4DBC | pdb_00004dbc

Substrate Activation in Aspartate Aminotransferase

• PDB DOI: https://doi.org/10.2210/pdb4DBC/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2012-01-14 Released: 2012-12-05 
• Deposition Author(s): Toney, M.D., Fisher, A.J., Griswold, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.194 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Ground-state electronic destabilization via hyperconjugation in aspartate aminotransferase.

Griswold, W.R., Castro, J.N., Fisher, A.J., Toney, M.D.

(2012) J Am Chem Soc 134: 8436-8438

• PubMed: 22551424 
• DOI: https://doi.org/10.1021/ja302809e
• Primary Citation Related Structures: 
  4DBC


• PubMed Abstract: 
  

  Binding isotope effects for l-aspartate reacting with the inactive K258A mutant of PLP-dependent aspartate aminotransferase to give a stable external aldimine intermediate are reported. They provide direct evidence for electronic ground-state destabilization via hyperconjugation. The smaller equilibrium isotope effect with deazaPLP-reconstituted K258A indicates that the pyridine nitrogen plays an important role in labilizing the Cα-H bond.

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Organizational Affiliation: 
• Department of Chemistry, University of California - Davis, 95616, 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: 44.37 kDa 
• Atom Count: 3,586 
• 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): 1  EC: 2.6.1.1
UniProt
Find proteins for P00509 (Escherichia coli (strain K12)) Explore P00509  Go to UniProtKB:  P00509

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3QP	G [auth A]	(E)-N-{2-hydroxy-3-methyl-6-[(phosphonooxy)methyl]benzylidene}-L-aspartic acid C13 H16 N O9 P CMDDKMGWJXISQE-ZFGNZVLRSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.194 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.29	α = 90
b = 155.25	β = 90
c = 77.96	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
DENZO	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Toney, M.D., Fisher, A.J., Griswold, W.R.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2018-08-29
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations