9AAT

X-RAY STRUCTURE REFINEMENT AND COMPARISON OF THREE FORMS OF MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray structure refinement and comparison of three forms of mitochondrial aspartate aminotransferase.

McPhalen, C.A.Vincent, M.G.Jansonius, J.N.

(1992) J Mol Biol 225: 495-517

  • DOI: 10.1016/0022-2836(92)90935-d
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The X-ray crystal structures of three forms of the enzyme aspartate aminotransferase (EC 2.6.1.1) from chicken heart mitochondria have been refined by least-squares methods: holoenzyme with the co-factor pyridoxal-5'-phosphate bound at pH 7.5 (1.9 A ...

    The X-ray crystal structures of three forms of the enzyme aspartate aminotransferase (EC 2.6.1.1) from chicken heart mitochondria have been refined by least-squares methods: holoenzyme with the co-factor pyridoxal-5'-phosphate bound at pH 7.5 (1.9 A resolution), holoenzyme with pyridoxal-5'-phosphate bound at pH 5.1 (2.3 A resolution) and holoenzyme with the co-factor pyridoxamine-5'-phosphate bound at pH 7.5 (2.2 A resolution). The crystallographic agreement factors [formula: see text] for the structures are 0.166, 0.130 and 0.131, respectively, for all data in the resolution range from 10.0 A to the limit of diffraction for each structure. The secondary, super-secondary and domain structures of the pyridoxal-phosphate holoenzyme at pH 7.5 are described in detail. The surface area of the interface between the monomer subunits of this dimeric alpha 2 protein is unusually large, indicating a very stable dimer. This is consistent with biochemical data. Both subunit and domain interfaces are relatively smooth compared with other proteins. The interactions of the protein with its co-factor are described and compared among the three structures. Observed changes in co-factor conformation may be related to spectral changes and the energetics of the catalytic reaction. Small but significant adjustments of the protein to changes in co-factor conformation are seen. These adjustments may be accommodated by small rigid-body shifts of secondary structural elements, and by packing defects in the protein core.


    Related Citations: 
    • The Open(Slash)Closed Conformational Equilibrium of Aspartate Aminotransferase: Studies in the Crystalline State and with a Fluorescent Probe in Solution
      Picot, D., Sandmeier, E., Thaller, C., Vincent, M.G., Christen, P., Jansonius, J.N.
      (1991) Eur J Biochem 196: 329
    • Mechanism of Action of Aspartate Aminotransferase Proposed on the Basis of its Spatial Structure
      Kirsch, J.F., Eichele, G., Ford, G.C., Vincent, M.G., Jansonius, J.N., Gehring, H., Christen, P.
      (1984) J Mol Biol 174: 497
    • Three-Dimensional Structure of a Pyridoxal-Phosphate-Dependent Enzyme, Mitochondrial Aspartate Aminotransferase
      Ford, G.C., Eichele, G., Jansonius, J.N.
      (1980) Proc Natl Acad Sci U S A 77: 2559

    Organizational Affiliation

    Department of Structural Biology, University of Basel, Switzerland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ASPARTATE AMINOTRANSFERASEA, B401Gallus gallusMutation(s): 0 
Gene Names: GOT2
EC: 2.6.1.1 (PDB Primary Data), 2.6.1.7 (UniProt)
Find proteins for P00508 (Gallus gallus)
Explore P00508 
Go to UniProtKB:  P00508
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMP
Query on PMP

Download CCD File 
A, B
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.131 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.67α = 85.2
b = 58.66β = 109.3
c = 75.79γ = 115.7
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other