5YZF image
Entry Detail
PDB ID:
5YZF
Title:
X-ray crystal structure of met K42C sperm whale myoglobin
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2017-12-14
Release Date:
2018-03-07
Method Details:
Experimental Method:
Resolution:
1.77 Å
R-Value Free:
0.20
R-Value Work:
0.15
R-Value Observed:
0.16
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:sperm whale myoglobin
Mutations:K43C
Chain IDs:A
Chain Length:154
Number of Molecules:1
Biological Source:Physeter catodon
Ligand Molecules
Primary Citation
Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen
J. Inorg. Biochem. 182 141 149 (2018)
PMID: 29477977 DOI: 10.1016/j.jinorgbio.2018.02.011

Abstact

The structure and function of heme proteins are regulated by diverse post-translational modifications including heme-protein cross-links, with the underlying mechanisms not well understood. In this study, we introduced a Cys (K42C) close to the heme 4-vinyl group in sperm whale myoglobin (Mb) and solved its X-ray crystal structure. Interestingly, we found that K42C Mb can partially form a Cys-heme cross-link (termed K42C Mb-X) under dithiothreitol-induced reductive conditions in presence of O(2), as suggested by guanidine hydrochloride-induced unfolding and heme extraction studies. Mass spectrometry (MS) studies, together with trypsin digestion studies, further indicated that a thioether bond is formed between Cys42 and the heme 4-vinyl group with an additional mass of 16 Da, likely due to hydroxylation of the alpha‑carbon. We then proposed a plausible mechanism for the formation of the novel Cys-heme cross-link based on MS, kinetic UV-vis and electron paramagnetic resonance (EPR) studies. Moreover, the Cys-heme cross-link was shown to fine-tune the protein reactivity toward activation of H(2)O(2). This study provides valuable insights into the post-translational modification of heme proteins, and also suggests that the Cys-heme cross-link can be induced to form in vitro, making it useful for design of new heme proteins with a non-dissociable heme and improved functions.

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