X-ray scattering using synchrotron radiation shows nitrite reductase from Achromobacter xylosoxidans to be a trimer in solution

Großmann, Joachim; Abraham, Z. H. L.; Adman, Elinor T.; Neu, M.; Eady, Robert R.; Smith, Barry E.; Hasnain, S. Samar

doi:10.1021/bi00080a005

Cited by 71 publications

(45 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The values in Table 1 show that for all three types of scattering the calculated profile is significantly closer to experiment when the solvent molecules are explicitly included. This result confirms previous studies indicating that it is necessary to take into account hydration effects in SAS studies (15,33,34). Fig.…”

Section: Resultssupporting

confidence: 92%

Is the first hydration shell of lysozyme of higher density than bulk water?

Merzel

Smith²

2002

Proc. Natl. Acad. Sci. U.S.A.

355

276

View full text Add to dashboard Cite

Characterization of the physical properties of protein surface hydration water is critical for understanding protein structure and folding. Here, using molecular dynamics simulation, we provide an explanation of recent x-ray and neutron solution scattering data that indicate that the density of water on the surface of lysozyme is significantly higher than that of bulk water. The simulationderived scattering profiles are in excellent agreement with the experiment. In the simulation, the 3-Å-thick first hydration layer is 15% denser than bulk water. About two-thirds of this increase is the result of a geometric contribution that would also be present if the water was unperturbed from the bulk. The remaining third arises from modification of the water structure and dynamics, involving approximately equal contributions from shortening of the average water-water O-O distance and an increase in the coordination number. Variation in the first hydration shell density is shown to be determined by topographical and electrostatic properties of the protein surface. On average, denser water is found in depressions on the surface in which the water dipoles tend to be aligned parallel to each other by the electrostatic field generated by the protein atoms.A characterization of protein hydration is essential for understanding protein structure, folding, and function. This characterization requires elucidating the effects of both the solvent on the protein and the protein on the solvent (1, 2). Concerning the latter effect, detailed information on ordering and dynamical properties of individual, highly perturbed, strongly bound water molecules has been furnished by highresolution x-ray crystallography and NMR spectroscopy (3-10). However, to obtain the data required for a complete thermodynamic description of protein hydration it is necessary to obtain a more global picture in which the solvent is described in terms of probability distributions. Recent work in this direction has used molecular dynamics (MD) simulation (11-13) and novel crystallographic methods (6,7,14) to enable radial distribution functions of water molecules around protein groups in crystals and related quantities to be obtained.It is of particular importance to determine how protein surface water is on average perturbed from the bulk. An intriguing result in this regard was reported by Svergun et al. (15), who combined small-angle scattering (SAS) of x-rays in H 2 O with that of neutrons in H 2 O and D 2 O to show that for lysozyme and other proteins the average density of the first hydration shell (0-3 Å from the surface) is significantly higher than that of bulk water. This finding is consistent with results from MD simulation (16) and the crystallographic work (14). The present article explains the physical origin of this effect. We use MD simulation of lysozyme in explicit water to determine the contributions to the hydration density profile. The MD allows detailed structural properties of the hydration water to be analyzed in the context of the SAS resul...

show abstract

Section: Resultssupporting

confidence: 92%

Is the first hydration shell of lysozyme of higher density than bulk water?

Merzel

Smith²

2002

Proc. Natl. Acad. Sci. U.S.A.

355

276

View full text Add to dashboard Cite

show abstract

“…This results in a signi®cant loss of ®xed nitrogen from the terrestrial environment (Payne, 1985;Zumft, 1997) Two types of NiRs are found in the denitrifying bacteria, the cytochrome cd 1 and copper NiRs (CuNiR); the latter are more widespread, being found in bacteria occupying a greater variety of habitats. The trimeric structures of several CuNiRs have now been established by X-ray crystallography [Achromobacter cyoclastes (AcNiR; Godden et al, 1991); Alcaligenes faecalis S-6 (AfNiR; Kukimoto et al, 1994) and Alcaligenes xylosoxidans (AxNiR; Dodd et al, 1998)] and solution X-ray scattering [AxNiR (Grossmann et al, 1993), Pseudomonas aureofaciens (PaNiR) and AfNiR (Grossmann & Hasnain, 1997)]. The crystal structures of the three CuNiRs show that they are similar, with the monomer consisting of two domains with Greek key -barrels similar to those found in cupredoxins.…”

Section: Introductionmentioning

confidence: 99%

X-ray structure of a blue copper nitrite reductase at high pH and in copper-free form at 1.9 Å resolution

Ellis

Dodd

Strange

et al. 2001

Acta Crystallogr D Biol Crystallogr

Self Cite

View full text Add to dashboard Cite

Copper‐containing nitrite reductases possess a trimeric structure where the catalytic Cu site, located at the monomer–monomer interface, resembles the catalytic sites of a number of Zn enzymes. Nitrite reductase from Alcaligenes xylosoxidans has optimum activity at pH 5.2 which decreases to a negligible level at pH 8. The structure of this nitrite reductase has previously been determined at pH 4.6. It has now been crystallized under new conditions at pH 8.5. Its crystallographic structure provides a structural explanation for the greatly reduced activity of the enzyme at high pH. Characterization of overexpressed protein in solution by EXAFS suggested that the protein lacked Cu in the catalytic type 2 Cu site and that the site was most probably occupied by Zn. Using the anomalous signals from Cu and Zn, the crystal structure revealed that the expressed protein was devoid of Cu in the catalytic site and that only a trace amount (<10%) of Zn was present at this site in the crystal. Despite the close structural similarity of the catalytic site to a number of Zn enzymes, these data suggest that Zn, if it binds at the catalytic copper site, binds weakly in nitrite reductase.

show abstract

“…NCIMB 11015, Achromobacter xylosoxidans or Pseudomonas denitri®cans), the reduction of nitrite to nitric oxide is accomplished by a copper-containing nitrite reductase Grossmann et al, 1993;Strange et al, 1995). Two classes of blue copper proteins, pseudoazurin and azurin, have so far been implicated in donating electrons to nitrite reductase; pseudoazurin to the green nitrite reductases of A. faecalis S-6 and Achrom.…”

Section: Introductionmentioning

confidence: 99%

Structures of oxidized and reduced azurin II fromAlcaligenes xylosoxidansat 1.75 Å resolution

Dodd

Abraham

Eady

et al. 2000

Acta Crystallogr D Biol Cryst

Self Cite

View full text Add to dashboard Cite

Crystallographic structures of oxidized and reduced forms of azurin II are reported at 1.75 A Ê resolution. Data were collected using one crystal in each case and by translating the crystal after each oscillation range to minimize photoreduction. Very small differences are observed at the Cu site upon reduction and these cannot be determined with con®dence at current resolution. A comparison with the three-dimensional EXAFS reveals a good correspondence for all the ligand distances except for CuÐHis46, where a larger deviation of $0.12±0.18 A Ê is observed, indicating that this ligand is more tightly restrained in the crystallographic re®nement at the current resolution.

show abstract

X-ray scattering using synchrotron radiation shows nitrite reductase from Achromobacter xylosoxidans to be a trimer in solution

Cited by 71 publications

References 19 publications

Is the first hydration shell of lysozyme of higher density than bulk water?

Is the first hydration shell of lysozyme of higher density than bulk water?

X-ray structure of a blue copper nitrite reductase at high pH and in copper-free form at 1.9 Å resolution

Structures of oxidized and reduced azurin II fromAlcaligenes xylosoxidansat 1.75 Å resolution

Contact Info

Product

Resources

About