5EVY | pdb_00005evy

Salicylate hydroxylase substrate complex

• PDB DOI: https://doi.org/10.2210/pdb5EVY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-20 Released: 2015-12-16 
• Deposition Author(s): Morimoto, Y., Uemura, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

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

• PubMed: 26616054 
• DOI: https://doi.org/10.1016/j.bbrc.2015.11.087
• Primary Citation Related Structures: 
  5EVY


• 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 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.

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Organizational Affiliation: 
• Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan; Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494, Japan.
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: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 48.12 kDa 
• Atom Count: 3,240 
• Modeled Residue Count: 411 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Salicylate hydroxylase	A [auth X]	438	Pseudomonas putida	Mutation(s): 0  Gene Names: sal EC: 1.14.13.1
UniProt
Find proteins for Q59713 (Pseudomonas putida) Explore Q59713  Go to UniProtKB:  Q59713

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth X]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SAL	C [auth X]	2-HYDROXYBENZOIC ACID C7 H6 O3 YGSDEFSMJLZEOE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.33	α = 90
b = 142.33	β = 90
c = 62.35	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
MOSFLM	data collection
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-16 
Deposition Author(s): Morimoto, Y., Uemura, T.

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2016-01-13
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references