The Structure of Copper-nitrite Reductase from Achromobacter cycloclastes at Five pH Values, with NO-2 Bound and with Type II Copper Depleted

Adman, Elinor T.; Godden, Jeffrey W.; Turley, S.

doi:10.1074/jbc.270.46.27458

Cited by 230 publications

(334 citation statements)

References 34 publications

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“…To quantify the extent to which the tetrahedral type 2 copper site geometry is distorted, the angle between the two planes N 338 -Cu-O and N 131 -Cu-N 166 is measured (residues are numbered according to RsNiR). Källrot et al (39) propose two structures for the type 2 copper site in NiRs, one that is almost perfectly tetrahedral with a angle close to 90°like the copper site in NiR from Achromobacter cycloclastes (6) and one that is more distorted and thereby less tetrahedral with a smaller angle, like the structure in NiR from Alcaligenes faecalis (40). They further suggest that these two solvent ligand positions are equally favored if the solvent ligand is a hydroxyl ion and the catalytic aspartate residue is protonated, but when the pH is such that the ligand is protonated the more tetrahedral geometry is energetically preferred.…”

Section: Resultsmentioning

confidence: 99%

“…Nitrite binds directly to the type 2 copper ion (14), with both oxygen atoms ligating the copper site in a bidentate fashion (6,13). After an electron is passed to the type 1 copper site from the electron donor protein, the electron is transferred on to nitrite via the type 2 copper ion (15).…”

mentioning

confidence: 99%

“…NiR reduces nitrite to produce NO (g) , and NO reductase reduces NO to N 2 O, where NO is the first gaseous compound in the pathway. There are two main categories of NiRs; those that are heme-containing (cd1-NiRs) (3,4) and those that are copper-containing (Cu-NiRs) (5)(6)(7)(8). The overall enzymatic reaction performed by NiRs is NO 2 Ϫ ϩ 2H ϩ ϩ e Ϫ 3 NO (g) ϩ H 2 O. Cu-NiRs are blue or green in color, showing visible absorption at 460 and 600 nm (1).…”

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confidence: 99%

“…Near the type 2 site there are also the catalytic residues Asp-129 and His-287, which have been found to be crucial to enzyme activity and nitrite binding (9, 16, 19 -22). These residues are bridged by a solvent molecule referred to as the "bridging water," and Asp-129 forms an H-bond to one of the oxygen atoms when nitrite is bound or to the water ligand in the absence of nitrite (6). All details concerning the catalytic role of His-287 are not entirely clear, but this residue is believed to be involved in supplying the proton needed for the enzymatic reaction to occur (6) and has in Rhodobacter sphaeroides been seen to disorder at high pH, most likely due to loss of H-bond interactions (12).…”

mentioning

confidence: 99%

“…These residues are bridged by a solvent molecule referred to as the "bridging water," and Asp-129 forms an H-bond to one of the oxygen atoms when nitrite is bound or to the water ligand in the absence of nitrite (6). All details concerning the catalytic role of His-287 are not entirely clear, but this residue is believed to be involved in supplying the proton needed for the enzymatic reaction to occur (6) and has in Rhodobacter sphaeroides been seen to disorder at high pH, most likely due to loss of H-bond interactions (12). Nitrite reductase is highly pH-dependent and has an activity maximum between pH 5 and 6 (23,24).…”

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confidence: 99%

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pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

Jacobson

Pistorius

Farkas

et al. 2007

Journal of Biological Chemistry

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Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

Jacobson

Pistorius

Farkas

et al. 2007

Journal of Biological Chemistry

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Protein fold analysis of the B30.2-like domain

Seto¹,

Liu²,

Zajchowski³

et al. 1999

Proteins

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The B30.2-like domain occurs in some members of a diverse and growing family of proteins containing zinc-binding B-box motifs, whose functions include regulation of cell growth and differentiation. The B30.2-like domain is also found in proteins without the zinc-binding motifs, such as butyrophilin (a transmembrane glycoprotein) and stonustoxin (a secreted cytolytic toxin). Currently, the function for the B30.2-like domain is not clear and the structure of a protein containing this domain has not been solved. The secondary structure prediction methods indicate that the B30.2-like domain consists of fifteen or fewer beta-strands. Fold recognition methods identified different structural topologies for the B30.2-like domains. Secondary structure prediction, deletion and lack of local sequence identity at the C-terminal region for certain members of the family, and packing of known core structures suggest that a structure containing two beta domains is the most probable of these folds. The most C-terminal sequence motif predicted to be a beta-strand in all B30.2-like domains is a potential subdomain boundary based on the sequence-structure alignments. Models of the B30.2-like domains were built based on immunoglobulin-like folds identified by the fold recognition methods to evaluate the possibility of the B30.2 domain adopting known folds and infer putative functional sites. The SPRY domain has been identified as a subdomain within the B30.2-like domain. If the B30.2-like domain is a subclass of the SPRY domain family, then this analysis would suggest that the SPRY domains are members of the immunoglobulin superfamily.

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Protein strain in blue copper proteins studied by free energy perturbations

Kerpel

Ryde

1999

Proteins

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Free energy perturbations have been performed on two blue copper proteins, plasto-cyanin and nitrite reductase. By changing the copper coordination geometry, force constants, and charges, we have estimated the maximum energy with which the proteins may distort the copper coordination sphere. By comparing this energy with the quantum chemical energy cost for the same perturbation on the isolated copper complex, various hypotheses about protein strain have been tested. The calculations show that the protein can only modify the copper-methionine bond length by a modest amount of energy-F5 kJ/mol-and they lend no support to the suggestion that the quite appreciable difference in the copper coordination geometry encountered in the two proteins is a result of the proteins enforcing different Cu-methionine bond lengths. On the contrary, this bond is very flexible, and neither the geometry nor the electronic structure change appreciably when the bond length is changed. Moreover, the proteins are rather indifferent to the length of this bond. Instead, the Cu(II) coordination geometries in the two proteins represent two distinct minima on the potential surface of the copper ligand sphere, characterized by different electronic structures, a tetragonal, mainly-bonded, structure in nitrite reductase and a trigonal,-bonded, structure in plastocyanin. In vacuum, the structures have almost the same energy, and they are stabilized in the proteins by a combination of geometric and electrostatic interactions. Plastocya-nin favors the bond lengths and electrostatics of the trigonal structure, whereas in nitrite reductase, the angles are the main discriminating factor. Proteins 1999;36:157-174.

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The Structure of Copper-nitrite Reductase from Achromobacter cycloclastes at Five pH Values, with NO-2 Bound and with Type II Copper Depleted

Cited by 230 publications

References 34 publications

pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase

Protein fold analysis of the B30.2-like domain

Protein strain in blue copper proteins studied by free energy perturbations

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