5XL0

met-aquo form of sperm whale myoglobin reconstituted with 7-PF, a heme possesseing CF3 group as side chain

Summary for 5XL0

• Entry DOI: 10.2210/pdb5xl0/pdb
• Descriptor: Myoglobin, fluorinated heme, SULFATE ION, ... (4 entities in total)
• Functional Keywords: sperm whale, myoglobin, trifluoromethyl group, fluorinated heme, heme orientational disorder, oxygen transport
• Biological source: Physeter catodon (Sperm whale)
• Total number of polymer chains: 1
• Total formula weight: 18012.45

Authors

Kanai, Y.,Harada, A.,Shibata, T.,Nishimura, R.,Namiki, K.,Watanabe, M.,Nakamura, S.,Yumoto, F.,Senda, T.,Suzuki, A.,Neya, S.,Yamamoto, Y. (deposition date: 2017-05-10, release date: 2017-08-16, Last modification date: 2024-03-27)

Primary citation

Kanai, Y.,Harada, A.,Shibata, T.,Nishimura, R.,Namiki, K.,Watanabe, M.,Nakamura, S.,Yumoto, F.,Senda, T.,Suzuki, A.,Neya, S.,Yamamoto, Y.
Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor
Biochemistry, 56:4500-4508, 2017

PubMed Abstract: The orientation of a CF-substituted heme in sperm whale myoglobin and L29F, H64L, L29F/H64Q, and H64Q variant proteins has been investigated using F NMR spectroscopy to elucidate structural factors responsible for the thermodynamic stability of the heme orientational disorder, i.e., the presence of two heme orientations differing by a 180° rotation about the 5-15 meso axis, with respect to the protein moiety. Crystal structure of the met-aquo form of the wild-type myoglobin reconstituted with 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7-trifluoromethylporphyrinatoiron(III), determined at resolution of 1.25 Å, revealed the presence of the heme orientational disorder. Alterations of the salt bridge between the heme 13-propionate and Arg45(CD3) side chains due to the mutations resulted in equilibrium constants of the heme orientational disorder ranging between 0.42 and 1.4. Thus, the heme orientational disorder is affected by the salt bridge associated with the heme 13-propionate side chain, confirming the importance of the salt bridge in the heme binding to the protein.

PubMed: 28758387
DOI: 10.1021/acs.biochem.7b00457

Experimental method

X-RAY DIFFRACTION (1.25 Å)