6H6J

Carbomonoxy murine neuroglobin Gly-loop mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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

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

(2019) Sci Rep 9: 5326-5326

  • DOI: 10.1038/s41598-019-41780-3
  • Primary Citation of Related Structures:  

  • PubMed 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 i ...

    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.


    Organizational Affiliation

    Dip. di Chimica "Ugo Schiff", Università di Firenze, Via delle Lastruccia 3-13, 50019, Sesto Fiorentino (FI), Italy.,Department of Physiology and Cellular Biophysics, Russ Berrie Pavilion, Columbia University Medical Center, 1150 St Nicholas Ave, 10032, New York, USA.,Neuroscience Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, 10031, New York, USA.,CNR Institute of Molecular Biology and Pathology, P.le A. Moro 5, 00185, Rome, Italy.,Institute for Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Istituto Pasteur-Fondazione Cenci Bolognetti, Dip. di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy. beatrice.vallone@uniroma1.it.,Istituto Pasteur-Fondazione Cenci Bolognetti, Dip. di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.,CNR Institute of Molecular Biology and Pathology, P.le A. Moro 5, 00185, Rome, Italy. beatrice.vallone@uniroma1.it.,Dip. di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy. beatrice.vallone@uniroma1.it.,Dip. di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neuroglobin
A
150Mus musculusMutation(s): 0 
Gene Names: Ngb
Find proteins for Q9ER97 (Mus musculus)
Go to UniProtKB:  Q9ER97
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
CMO
Query on CMO

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Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.194 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.859α = 90.00
b = 74.859β = 90.00
c = 77.229γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionItaly637295

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release