2AY4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 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
  • Primary Citation of Related Structures:  

  • 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.(Tokyo) 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 AMINOTRANSFERASE
A, B
394Paracoccus denitrificansMutation(s): 0 
Gene Names: tyrB
EC: 2.6.1.57
Find proteins for P95468 (Paracoccus denitrificans)
Go to UniProtKB:  P95468
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
PPT
Query on PPT

Download SDF File 
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 BINDINGMOAD
PPTKd: 1240000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 124.200α = 90.00
b = 121.790β = 90.00
c = 55.170γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
PROCESSdata scaling
X-PLORrefinement
X-PLORphasing
PROCESSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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