. J Biol Chem 2000; 275:23957-64. [PMID: 10811642 DOI: 10.1074/jbc.m001859200] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two active site residues, Asp-98 and His-255, of copper-containing nitrite reductase (NIR) from Alcaligenes faecalis have been mutated to probe the catalytic mechanism. Three mutations at these two sites (D98N, H255D, and H255N) result in large reductions in activity relative to native NIR, suggesting that both residues are involved intimately in the reaction mechanism. Crystal structures of these mutants have been determined using data collected to better than 1. 9-A resolution. In the native structure, His-255 Nepsilon2 forms a hydrogen bond through a bridging water molecule to the side chain of Asp-98, which also forms a hydrogen bond to a water or nitrite oxygen ligated to the active site copper. In the D98N mutant, reorientation of the Asn-98 side chain results in the loss of the hydrogen bond to the copper ligand water, consistent with a negatively charged Asp-98 directing the binding and protonation of nitrite in the native enzyme. An additional solvent molecule is situated between residues 255 and the bridging water in the H255N and H255D mutants and likely inhibits nitrite binding. The interaction of His-255 with the bridging water appears to be necessary for catalysis and may donate a proton to reaction intermediates in addition to Asp-98.
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Affiliation(s)
- M J Boulanger
- Departments of Biochemistry and Molecular Biology and of Microbiology and Immunology, University of British Columbia, Vancouver V6T 1Z3, Canada
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154
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Zhang H, Boulanger MJ, Mauk AG, Murphy MEP. Carbon Monoxide Binding to Copper-Containing Nitrite Reductase from Alcaligenes faecalis. J Phys Chem B 2000. [DOI: 10.1021/jp000745r] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haoming Zhang
- Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Martin J. Boulanger
- Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - A. Grant Mauk
- Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E. P. Murphy
- Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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155
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Bu XH, Lu SL, Zhang RH, Liao DZ, Aoki S, Clifford T, Kimura E. The first dicopper(II) complex of a new bis(1,5,9-triazacyclododecane) ligand: synthesis, crystal structure and magnetic coupling of the complex. Inorganica Chim Acta 2000. [DOI: 10.1016/s0020-1693(99)00410-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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156
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Fülöp V, Watmough NJ, Ferguson SJ. Structure and enzymology of two bacterial diheme enzymes: Cytochrome cd1 nitrite reductase and cytochrome c peroxidase. ADVANCES IN INORGANIC CHEMISTRY 2000. [DOI: 10.1016/s0898-8838(00)51003-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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157
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Suzuki S, Kataoka K, Yamaguchi K, Inoue T, Kai Y. Structure–function relationships of copper-containing nitrite reductases. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(99)00069-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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158
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Abstract
The structure-function relationships in nitrite reductases, key enzymes in the dissimilatory denitrification pathway which reduce nitrite to nitric oxide (NO), are reviewed in this paper. The mechanisms of NO production are discussed in detail and special attention is paid to new structural information, such as the high resolution structure of the copper- and heme-containing enzymes from different sources. Finally, some implications relevant to regulation of the steady state levels of NO in denitrifiers are presented.
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Affiliation(s)
- F Cutruzzolà
- Dipartimento di Scienze Biochimiche, Università di Roma 'La Sapienza', P.le A. Moro, 5, 00185, Rome, Italy.
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159
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Watmough NJ, Butland G, Cheesman MR, Moir JW, Richardson DJ, Spiro S. Nitric oxide in bacteria: synthesis and consumption. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1411:456-74. [PMID: 10320675 DOI: 10.1016/s0005-2728(99)00032-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- N J Watmough
- School of Biological Sciences, Centre for Metalloprotein Spectroscopy and Biology, University of East Anglia, Norwich NR4 7TJ, UK.
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160
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Strange RW, Murphy LM, Dodd FE, Abraham ZH, Eady RR, Smith BE, Hasnain SS. Structural and kinetic evidence for an ordered mechanism of copper nitrite reductase. J Mol Biol 1999; 287:1001-9. [PMID: 10222206 DOI: 10.1006/jmbi.1999.2648] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystallographic structures of several copper-containing nitrite reductases are now available. Despite this wealth of structural data, no definitive information is available as to whether the reaction proceeds by an ordered mechanism where nitrite binds to the oxidised type 2 site, followed by an internal electron transfer from the type 1 Cu, or whether binding occurs to the reduced type 2 Cu centre, or a random mechanism operates. We present here the first structural information on both types of Cu centres for the reduced form of NiR from Alcaligenes xylosoxidans (AxNiR) using X-ray absorption spectroscopy. The reduced type 2 Cu site EXAFS shows striking similarity to the EXAFS data for reduced bovine superoxide dismutase (Cu2Zn2 SOD), providing strong evidence for the loss of the water molecule from the catalytic Cu site in NiR on reduction resulting in a tri-coordinate Cu site similar to that in Cu2Zn2 SOD. The reduced type 2 Cu site of AxNiR is shown to be unable to bind inhibitory ligands such as azide, and to react very sluggishly with nitrite leading to only a slow re-oxidation of the the type 1 centre. These observations provide strong evidence that turnover of AxNiR proceeds by an ordered mechanism in which nitrite binds to the oxidised type 2 Cu centres before electron transfer from the reduced type 1 centre occurs. We propose that the two links between the Cu sites of AxNiR, namely His129-Cys130 and His89-Asp92-His94 are utilised for electron transfer and for communicating the status of the type 2 Cu site, respectively. Nitrite binding at type 2 Cu is sensed by the proton abstracting group Asp92 and the type 2 Cu ligand His94, and relayed to the type 1 Cu site via His89 thus triggering an internal electron transfer. The similarity of the type 2 Cu NiR catalytic site to the reduced Cu site of SOD is examined in some detail together with the biochemical evidence for the SOD activity of AxNiR.
