2AY4

AROMATIC AMINO ACID AMINOTRANSFERASE WITH 3-(P-TOLYL)PROPIONIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The active site of Paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: flexibility and rigidity.

Okamoto, A.Ishii, S.Hirotsu, K.Kagamiyama, H.

(1999) Biochemistry 38: 1176-1184

  • DOI: 10.1021/bi981921d
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Paracoccus denitrificans aromatic amino acid aminotransferase (EC 2. 6.1.57; pdAroAT) binds with a series of aliphatic monocarboxylates attached to the bulky hydrophobic groups. To analyze the properties of the active site in this enzyme, we determin ...

    Paracoccus denitrificans aromatic amino acid aminotransferase (EC 2. 6.1.57; pdAroAT) binds with a series of aliphatic monocarboxylates attached to the bulky hydrophobic groups. To analyze the properties of the active site in this enzyme, we determined the tertiary structures of pdAroAT complexed with nine different inhibitors. Comparison of these active site structures showed that the active site of pdAroAT consists of two parts with contrary properties: rigidity and flexibility. The regions that interact with the carboxylates and methylene chains of the inhibitors gave essentially the same structures among these complexes, exhibiting the rigid property, which would involve fixing the substrate at the proper orientation for efficient catalysis. The region that interacts with the terminal hydrophobic groups of the inhibitors gave versatile structures according to the structures of the terminal groups, showing that this region is structurally flexible. This is mainly achieved by the conformational versatility of the side chains of Asp15, Lys16, Asn142, Arg292, and Ser296. These residues formed in the active site hydrogen bond networks, which were adaptable for the structures of the terminal hydrophobic groups of the inhibitors, with a small deformation or partial destruction according to the shapes and sizes of the inhibitors. These observations illustrate how the flexibility and rigidity in the active site can be used for the substrate binding and recognition.


    Related Citations: 
    • Crystal Structures of Paracoccus Denitrificans Aromatic Amino Acid Aminotransferase: A Substrate Recognition Site Constructed by Rearrangement of Hydrogen Bond Network
      Okamoto, A., Nakai, Y., Hayashi, H., Hirotsu, K., Kagamiyama, H.
      (1998) J Mol Biol 280: 443
    • Paracoccus Denitrificans Aromatic Amino Acid Aminotransferase: A Model Enzyme for the Study of Dual Substrate Recognition Mechanism
      Oue, S., Okamoto, A., Nakai, Y., Nakahira, M., Shibatani, T., Hayashi, H., Kagamiyama, H.
      (1997) J Biochem 121: 161

    Organizational Affiliation

    Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AROMATIC AMINO ACID AMINOTRANSFERASEA, B394Paracoccus denitrificansMutation(s): 0 
Gene Names: tyrB
EC: 2.6.1.57
Find proteins for P95468 (Paracoccus denitrificans)
Explore P95468 
Go to UniProtKB:  P95468
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
PPT
Query on PPT

Download CCD File 
B
3-(P-TOLYL)PROPIONIC ACID
C10 H12 O2
LDYGRLNSOKABMM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PPTKd:  1240000   nM  Binding MOAD
PPTKd :  1240000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.2α = 90
b = 121.79β = 90
c = 55.17γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-02
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other