5VJZ

Joint X-ray/neutron structure of aspartate aminotransferase with alpha-methyl-aspartate at pH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.197 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 2.0 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: 10.1038/s41467-017-01060-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enzymes dependent on pyridoxal 5'-phosphate (PLP, the active form of vitamin B6) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active s ...

    Enzymes dependent on pyridoxal 5'-phosphate (PLP, the active form of vitamin B6) 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate aminotransferase, cytoplasmic
A
412Sus scrofaMutation(s): 0 
Gene Names: GOT1
EC: 2.6.1.1, 2.6.1.3
Find proteins for P00503 (Sus scrofa)
Go to Gene View: GOT1
Go to UniProtKB:  P00503
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aspartate aminotransferase, cytoplasmic
B
412Sus scrofaMutation(s): 0 
Gene Names: GOT1
EC: 2.6.1.1, 2.6.1.3
Find proteins for P00503 (Sus scrofa)
Go to Gene View: GOT1
Go to UniProtKB:  P00503
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLA
Query on PLA

Download SDF File 
Download CCD File 
A
2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID
N-PYRIDOXYL-2-METHYLASPARTIC ACID-5-MONOPHOSPHATE
C13 H19 N2 O9 P
ZFKRUCNEKPIDBK-ZDUSSCGKSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A, B
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.532α = 90.00
b = 124.986β = 90.00
c = 130.444γ = 90.00
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.234 
Software Package:
Software NamePurpose
nCNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DOE-BattelleUnited StatesN-125688-01

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 2.0: 2019-01-30
    Type: Atomic model, Data collection