1dy7

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spinqualitylabelsall models 1dy7, resolution 1.6Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

CYTOCHROME CD1 NITRITE REDUCTASE, CO COMPLEX

Overview

We have investigated dynamic events after flash photolysis of CO from, reduced cytochrome cd(1) nitrite reductase (NiR) from Paracoccus, pantotrophus (formerly Thiosphaera pantotropha). Upon pulsed illumination, of the cytochrome cd(1)-CO complex, at 460 nm, a rapid (<50 ns) absorbance, change, attributed to dissociation of CO, was observed. This was followed, by a biphasic rearrangement with rate constants of 1.7 x 10(4) and 2.5 x, 10(3) s(-1) at pH 8.0. Both parts of the biphasic rearrangement phases, displayed the same kinetic difference spectrum in the region of 400-660, nm. The slower of the two processes was accompanied by proton uptake from, solution (0.5 proton per active site at pH 7.5-8.5). After, photodissociation, the CO ligand recombined at a rate of 12 s(-1) (at 1 mM, CO and pH 8.0), accompanied by proton release. The crystal structure of, reduced cytochrome cd(1) in complex with CO was determined to a resolution, of 1.57 A. The structure shows that CO binds to the iron of the d(1) heme, in the active site. The ligation of the c heme is unchanged in the, complex. A comparison of the structures of the reduced, unligated NiR and, the NiR-CO complex indicates changes in the puckering of the d(1) heme as, well as rearrangements in the hydrogen-bonding network and solvent, organization in the substrate binding pocket at the d(1) heme. Since the, CO ligand binds to heme d(1) and there are structural changes in the d(1), pocket upon CO binding, it is likely that the proton uptake or release, observed after flash-induced CO dissociation is due to changes of the, protonation state of groups in the active site. Such proton-coupled, structural changes associated with ligand binding are likely to affect the, redox potential of heme d(1) and may regulate the internal electron, transfer from heme c to heme d(1).

About this Structure

1DY7 is a Single protein structure of sequence from Paracoccus pantotrophus with SO4, DHE, CMO, HEC and GOL as ligands. Active as Transferred entry: 1.7.2.1, with EC number 1.9.3.2 Structure known Active Sites: C1B, D1A and D1B. Full crystallographic information is available from OCA.

Reference

Proton-coupled structural changes upon binding of carbon monoxide to cytochrome cd1: a combined flash photolysis and X-ray crystallography study., Sjogren T, Svensson-Ek M, Hajdu J, Brzezinski P, Biochemistry. 2000 Sep 12;39(36):10967-74. PMID:10998233

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