4W5K

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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This is version 1.3 of the entry. See complete history. 


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

  • DOI: 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate aminotransferase, mitochondrialA, B396Trypanosoma brucei brucei TREU927Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ385Q9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N		 Ligand Interaction
MLT
Query on MLT
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.39α = 90
b = 96.66β = 111.03
c = 81.61γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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