5B84

X-ray crystal structure of met I107Y sperm whale myoglobin

Summary for 5B84

• Entry DOI: 10.2210/pdb5b84/pdb
• Related: 5B85
• Descriptor: Myoglobin, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: oxygen storage
• Biological source: Physeter catodon (Sperm whale)
• Total number of polymer chains: 1
• Total formula weight: 17901.46

Authors

Yuan, H. (deposition date: 2016-06-12, release date: 2016-08-24, Last modification date: 2023-11-08)

Primary citation

Liao, F.,Yuan, H.,Du, K.J.,You, Y.,Gao, S.Q.,Wen, G.B.,Lin, Y.W.,Tan, X.
Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin
Mol Biosyst, 12:3139-3145, 2016

PubMed Abstract: A hydrogen-bond (H-bond) network, specifically a Tyr-associated H-bond network, plays key roles in regulating the structure and function of proteins, as exemplified by abundant heme proteins in nature. To explore an approach for fine-tuning the structure and function of artificial heme proteins, we herein used myoglobin (Mb) as a model protein and introduced a Tyr residue in the secondary sphere of the heme active site at two different positions (107 and 138). We performed X-ray crystallography, UV-Vis spectroscopy, stopped-flow kinetics, and electron paramagnetic resonance (EPR) studies for the two single mutants, I107Y Mb and F138Y Mb, and compared to that of wild-type Mb under the same conditions. The results showed that both Tyr107 and Tyr138 form a distinct H-bond network involving water molecules and neighboring residues, which fine-tunes ligand binding to the heme iron and enhances the protein stability, respectively. Moreover, the Tyr107-associated H-bond network was shown to fine-tune both H2O2 binding and activation. With two cases demonstrated for Mb, this study suggests that the Tyr-associated H-bond network has distinct roles in regulating the protein structure, properties and functions, depending on its location in the protein scaffold. Therefore, it is possible to design a Tyr-associated H-bond network in general to create other artificial heme proteins with improved properties and functions.

PubMed: 27476534
DOI: 10.1039/c6mb00537c

Experimental method

X-RAY DIFFRACTION (1.61 Å)