PDBsum entry 4lpi

Oxygen transport

PDB id: 4lpi

Contents

Protein chain

153 a.a.

Ligands

HEM

Waters ×199

PDB id:

4lpi

Name:

Oxygen transport

Title:

A sperm whale myoglobin double mutant l29h/f43y mb with a distal hydrogen-bonding network

Structure:

Myoglobin. Chain: a. Engineered: yes. Mutation: yes

Source:

Physeter catodon. Sperm whale. Organism_taxid: 9755. Gene: mb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.36Å R-factor: 0.181 R-free: 0.199

Authors:

Y.Lin

Key ref:

D.J.Yan et al. (2015). How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin. Dalton Trans, 44, 18815-18822. PubMed id: 26458300 DOI: 10.1039/c5dt03040d

Date:

16-Jul-13 Release date: 16-Jul-14

Protein chain

P02185  (MYG_PHYMC) -  Myoglobin from Physeter macrocephalus

Seq: 154 a.a.

Struc: 153 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1039/c5dt03040d

Dalton Trans 44:18815-18822 (2015)

PubMed id: 26458300

How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin.

D.J.Yan, H.Yuan, W.Li, Y.Xiang, B.He, C.M.Nie, G.B.Wen, Y.W.Lin, X.Tan.

ABSTRACT

A heme-protein cross-link is a key post-translational modification (PTM) of heme proteins. Meanwhile, the structural and functional consequences of heme-protein cross-links are not fully understood, due to limited studies on a direct comparison of the same protein with and without the cross-link. A Tyr-heme cross-link with a C-O bond is a newly discovered PTM of heme proteins, and is spontaneously formed in F43Y myoglobin (Mb) between the Tyr hydroxyl group and the heme 4-vinyl group in vivo. In this study, we found that with an additional distal His29 introduced in the heme pocket, the double mutant L29H/F43Y Mb can form two distinct forms under different protein purification conditions, with and without a novel Tyr-heme cross-link. By solving the X-ray structures of both forms of L29H/F43Y Mb and performing spectroscopic studies, we made a direct structural and functional comparison in the same protein scaffold. It revealed that the Tyr-heme cross-link regulates the heme distal hydrogen-bonding network, and fine-tunes not only the spectroscopic and ligand binding properties, but also the protein reactivity. Moreover, the formation of the Tyr-heme cross-link in the double mutant L29H/F43Y Mb was investigated in vitro. This study addressed the key issue of how Tyr-heme cross-link fine-tunes the structure and functions of the heme protein, and provided a plausible mechanism for the formation of the newly discovered Tyr-heme cross-link.