4FMX

Crystal Structure of Substrate-Bound P450cin

Summary for 4FMX

• Entry DOI: 10.2210/pdb4fmx/pdb
• Related: 4FB2
• Descriptor: P450cin, PROTOPORPHYRIN IX CONTAINING FE, 1,3,3-TRIMETHYL-2-OXABICYCLO[2.2.2]OCTANE, ... (6 entities in total)
• Functional Keywords: p450, heme, monooxygenase, cindoxin, oxidoreductase
• Biological source: Citrobacter braakii
• Total number of polymer chains: 2
• Total formula weight: 91585.64

Authors

Madrona, Y.,Tripathi, S.M.,Huiying, L.,Poulos, T.L. (deposition date: 2012-06-18, release date: 2012-07-25, Last modification date: 2023-09-13)

Primary citation

Madrona, Y.,Tripathi, S.,Li, H.,Poulos, T.L.
Crystal structures of substrate-free and nitrosyl cytochrome p450cin: implications for o(2) activation.
Biochemistry, 51:6623-6631, 2012

PubMed Abstract: The crystal structure of the P450cin substrate-bound nitric oxide complex and the substrate-free form have been determined revealing a substrate-free structure that adopts an open conformation relative to the substrate-bound structure. The region of the I helix that forms part of the O(2) binding pocket shifts from an α helix in the substrate-free form to a π helix in the substrate-bound form. Unique to P450cin is an active site residue, Asn242, in the I helix that H-bonds with the substrate. In most other P450s this residue is a Thr and plays an important role in O(2) activation by participating in an H-bonding network required for O(2) activation. The π/α I helix transition results in the carbonyl O atom of Gly238 moving in to form an H-bond with the water/hydroxide ligand in the substrate-free form. The corresponding residue, Gly248, in the substrate-free P450cam structure experiences a similar motion. Most significantly, in the oxy-P450cam complex Gly248 adopts a position midway between the substrate-free and -bound states. A comparison between these P450cam and the new P450cin structures provides insights into differences in how the two P450s activate O(2). The structure of P450cin complexed with nitric oxide, a close mimic of the O(2) complex, shows that Gly238 is likely to form tighter interactions with ligands than the corresponding Gly248 in P450cam. Having a close interaction between an H-bond acceptor, the Gly238 carbonyl O atom, and the distal oxygen atom of O(2) will promote protonation and hence further reduction of the oxy complex to the hydroperoxy intermediate resulting in heterolytic cleavage of the peroxide O-O bond and formation of the active ferryl intermediate required for substrate hydroxylation.

PubMed: 22775403
DOI: 10.1021/bi300666u

Experimental method

X-RAY DIFFRACTION (1.554 Å)