1DY7

Cytochrome cd1 Nitrite Reductase, CO complex

Summary for 1DY7

• Entry DOI: 10.2210/pdb1dy7/pdb
• Related: 1AOF 1AOM 1AOQ 1E2R 1QKS
• Descriptor: NITRITE REDUCTASE, HEME D, CARBON MONOXIDE, ... (7 entities in total)
• Functional Keywords: enzyme, nitrite reductase, oxidoreductase
• Biological source: PARACOCCUS PANTOTROPHUS
• Total number of polymer chains: 2
• Total formula weight: 127757.04

Authors

Sjogren, T.,Svensson-Ek, M.,Hajdu, J.,Brzezinski, P. (deposition date: 2000-01-28, release date: 2000-09-24, Last modification date: 2023-12-06)

Primary citation

Sjogren, T.,Svensson-Ek, M.,Hajdu, J.,Brzezinski, P.
Proton-Coupled Structural Changes Upon Binding of Carbon Monoxide to Cytochrome Cd(1): A Combined Flash Photolysis and X-Ray Crystallography Study
Biochemistry, 39:10967-, 2000

PubMed Abstract: 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).

PubMed: 10998233
DOI: 10.1021/BI000179Q

Experimental method

X-RAY DIFFRACTION (1.6 Å)