4H3E | pdb_00004h3e

Crystal structure of a putative iron superoxide dismutase from Trypanosoma cruzi bound to iron

• PDB DOI: https://doi.org/10.2210/pdb4H3E/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma cruzi strain CL Brener
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-13 Released: 2012-09-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.212 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Iron superoxide dismutases in eukaryotic pathogens: new insights from Apicomplexa and Trypanosoma structures.

Phan, I.Q., Davies, D.R., Moretti, N.S., Shanmugam, D., Cestari, I., Anupama, A., Fairman, J.W., Edwards, T.E., Stuart, K., Schenkman, S., Myler, P.J.

(2015) Acta Crystallogr F Struct Biol Commun 71: 615-621

• PubMed: 25961325 
• DOI: https://doi.org/10.1107/S2053230X15004185
• Primary Citation Related Structures: 
  4F2N, 4H3E, 4YET


• PubMed Abstract: 
  

  Prior studies have highlighted the potential of superoxide dismutases as drug targets in eukaryotic pathogens. This report presents the structures of three iron-dependent superoxide dismutases (FeSODs) from Trypanosoma cruzi, Leishmania major and Babesia bovis. Comparison with existing structures from Plasmodium and other trypanosome isoforms shows a very conserved overall fold with subtle differences. In particular, structural data suggest that B. bovis FeSOD may display similar resistance to peroxynitrite-mediated inactivation via an intramolecular electron-transfer pathway as previously described in T. cruzi FeSOD isoform B, thus providing valuable information for structure-based drug design. Furthermore, lysine-acetylation results in T. cruzi indicate that acetylation occurs at a position close to that responsible for the regulation of acetylation-mediated activity in the human enzyme.

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Organizational Affiliation: 
• Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.
Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA.
CSIR-National Chemical Laboratory, Pune 411 008, India.
Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil.

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: 54.59 kDa 
• Atom Count: 3,703 
• Modeled Residue Count: 428 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B	241	Trypanosoma cruzi strain CL Brener	Mutation(s): 0  Gene Names: Tc00.1047053509775.40 EC: 1.15.1.1
UniProt
Find proteins for Q4DCQ3 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DCQ3  Go to UniProtKB:  Q4DCQ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	C [auth A], D [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.212 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34H3E

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.65	α = 90
b = 75.68	β = 90
c = 117.45	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2015-06-03
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description