5EVY

Salicylate hydroxylase substrate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The catalytic mechanism of decarboxylative hydroxylation of salicylate hydroxylase revealed by crystal structure analysis at 2.5 angstrom resolution

Uemura, T.Kita, A.Watanabe, Y.Adachi, M.Kuroki, R.Morimoto, Y.

(2016) Biochem.Biophys.Res.Commun. 469: 158-163

  • DOI: 10.1016/j.bbrc.2015.11.087

  • PubMed Abstract: 
  • The X-ray crystal structure of a salicylate hydroxylase from Pseudomonas putida S-1 complexed with coenzyme FAD has been determined to a resolution of 2.5 Å. Structural conservation with p- or m-hydroxybenzoate hydroxylase is very good throughout the ...

    The X-ray crystal structure of a salicylate hydroxylase from Pseudomonas putida S-1 complexed with coenzyme FAD has been determined to a resolution of 2.5 Å. Structural conservation with p- or m-hydroxybenzoate hydroxylase is very good throughout the topology, despite a low amino sequence identity of 20-40% between these three hydroxylases. Salicylate hydroxylase is composed of three distinct domains and includes FAD between domains I and II, which is accessible to solvent. In this study, which analyzes the tertiary structure of the enzyme, the unique reaction of salicylate, i.e. decarboxylative hydroxylation, and the structural roles of amino acids surrounding the substrate, are considered.


    Organizational Affiliation

    Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494, Japan.,Quantum Beam Science Center, Japan Atomic Energy Agency, Ibaraki 319-1195, Japan.,Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494, Japan. Electronic address: morimoto@rri.kyoto-u.ac.jp.,Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Salicylate hydroxylase
X
438Pseudomonas putidaMutation(s): 0 
Gene Names: sal
Find proteins for Q59713 (Pseudomonas putida)
Go to UniProtKB:  Q59713
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
X
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
SAL
Query on SAL

Download SDF File 
Download CCD File 
X
2-HYDROXYBENZOIC ACID
SALICYLIC ACID
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 142.330α = 90.00
b = 142.330β = 90.00
c = 62.350γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
MOSFLMdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-01-13
    Type: Database references