8RKP image
Deposition Date 2023-12-27
Release Date 2024-12-04
Last Version Date 2024-12-04
Entry Detail
PDB ID:
8RKP
Title:
Cytochrome c prime from Hydrogenophilus thermoluteolus: Ferrous recombinant native with bound NO
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.63 Å
R-Value Free:
0.21
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 62 2 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c prime
Gene (Uniprot):cytc
Chain IDs:A
Chain Length:134
Number of Molecules:1
Biological Source:Hydrogenophilus thermoluteolus
Primary Citation
Conformational rigidity of cytochrome c'-alpha from a thermophile is associated with slow NO binding.
Biophys.J. 123 2594 2603 (2024)
PMID: 38937973 DOI: 10.1016/j.bpj.2024.06.026

Abstact

Cytochromes c'-α are nitric oxide (NO)-binding heme proteins derived from bacteria that can thrive in a wide range of temperature environments. Studies of mesophilic Alcaligenes xylosoxidans cytochrome c'-α (AxCP-α) have revealed an unusual NO-binding mechanism involving both heme faces, in which NO first binds to form a distal hexa-coordinate Fe(II)-NO (6cNO) intermediate and then displaces the proximal His to form a proximal penta-coordinate Fe(II)-NO (5cNO) final product. Here, we characterize a thermally stable cytochrome c'-α from thermophilic Hydrogenophilus thermoluteolus (PhCP-α) to understand how protein thermal stability affects NO binding. Electron paramagnetic and resonance Raman spectroscopies reveal the formation of a PhCP-α 5cNO product, with time-resolved (stopped-flow) UV-vis absorbance indicating the involvement of a 6cNO intermediate. Relative to AxCP-α, the rates of 6cNO and 5cNO formation in PhCP-α are ∼11- and ∼13-fold lower, respectively. Notably, x-ray crystal structures of PhCP-α in the presence and absence of NO suggest that the sluggish formation of the proximal 5cNO product results from conformational rigidity: the Arg-132 residue (adjacent to the proximal His ligand) is held in place by a salt bridge between Arg-75 and Glu-135 (an interaction not present in AxCP-α or a psychrophilic counterpart). Overall, our data provide fresh insights into structural factors controlling NO binding in heme proteins, including 5cNO complexes relevant to eukaryotic NO sensors.

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