5VWR | pdb_00005vwr

E.coli Aspartate aminotransferase-(1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP)-alpha-ketoglutarate

• PDB DOI: https://doi.org/10.2210/pdb5VWR/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-22 Released: 2017-09-13 
• Deposition Author(s): Mascarenhas, R., Liu, D., Le, H., Silverman, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.190 (Depositor) 
• R-Value Work: 
  0.167 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover.

Mascarenhas, R., Le, H.V., Clevenger, K.D., Lehrer, H.J., Ringe, D., Kelleher, N.L., Silverman, R.B., Liu, D.

(2017) Biochemistry 56: 4951-4961

• PubMed: 28816437 
• DOI: https://doi.org/10.1021/acs.biochem.7b00499
• Primary Citation Related Structures: 
  5VWO, 5VWQ, 5VWR


• PubMed Abstract: 
  

  Potent mechanism-based inactivators can be rationally designed against pyridoxal 5'-phosphate (PLP)-dependent drug targets, such as ornithine aminotransferase (OAT) or γ-aminobutyric acid aminotransferase (GABA-AT). An important challenge, however, is the lack of selectivity toward other PLP-dependent, off-target enzymes, because of similarities in mechanisms of all PLP-dependent aminotransferase reactions. On the basis of complex crystal structures, we investigate the inactivation mechanism of OAT, a hepatocellular carcinoma target, by (1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP), a known inactivator of GABA-AT. A crystal structure of OAT and FCP showed the formation of a ternary adduct. This adduct can be rationalized as occurring via an enamine mechanism of inactivation, similar to that reported for GABA-AT. However, the crystal structure of an off-target, PLP-dependent enzyme, aspartate aminotransferase (Asp-AT), in complex with FCP, along with the results of attempted inhibition assays, suggests that FCP is not an inactivator of Asp-AT, but rather an alternate substrate. Turnover of FCP by Asp-AT is also supported by high-resolution mass spectrometry. Amid existing difficulties in achieving selectivity of inactivation among a large number of PLP-dependent enzymes, the obtained results provide evidence that a desirable selectivity could be achieved, taking advantage of subtle structural and mechanistic differences between a drug-target enzyme and an off-target enzyme, despite their largely similar substrate binding sites and catalytic mechanisms.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, Loyola University Chicago , Chicago, Illinois 60660, United States.
Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208, United States.
Department of BioMolecular Sciences and Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi , University, Mississippi 38677, United States.
Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University , Waltham, Massachusetts 02454-9110, United States.

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: 44.46 kDa 
• Atom Count: 3,526 
• Modeled Residue Count: 396 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate aminotransferase	A	396	Escherichia coli K-12	Mutation(s): 0  Gene Names: aspC, b0928, JW0911 EC: 2.6.1.1
UniProt
Find proteins for P00509 (Escherichia coli (strain K12)) Explore P00509  Go to UniProtKB:  P00509

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PL6	B [auth A]	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid C13 H17 N2 O9 P ZZRWFCMLYWHYGX-XSFFOXFNSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.190 (Depositor) 
• R-Value Work:  0.167 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.4	α = 90
b = 155.521	β = 90
c = 77.409	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Mascarenhas, R., Liu, D., Le, H., Silverman, R.

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Database references, Refinement description
• Version 1.2: 2017-10-04
  Changes: Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references