5VK7

aspartate aminotransferase pH 4.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme.

Dajnowicz, S.Johnston, R.C.Parks, J.M.Blakeley, M.P.Keen, D.A.Weiss, K.L.Gerlits, O.Kovalevsky, A.Mueser, T.C.

(2017) Nat Commun 8: 955-955

  • DOI: https://doi.org/10.1038/s41467-017-01060-y
  • Primary Citation of Related Structures:  
    5VJZ, 5VK7

  • PubMed Abstract: 

    Enzymes dependent on pyridoxal 5'-phosphate (PLP, the active form of vitamin B 6 ) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active site. Neutron crystallography has the unique ability of visualizing the nuclear positions of hydrogen atoms in macromolecules. Here we present a room-temperature neutron structure of a homodimeric PLP-dependent enzyme, aspartate aminotransferase, which was reacted in situ with α-methylaspartate. In one monomer, the PLP remained as an internal aldimine with a deprotonated Schiff base. In the second monomer, the external aldimine formed with the substrate analog. We observe a deuterium equidistant between the Schiff base and the C-terminal carboxylate of the substrate, a position indicative of a low-barrier hydrogen bond. Quantum chemical calculations and a low-pH room-temperature X-ray structure provide insight into the physical phenomena that control the electronic modulation in aspartate aminotransferase.Pyridoxal 5'-phosphate (PLP) is a ubiquitous co factor for diverse enzymes, among them aspartate aminotransferase. Here the authors use neutron crystallography, which allows the visualization of the positions of hydrogen atoms, and computation to characterize the catalytic mechanism of the enzyme.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, 43606, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate aminotransferase, cytoplasmic
A, B
414Sus scrofaMutation(s): 0 
Gene Names: GOT1
EC: 2.6.1.1 (PDB Primary Data), 2.6.1.3 (PDB Primary Data)
UniProt
Find proteins for P00503 (Sus scrofa)
Explore P00503 
Go to UniProtKB:  P00503
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00503
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.732α = 90
b = 125.249β = 90
c = 131.116γ = 90
Software Package:
Software NamePurpose
SHELXLrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release