Structural and kinetic evidence for an ordered mechanism of copper nitrite reductase

Strange, R.W.; Murphy, Loretta M.; Dodd, F.E.; Abraham, Z. H. L.; Eady, Robert R.; Smith, Barry E.; Hasnain, S. Samar

doi:10.1006/jmbi.1999.2648

Cited by 110 publications

(137 citation statements)

References 29 publications

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“…As a result, His-63 adopts a position structurally analogous to His-249 in AxNIR and His-255 in AfNIR. Interestingly, SOD activity has been observed previously in NIR from Rhodopseudomonas sphaeroides (20) and is localized at the type II copper center in AxNIR (14). Together, these findings show an important catalytic role for His-63 in SOD and are suggestive of a similar role for the His-255 analogue in AfNIR.…”

supporting

confidence: 81%

“…Nitrite displaces the ligand water at the type II site as shown by crystallographic structures (10,11) and electron nuclear double resonance spectroscopy (12,13). Steady-state kinetics (14) are consistent with a proposed catalytic mechanism that proceeds by an ordered process where nitrite binds to the oxidized type II copper center before an electron is transferred from the type I copper (10,11).…”

supporting

confidence: 78%

“…A catalytic role for His-255 has been suggested from a comparison to the SOD copper center that is ligated by four histidine ligands in a plane and a water molecule in the apical position (18). The recent crystal structure of the reduced yeast SOD (19) demonstrates a structural rearrangement following protonation of a histidine ligand (His-63) resulting in a more tetrahedral coordination of the copper similar to that found in AxNIR (14). As a result, His-63 adopts a position structurally analogous to His-249 in AxNIR and His-255 in AfNIR.…”

mentioning

confidence: 84%

“…The green color of the crystals indicates that the type I site contains primarily copper. Crystal structures of preparations of type II-depleted AxNIR do not show the presence of zinc in the active site despite EXAFS evidence consistent with zinc binding to surface residues (14). Furthermore, anomalous scattering experiments of M150E AfNIR showed the presence of zinc bound to the mutated type I site with negligible binding at the type II site (17).…”

Section: D98nmentioning

confidence: 94%

“…Additional insight into the mechanism has come from structural comparisons of the active sites of copper-containing A. xylosoxidans NIR (AxNIR) and AfNIR to the zinc sites in superoxide dismutase (SOD), thermolysin, astacin, and carbonic anhydrase (11,14,15,17). The common structural motif of carbonic anhydrase, astacin, and NIR is a metal site with three protein ligands, a fourth distal ligand water, and a proton-abstracting group (a carboxyl or hydroxyl group) forming a hydrogen bond to the ligand water (15).…”

mentioning

confidence: 99%

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Catalytic Roles for Two Water Bridged Residues (Asp-98 and His-255) in the Active Site of Copper-containing Nitrite Reductase

Boulanger¹,

Kukimoto²,

Nishiyama³

et al. 2000

Journal of Biological Chemistry

127

154

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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-Å resolution. In the native structure, His-255 N⑀2 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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supporting

confidence: 81%

supporting

confidence: 78%

mentioning

confidence: 84%

Section: D98nmentioning

confidence: 94%

mentioning

confidence: 99%

See 3 more Smart Citations

Catalytic Roles for Two Water Bridged Residues (Asp-98 and His-255) in the Active Site of Copper-containing Nitrite Reductase

Boulanger¹,

Kukimoto²,

Nishiyama³

et al. 2000

Journal of Biological Chemistry

127

154

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Copper Nitrite Reductase

Adman

Murphy

2004

Handbook of Metalloproteins

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Copper nitrite reductase catalyzes the one electron reduction of nitrite to nitric oxide as part of the dissimilatory denitrification pathway. Copper nitrite reductases are found in some fungi and archaea and in many divisions of bacteria. The crystal structure of the enzyme reveals a homotrimer, each of which has a type 1 Cu site that mediates electron transfer to a type 2 Cu site. The three type 2 Cu sites are found at the subunit interfaces and catalyze nitrite reduction. Extensive mutagenic, spectroscopic, kinetic, and crystallographic studies have explored the catalytic mechanism that is proposed to include a copper–nitrosyl intermediate.

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Copper Enzymes in Denitrification

Dooley

Chan

2005

Encyclopedia of Inorganic Chemistry

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Denitrification is an intrinsic part of the global nitrogen cycle, balancing the cycle by returning fixed nitrogen to the atmosphere. During denitrification, a bacterial respiratory process, nitrate or nitrite is reduced to nitrogenous oxides. All of the redox reactions of denitrification are catalyzed by metalloenzymes, two of which contain copper. This chapter reviews the structures, mechanisms, and assembly of these copper‐containing enzymes, copper nitrite reductase and nitrous oxide reductase.

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Structural and kinetic evidence for an ordered mechanism of copper nitrite reductase

Cited by 110 publications

References 29 publications

Catalytic Roles for Two Water Bridged Residues (Asp-98 and His-255) in the Active Site of Copper-containing Nitrite Reductase

Catalytic Roles for Two Water Bridged Residues (Asp-98 and His-255) in the Active Site of Copper-containing Nitrite Reductase

Copper Nitrite Reductase

Copper Enzymes in Denitrification

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