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Affiliation(s)
- R W Strange
- CCLRC Daresbury Laboratory, Warrington, Cheshire, WA4 4AD, UK
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161
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Suzuki E, Horikoshi N, Kohzuma T. Cloning, sequencing, and transcriptional studies of the gene encoding copper-containing nitrite reductase from Alcaligenes xylosoxidans NCIMB 11015. Biochem Biophys Res Commun 1999; 255:427-31. [PMID: 10049725 DOI: 10.1006/bbrc.1998.9932] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gene encoding of the blue copper-containing nitrite reductase (nir) from Alcaligenes xylosoxidans NCIMB 11015 has been cloned and characterized. The nir is translated into a polypeptide of 360 amino acid residues as a precursor, and the N-terminal 24 residues are subsequently removed upon transport into the periplasm as a mature protein. A specific transcription product of nir was detected only in the presence of nitrate. The aeration level of the culture medium did not show a significant effect on the transcriptional level. A varsigma54 binding sequence is identified upstream of the transcriptional initiation at 53 to 26 nucleotides. A putative fnr box has also been identified in the sequence of the upstream region. The mature polypeptide showed 70% sequence identity with those of the Achromobacter cycloclastes enzyme. The transcriptional start point has been determined at 92 nucleotides upstream of the initiation codon and is preceded by the binding sites for varsigma54 and the fnr box. These results suggest that gene expression depends on the presence of nitrate and is stimulated under an anaerobic environment.
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Affiliation(s)
- E Suzuki
- Faculty of Science, Ibaraki University, Japan
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162
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Farver O, Eady RR, Abraham ZH, Pecht I. The intramolecular electron transfer between copper sites of nitrite reductase: a comparison with ascorbate oxidase. FEBS Lett 1998; 436:239-42. [PMID: 9781686 DOI: 10.1016/s0014-5793(98)01120-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The intramolecular electron transfer (ET) between the type 1 Cu(I) and the type 2 Cu(II) sites of Alcaligenes xylosoxidans dissimilatory nitrite reductase (AxNiR) has been studied in order to compare it with the analogous process taking place in ascorbate oxidase (AO). This internal process is induced following reduction of the type 1 Cu(II) by radicals produced by pulse radiolysis. The reversible ET reaction proceeds with a rate constant kET = k(1-->2) + k(2-->1) of 450 +/- 30 s(-1) at pH 7.0 and 298 K. The equilibrium constant K was determined to be 0.7 at 298 K from which the individual rate constants for the forward and backward reactions were calculated to be: k(1-->2) = 185 +/- 12 s(-1) and k(2-->1) 265 +/- 18 s(-1). The temperature dependence of K allowed us to determine the deltaH(o) value of the ET equilibrium to be 12.1 kJ mol(-1). Measurements of the temperature dependence of the ET process yielded the following activation parameters: forward reaction, deltaH* = 22.7 +/- 3.4 kJ mol(-1) and deltaS* = -126 +/- 11 J K(-1) mol(-1); backward reaction, deltaH* = 10.6 +/- 1.7 kJ mol(-1) and deltaS* = -164 +/- 15 J K(-1) mol(-1). X-ray crystallographic studies of NiRs suggest that the most probable ET pathway linking the two copper sites consists of Cys136, which provides the thiolate ligand to the type 1 copper ion, and the adjacent His135 residue with its imidazole being one of the ligands to the type 2 Cu ion. This pathway is essentially identical to that operating between the type 1 Cu(I) and the trinuclear copper centre in ascorbate oxidase, and the characteristics of the internal ET processes of these enzymes are compared. The data are consistent with the faster ET observed in nitrite reductase arising from a more advantageous entropy of activation when compared with ascorbate oxidase.
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Affiliation(s)
- O Farver
- Institute of Chemistry, Royal Danish School of Pharmacy, Copenhagen
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163
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Abstract
The minimal nitrogen cycle involves five reduction reactions and three oxidation reactions, each of which poses interesting problems in bioinorganic chemistry, energy transduction and protein structure/function relationships. Many of the major recent developments in this field have depended on the acquisition of protein crystal structures, including structures of enzymes with bound substrates or products and in protein-protein complexes. These enzymes include nitrogenase, nitrite reductases, hydroxylamine oxidoreductase and a fungal nitric oxide reductase.
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Affiliation(s)
- S J Ferguson
- Department of Biochemistry, Oxford Centre for Molecular Sciences, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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