2IG9

Structure of a full-length Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in a new spacegroup.

• PDB DOI: https://doi.org/10.2210/pdb2IG9/pdb

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


• Deposited: 2006-09-22 Released: 2007-04-24 
• Deposition Author(s): Kovaleva, E.G., Lipscomb, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates

Kovaleva, E.G., Lipscomb, J.D.

(2007) Science 316: 453-457

• PubMed: 17446402 
• DOI: https://doi.org/10.1126/science.1134697
• Primary Citation of Related Structures:  
  2IG9, 2IGA


• PubMed Abstract: 
  

  We report the structures of three intermediates in the O2 activation and insertion reactions of an extradiol ring-cleaving dioxygenase. A crystal of Fe2+-containing homoprotocatechuate 2,3-dioxygenase was soaked in the slow substrate 4-nitrocatechol in a low O2 atmosphere. The x-ray crystal structure shows that three different intermediates reside in different subunits of a single homotetrameric enzyme molecule. One of these is the key substrate-alkylperoxo-Fe2+ intermediate, which has been predicted, but not structurally characterized, in an oxygenase. The intermediates define the major chemical steps of the dioxygenase mechanism and point to a general mechanistic strategy for the diverse 2-His-1-carboxylate enzyme family.

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 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: 168.44 kDa 
• Atom Count: 13,106 
• Modelled Residue Count: 1,436 
• Deposited Residue Count: 1,460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoprotocatechuate 2,3-dioxygenase	A, B, C, D	365	Brevibacterium fuscum	Mutation(s): 0  Gene Names: hpcd EC: 1.13.11.15
UniProt
Find proteins for Q45135 (Brevibacterium fuscum) Go to UniProtKB:  Q45135

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.445	α = 90
b = 152.802	β = 90
c = 99.714	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
d*TREK	data reduction
d*TREK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Kovaleva, E.G., Lipscomb, J.D.

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description