1XMB

X-ray structure of IAA-aminoacid hydrolase from Arabidopsis thaliana gene AT5G56660


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

X-ray structure of ILL2, an auxin-conjugate amidohydrolase from Arabidopsis thaliana.

Bitto, E.Bingman, C.A.Bittova, L.Houston, N.L.Boston, R.S.Fox, B.G.Phillips Jr., G.N.

(2009) Proteins 74: 61-71

  • DOI: 10.1002/prot.22124

  • PubMed Abstract: 
  • The plant hormone indole-3-acetic acid (IAA) is the most abundant natural auxin involved in many aspects of plant development and growth. The IAA levels in plants are modulated by a specific group of amidohydrolases from the peptidase M20D family tha ...

    The plant hormone indole-3-acetic acid (IAA) is the most abundant natural auxin involved in many aspects of plant development and growth. The IAA levels in plants are modulated by a specific group of amidohydrolases from the peptidase M20D family that release the active hormone from its conjugated storage forms. Here, we describe the X-ray crystal structure of IAA-amino acid hydrolase IAA-leucine resistantlike gene 2 (ILL2) from Arabidopsis thaliana at 2.0 A resolution. ILL2 preferentially hydrolyses the auxin-amino acid conjugate N-(indol-3-acetyl)-alanine. The overall structure of ILL2 is reminiscent of dinuclear metallopeptidases from the M20 peptidase family. The structure consists of two domains, a larger catalytic domain with three-layer alpha beta alpha sandwich architecture and aminopeptidase topology and a smaller satellite domain with two-layer alphabeta-sandwich architecture and alpha-beta-plaits topology. The metal-coordinating residues in the active site of ILL2 include a conserved cysteine that clearly distinguishes this protein from previously structurally characterized members of the M20 peptidase family. Modeling of N-(indol-3-acetyl)-alanine into the active site of ILL2 suggests that Leu175 serves as a key determinant for the amino acid side-chain specificity of this enzyme. Furthermore, a hydrophobic pocket nearby the catalytic dimetal center likely recognizes the indolyl moiety of the substrate. Finally, the active site of ILL2 harbors an absolutely conserved glutamate (Glu172), which is well positioned to act as a general acid-base residue. Overall, the structure of ILL2 suggests that this enzyme likely uses a catalytic mechanism that follows the paradigm established for the other enzymes of the M20 peptidase family.


    Organizational Affiliation

    Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IAA-amino acid hydrolase homolog 2
A
418Arabidopsis thalianaGene Names: ILL2
EC: 3.5.1.-
Find proteins for P54970 (Arabidopsis thaliana)
Go to UniProtKB:  P54970
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.157 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.264α = 90.00
b = 75.264β = 90.00
c = 130.880γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
RESOLVEphasing
SCALEPACKdata scaling
SOLVEphasing
DENZOdata reduction
ARP/wARPmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-02-04
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-01-30
    Type: Database references, Structure summary
  • Version 1.4: 2017-10-11
    Type: Refinement description