5VJZ

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


Experimental Data Snapshot

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.197 

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:  
    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 ...

    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. timothy.mueser@utoledo.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate aminotransferase, cytoplasmicA412Sus 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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate aminotransferase, cytoplasmicB412Sus 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLA (Subject of Investigation/LOI)
Query on PLA

Download Ideal Coordinates CCD File 
C [auth A]2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID
C13 H19 N2 O9 P
ZFKRUCNEKPIDBK-ZDUSSCGKSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
BL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 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
b = 124.986β = 90
c = 130.444γ = 90
Software Package:
Software NamePurpose
nCNSrefinement

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DOE-BattelleUnited StatesN-125688-01

Revision History  (Full details and data files)

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