4EU1

Structure of a mitochondrial aspartate aminotransferase from Trypanosoma brucei

• PDB DOI: https://doi.org/10.2210/pdb4EU1/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma brucei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-25 Released: 2012-05-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.245 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

Structures of aspartate aminotransferases from Trypanosoma brucei, Leishmania major and Giardia lamblia.

Abendroth, J., Choi, R., Wall, A., Clifton, M.C., Lukacs, C.M., Staker, B.L., Van Voorhis, W., Myler, P., Lorimer, D.D., Edwards, T.E.

(2015) Acta Crystallogr Sect F Struct Biol Cryst Commun 71: 566-571

• PubMed: 25945710 
• DOI: https://doi.org/10.1107/S2053230X15001831
• Primary Citation of Related Structures:  
  3MEB, 4EU1, 4H51, 4W5K


• PubMed Abstract: 
  

  The structures of three aspartate aminotransferases (AATs) from eukaryotic pathogens were solved within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). Both the open and closed conformations of AAT were observed. Pyridoxal phosphate was bound to the active site via a Schiff base to a conserved lysine. An active-site mutant showed that Trypanosoma brucei AAT still binds pyridoxal phosphate even in the absence of the tethering lysine. The structures highlight the challenges for the structure-based design of inhibitors targeting the active site, while showing options for inhibitor design targeting the N-terminal arm.

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Organizational Affiliation: 

Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 91.14 kDa 
• Atom Count: 6,249 
• Modelled Residue Count: 764 
• Deposited Residue Count: 818 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial aspartate aminotransferase	A, B	409	Trypanosoma brucei	Mutation(s): 0  Gene Names: Tb11.02.2740 EC: 2.6.1.1
UniProt
Find proteins for Q385Q9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q385Q9  Go to UniProtKB:  Q385Q9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], G [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.245 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M34EU1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.26	α = 90
b = 96.25	β = 111.62
c = 81.32	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2015-05-06
  Changes: Database references
• Version 1.2: 2015-05-13
  Changes: Database references
• Version 1.3: 2015-05-20
  Changes: Database references
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-12-06
  Changes: Data collection