3ECJ | pdb_00003ecj

Structure of E323L mutant of Homoprotocatechuate 2,3-Dioxygenase from Brevibacterium fuscum at 1.65A resolution

• PDB DOI: https://doi.org/10.2210/pdb3ECJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brevibacterium fuscum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-08-31 Released: 2008-10-07 
• Deposition Author(s): Kovaleva, E.G., Lipscomb, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.194 (Depositor) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Intermediate in the O-O Bond Cleavage Reaction of an Extradiol Dioxygenase.

Kovaleva, E.G., Lipscomb, J.D.

(2008) Biochemistry 47: 11168-11170

• PubMed: 18826259 
• DOI: https://doi.org/10.1021/bi801459q
• Primary Citation of Related Structures:  
  3ECJ, 3ECK


• PubMed Abstract: 
  

  The reactive oxy intermediate of the catalytic cycle of extradiol aromatic ring-cleaving dioxygenases is formed by binding the catecholic substrate and O2 in adjacent ligand positions of the active site metal [usually Fe(II)]. This intermediate and the following Fe(II)-alkylperoxo intermediate resulting from oxygen attack on the substrate have been previously characterized in a crystal of homoprotocatechuate 2,3-dioxygenase (HPCD). Here a subsequent intermediate in which the O-O bond is broken to yield a gem diol species is structurally characterized. This new intermediate is stabilized in the crystal by using the alternative substrate, 4-sulfonylcatechol, and the Glu323Leu variant of HPCD, which alters the crystal packing.

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Organizational Affiliation: 
• Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, 321 Church Street SE, University of Minnesota, Minneapolis, Minnesota 55455, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 167.92 kDa 
• Atom Count: 13,558 
• Modeled Residue Count: 1,437 
• Deposited Residue Count: 1,460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (Homoprotocatechuate 2,3-dioxygenase)	A, B, C, D	365	Brevibacterium fuscum	Mutation(s): 1  Gene Names: hpcd EC: 1.13.11.15
UniProt
Find proteins for Q45135 (Brevibacterium fuscum) Explore Q45135  Go to UniProtKB:  Q45135

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2	E [auth A], H [auth B], L [auth C], P [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CA	I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A], J [auth B], M [auth C], Q [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.194 (Depositor) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.711	α = 90
b = 163.403	β = 90
c = 101.584	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Kovaleva, E.G., Lipscomb, J.D.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description