3ECK

Structure of E323L Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum in complex with putative O-O bond cleavage intermediate formed via in crystallo reaction with 4-sulfonyl catechol at low oxygen concentrations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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

Kovaleva, E.G.Lipscomb, J.D.

(2008) Biochemistry 47: 11168-11170

  • 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.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (Homoprotocatechuate 2,3-dioxygenase)
A, B, C, D
365Brevibacterium fuscumMutation(s): 1 
Gene Names: hpcd
EC: 1.13.11.15
UniProt
Find proteins for Q45135 (Brevibacterium fuscum)
Explore Q45135 
Go to UniProtKB:  Q45135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45135
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XXG
Query on XXG

Download Ideal Coordinates CCD File 
N [auth C],
S [auth D]
3,3-dihydroxy-4-oxocyclohexa-1,5-diene-1-sulfonic acid
C6 H6 O6 S
JGCZOYLBGVHOFP-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
K [auth B]
O [auth C]
P [auth C]
T [auth D]
G [auth A],
K [auth B],
O [auth C],
P [auth C],
T [auth D],
U [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C],
Q [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

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I [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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F [auth A],
J [auth B],
M [auth C],
R [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.735α = 90
b = 163.176β = 90
c = 101.373γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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