Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 43.98 kDa 
• Atom Count: 3357 
• Modelled Residue Count: 396 
• Deposited Residue Count: 396 
• Unique protein chains: 1

1AMR

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

• PDB DOI: 10.2210/pdb1AMR/pdb

• Classification: TRANSFERASE(AMINOTRANSFERASE)
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1994-07-01 Released: 1994-09-30 
• Deposition Author(s): Miyahara, I., Hirotsu, K., Hayashi, H., Kagamiyama, H.

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Experimental Data Snapshot

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

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

• PubMed: 7896726 
• 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 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.

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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 --: --

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE AMINOTRANSFERASE	A	396	Escherichia coli	Mutation(s): 0  EC: 2.6.1.1
UniProt
Find proteins for P00509 (Escherichia coli (strain K12)) Explore P00509  Go to UniProtKB:  P00509

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP	B [auth A]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N
MAE	C [auth A]	MALEIC ACID C4 H4 O4 VZCYOOQTPOCHFL-UPHRSURJSA-N

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 = 157.6	α = 90
b = 85.7	β = 90
c = 78.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
TOM	refinement
X-PLOR	phasing
TOM/FRODO	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-07-01 
• Released Date: 1994-09-30 
Deposition Author(s): Miyahara, I., Hirotsu, K., Hayashi, H., Kagamiyama, H.

Revision History  

• 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