4W5K | pdb_00004w5k

Structure of a mitochondrial aspartate aminotransferase from Trypanosoma brucei, K237A mutant

• PDB DOI: https://doi.org/10.2210/pdb4W5K/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-08-18 Released: 2014-09-24 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.183 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.153 (Depositor) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

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 F Struct Biol Commun 71: 566-571

• PubMed: 25945710 
• DOI: https://doi.org/10.1107/S2053230X15001831
• Primary Citation 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: 88.52 kDa 
• Atom Count: 6,708 
• Modeled Residue Count: 760 
• Deposited Residue Count: 792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate aminotransferase, mitochondrial	A, B	396	Trypanosoma brucei brucei TREU927	Mutation(s): 1  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MLT	D [auth A], G [auth B]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
EDO	E [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.183 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.153 (Depositor) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34W5K

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.39	α = 90
b = 96.66	β = 111.03
c = 81.61	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2015-05-06
  Changes: Database references
• Version 1.2: 2015-05-20
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Advisory, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary