PDBsum entry 6h6c

Oxygen binding

PDB id: 6h6c

Contents

Protein chain

151 a.a.

Ligands

HEM

CMO

SO4

DIO ×3

GOL ×2

Waters ×119

PDB id:

6h6c

Name:

Oxygen binding

Title:

Carbomonoxy murine neuroglobin f106a mutant

Structure:

Neuroglobin. Chain: a. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: ngb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: plyss

Resolution:

1.75Å R-factor: 0.135 R-free: 0.209

Authors:

C.Exertier,B.Vallone,C.Savino,I.Freda,L.C.Montemiglio,G.Cerutti, A.Scaglione,G.Parisi

Key ref:

C.Exertier et al. (2019). Proximal and distal control for ligand binding in neuroglobin: role of the CD loop and evidence for His64 gating. Sci Rep, 9, 5326. PubMed id: 30926858 DOI: 10.1038/s41598-019-41780-3

Date:

27-Jul-18 Release date: 10-Apr-19

Protein chain

Q9ER97  (NGB_MOUSE) -  Neuroglobin from Mus musculus

Seq: 151 a.a.

Struc: 151 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.7.-.-

DOI no: 10.1038/s41598-019-41780-3

Sci Rep 9:5326 (2019)

PubMed id: 30926858

Proximal and distal control for ligand binding in neuroglobin: role of the CD loop and evidence for His64 gating.

C.Exertier, L.Milazzo, I.Freda, L.C.Montemiglio, A.Scaglione, G.Cerutti, G.Parisi, M.Anselmi, G.Smulevich, C.Savino, B.Vallone.

ABSTRACT

Neuroglobin (Ngb) is predominantly expressed in neurons of the central and peripheral nervous systems and it clearly seems to be involved in neuroprotection. Engineering Ngb to observe structural and dynamic alterations associated with perturbation in ligand binding might reveal important structural determinants, and could shed light on key features related to its mechanism of action. Our results highlight the relevance of the CD loop and of Phe106 as distal and proximal controls involved in ligand binding in murine neuroglobin. We observed the effects of individual and combined mutations of the CD loop and Phe106 that conferred to Ngb higher CO binding velocities, which we correlate with the following structural observations: the mutant F106A shows, upon CO binding, a reduced heme sliding hindrance, with the heme present in a peculiar double conformation, whereas in the CD loop mutant "Gly-loop", the original network of interactions between the loop and the heme was abolished, enhancing binding via facilitated gating out of the distal His64. Finally, the double mutant, combining both mutations, showed a synergistic effect on CO binding rates. Resonance Raman spectroscopy and MD simulations support our findings on structural dynamics and heme interactions in wild type and mutated Ngbs.