6Q6P | pdb_00006q6p

Antarctic fish cytoglobin 1 from D.mawsoni

• PDB DOI: https://doi.org/10.2210/pdb6Q6P/pdb

• Classification: OXYGEN BINDING
• Organism(s): Dissostichus mawsoni
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-12-11 Released: 2020-01-15 
• Deposition Author(s): Giordano, D., Pesce, A., Vermeylen, S., Abbruzzetti, S., Nardini, M., Marchesani, F., Berghmans, H., Seira, C., Bruno, S., Luque, F.J., di Prisco, G., Ascenzi, P., Dewilde, S., Bolognesi, M., Viappiani, C., Verde, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structural and functional properties of Antarctic fish cytoglobins-1: Cold-reactivity in multi-ligand reactions.

Giordano, D., Pesce, A., Vermeylen, S., Abbruzzetti, S., Nardini, M., Marchesani, F., Berghmans, H., Seira, C., Bruno, S., Javier Luque, F., di Prisco, G., Ascenzi, P., Dewilde, S., Bolognesi, M., Viappiani, C., Verde, C.

(2020) Comput Struct Biotechnol J 18: 2132-2144

• PubMed: 32913582 
• DOI: https://doi.org/10.1016/j.csbj.2020.08.007
• Primary Citation Related Structures: 
  6Q6P


• PubMed Abstract: 
  

  While the functions of the recently discovered cytoglobin, ubiquitously expressed in vertebrate tissues, remain uncertain, Antarctic fish provide unparalleled models to study novel protein traits that may arise from cold adaptation. We report here the spectral, ligand-binding and enzymatic properties (peroxynitrite isomerization, nitrite-reductase activity) of cytoglobin-1 from two Antarctic fish, Chaenocephalus aceratus and Dissostichus mawsoni, and present the crystal structure of D. mawsoni cytoglobin-1. The Antarctic cytoglobins-1 display high O ₂ affinity, scarcely compatible with an O ₂ -supply role, a slow rate constant for nitrite-reductase activity, and do not catalyze peroxynitrite isomerization. Compared with mesophilic orthologues, the cold-adapted cytoglobins favor binding of exogenous ligands to the hexa -coordinated bis-histidyl species, a trait related to their higher rate constant for distal-His/heme-Fe dissociation relative to human cytoglobin. At the light of a remarkable 3D-structure conservation, the observed differences in ligand-binding kinetics may reflect Antarctic fish cytoglobin-1 specific features in the dynamics of the heme distal region and of protein matrix cavities, suggesting adaptation to functional requirements posed by the cold environment. Taken together, the biochemical and biophysical data presented suggest that in Antarctic fish, as in humans, cytoglobin-1 unlikely plays a role in O ₂ transport, rather it may be involved in processes such as NO detoxification.

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Organizational Affiliation: 
• Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy.
Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
Department of Physics, University of Genova, Via Dodecaneso 33, I-16121 Genova, Italy.
Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium.
Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy.
Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milano, Italy.
Department of Food and Drug, University of Parma, Parco Area delle Scienze 23A, 43124, Parma, Italy.
Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramenet E-08921, Spain.
Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146 Roma, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.46 kDa 
• Atom Count: 2,582 
• Modeled Residue Count: 313 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoglobin	A, B	179	Dissostichus mawsoni	Mutation(s): 2  Gene Names: CYGB1 EC: 1.15.1.1
UniProt
Find proteins for A0A192X9K5 (Dissostichus mawsoni) Explore A0A192X9K5  Go to UniProtKB:  A0A192X9K5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.658	α = 90
b = 105.647	β = 90
c = 127.328	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Giordano, D., Pesce, A., Vermeylen, S., Abbruzzetti, S., Nardini, M., Marchesani, F., Berghmans, H., Seira, C., Bruno, S., Luque, F.J., di Prisco, G., Ascenzi, P., Dewilde, S., Bolognesi, M., Viappiani, C., Verde, C.

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2020-09-30
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description