Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer -A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33125.63 
• Atom Count: 2395 
• Residue Count: 289 
• Unique protein chains: 2

3GKV

X-ray structure of an intermediate along the oxidation pathway of Trematomus bernacchii hemoglobin

• DOI: 10.2210/pdb3GKV/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Pseudotrematomus bernacchii


• Deposited: 2009-03-11 Released: 2009-05-05 
• Deposition Author(s): Merlino, A., Vitagliano, L., Sica, F., Vergara, A., Mazzarella, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.4 Å
• R-Value Free: 0.211 
• R-Value Work: 0.184 

Literature

Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins

Merlino, A., Vitagliano, L., Howes, B.D., Verde, C., di Prisco, G., Smulevich, G., Sica, F., Vergara, A.

(2009) Biopolymers 91: 1117-1125

• PubMed: 19373928 
• DOI: 10.1002/bip.21206
• Also Cited By: 4ESA


• PubMed Abstract: 
  

Recent studies have demonstrated that hemoglobins isolated from Antarctic fish undergo peculiar oxidation processes. Here we show, by combining crystallographic and spectroscopic data, that the oxidation pathway of Trematomus bernacchii hemoglobin (HbTb) is distinct from that observed for the major component of Trematomus newnesi (Hb1Tn), despite the high sequence identity of the two proteins and structural similarity of their ferrous and fully oxidized states. Resonance Raman analysis of HbTb autoxidation upon air-exposure reveals the absence of the oxidized pentacoordinated state that was observed for Hb1Tn. The HbTb oxidation pathway is characterized by two ferric species: an aquo hexacoordinated high spin state and a bis-histidyl hexacoordinated low spin form, which appear in the early stages of the oxidation process. The high resolution structure of an intermediate along the oxidation pathway has been determined at 1.4 A resolution. The analysis of the electron density of the heme pocket shows, for both the alpha and the beta iron, the coexistence of multiple binding states. In this partially oxidized form, HbTb exhibits significant deviations from the canonical R state both at the local and global level. The analysis of these modifications highlights the structural correlation between key functional regions of the protein.

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Related Citations: 

• Spectroscopic and crystallographic characterization of a tetrameric hemoglobin oxidation reveals structural features of the functional intermediate relaxed/tense state
  Vitagliano, L.,Vergara, A.,Bonomi, G.,Merlino, A.,Verde, C.,di Prisco, G.,Howes, B.D.,Smulevich, G.,Mazzarella, L.
  (2008) J.Am.Chem.Soc. 130: 10527




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Organizational Affiliation: 

Department of Chemistry, University of Naples, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hemoglobin subunit alpha	A	143	Pseudotrematomus bernacchii	Mutation(s): 0  Gene Names: hba
Find proteins for P80043 (Pseudotrematomus bernacchii) Go to UniProtKB:  P80043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Hemoglobin subunit beta	B	146	Pseudotrematomus bernacchii	Mutation(s): 0  Gene Names: hbb
Find proteins for P80044 (Pseudotrematomus bernacchii) Go to UniProtKB:  P80044

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CMO	A, B	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ACE	A	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.4 Å
• R-Value Free: 0.211 
• R-Value Work: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 86.880	α = 90.00
b = 87.647	β = 100.17
c = 55.339	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
SCALEPACK	data scaling
AMoRE	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-11 
• Released Date: 2009-05-05 
• Deposition Author(s): Merlino, A., Vitagliano, L., Sica, F., Vergara, A., Mazzarella, L.

Revision History 

• Version 1.0: 2009-05-05
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance