Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 39.63 kDa 
• Atom Count: 2684 
• Modelled Residue Count: 299 
• Deposited Residue Count: 336 
• Unique protein chains: 1

3QQQ

Crystal structure of non-symbiotic plant hemoglobin from Trema tomentosa

• PDB DOI: 10.2210/pdb3QQQ/pdb

• Classification: oxygen binding, METAL BINDING PROTEIN
• Organism(s): Trema tomentosum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-16 Released: 2011-04-27 
• Deposition Author(s): Kakar, S., Sturms, R., Savage, A., Nix, J.C., Dispirito, A., Hargrove, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.249 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

Crystal structures of Parasponia and Trema hemoglobins: differential heme coordination is linked to quaternary structure.

Kakar, S., Sturms, R., Tiffany, A., Nix, J.C., DiSpirito, A.A., Hargrove, M.S.

(2011) Biochemistry 50: 4273-4280

• PubMed: 21491905 
• DOI: 10.1021/bi2002423
• Primary Citation of Related Structures:  
  3QQQ, 3QQR


• PubMed Abstract: 
  

Hemoglobins from the plants Parasponia andersonii (ParaHb) and Trema tomentosa (TremaHb) are 93% identical in primary structure but differ in oxygen binding constants in accordance with their distinct physiological functions. Additionally, these proteins are dimeric, and ParaHb exhibits the unusual property of having different heme redox potentials for each subunit. To investigate how these hemoglobins could differ in function despite their shared sequence identity and to determine the cause of subunit heterogeneity in ParaHb, we have measured their crystal structures in the ferric oxidation state. Furthermore, we have made a monomeric ParaHb mutant protein (I43N) and measured its ferrous/ferric heme redox potential to test the hypothesized link between quaternary structure and heme heterogeneity in wild-type ParaHb. Our results demonstrate that TremaHb is a symmetric dimeric hemoglobin similar to other class 1 nonsymbiotic plant hemoglobins but that ParaHb has structurally distinct heme coordination in each of its two subunits that is absent in the monomeric I43N mutant protein. A mechanism for achieving structural heterogeneity in ParaHb in which the Ile(101(F4)) side chain contacts the proximal His(105(F8)) in one subunit but not the other is proposed. These results are discussed in the context of the evolution of plant oxygen transport hemoglobins, and other potential functions of plant hemoglobins.

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Organizational Affiliation: 

Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-symbiotic hemoglobin	A, B	168	Trema tomentosum	Mutation(s): 0  Gene Names: GLB1
UniProt
Find proteins for P07803 (Trema tomentosa) Explore P07803  Go to UniProtKB:  P07803

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.249 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.87	α = 90
b = 70.736	β = 90
c = 89.587	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
SOLVE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-16 
• Released Date: 2011-04-27 
Deposition Author(s): Kakar, S., Sturms, R., Savage, A., Nix, J.C., Dispirito, A., Hargrove, M.S.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-29
  Changes: Database references