1AMR

X-RAY CRYSTALLOGRAPHIC STUDY OF PYRIDOXAMINE 5'-PHOSPHATE-TYPE ASPARTATE AMINOTRANSFERASES FROM ESCHERICHIA COLI IN THREE FORMS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

X-ray crystallographic study of pyridoxamine 5'-phosphate-type aspartate aminotransferases from Escherichia coli in three forms.

Miyahara, I., Hirotsu, K., Hayashi, H., Kagamiyama, H.

(1994) J Biochem 116: 1001-1012

  • DOI: 10.1093/oxfordjournals.jbchem.a124620
  • Primary Citation of Related Structures:  
    1AMQ, 1AMR, 1AMS

  • PubMed Abstract: 

    • The three-dimensional structures of pyridoxamine 5'-phosphate-type aspartate aminotransferase from Escherichia coli and its complexes with maleate and glutarate have been determined by X-ray crystallography at 2.2, 2.1, and 2.7 A resolution, respectively ...

    The three-dimensional structures of pyridoxamine 5'-phosphate-type aspartate aminotransferase from Escherichia coli and its complexes with maleate and glutarate have been determined by X-ray crystallography at 2.2, 2.1, and 2.7 A resolution, respectively. The enzyme is a dimeric form comprising two identical subunits, each of which is divided into one large and one small domain. The complex with maleate showed that substrate (or inhibitor) binding induced a large conformational change from the "open" to the "closed" form, resulting in closure of the active site by the small domain movement, as was observed in the pyridoxal 5'-phosphate-type enzyme. In the open form, three hydrophobic residues (hydrophobic plug) at the entrance of the active site are exposed to solvent. Maleate binding make the active site more hydrophobic by charge compensation and release of water molecules, facilitating the movement of the hydrophobic plug into the active site pocket to induce a large conformational change in the enzyme. Maleate is fixed rigidly in the active site pocket by extensive salt bridges and a hydrogen bonding network, guaranteeing the stereo-specificity of the catalysis and giving a Michaelis complex model. Contrary to our expectation, the glutarate complex was in the open form, suggesting that the equilibrium between the open and closed forms lies far toward the open form in solution. The water molecules located in the active site pocket were almost completely conserved between Escherichia coli and chicken mitochondrial aspartate aminotransferase with the same type of cofactor and the same conformation.

    Related Citations: 
    • X-Ray Crystallographic Study of Pyridoxal 5'-Phosphate-Type Aspartate Aminotransferase from Esherichia Coli in Open and Closed Form
      Okamoto, A., Higuchi, T., Hirotsu, K., Kuramitsu, S.
      () To be published --: --
    Organizational Affiliation: 

    Department of Chemistry, Faculty of Science, Osaka City University.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ASPARTATE AMINOTRANSFERASEA396Escherichia coliMutation(s): 0 
EC: 2.6.1.1
UniProt
Find proteins for P00509 (Escherichia coli (strain K12))
Explore P00509 
Go to UniProtKB:  P00509
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMP (Subject of Investigation/LOI)
Query on PMP
Download Ideal Coordinates CCD File 
B [auth A]4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N		 Ligand Interaction
MAE
Query on MAE
Download Ideal Coordinates CCD File 
C [auth A]MALEIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-UPHRSURJSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.6α = 90
b = 85.7β = 90
c = 78.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
TOMrefinement
X-PLORphasing
TOM/FRODOrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-09-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other