2IG9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2007) Science 316: 453-457

  • DOI: 10.1126/science.1134697
  • Primary Citation of Related Structures:  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 ...

    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.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homoprotocatechuate 2,3-dioxygenase
A, B, C, D
365Brevibacterium fuscumN/A
Find proteins for Q45135 (Brevibacterium fuscum)
Go to UniProtKB:  Q45135
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

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A, B, C, D
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.445α = 90.00
b = 152.802β = 90.00
c = 99.714γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
d*TREKdata scaling
d*TREKdata reduction
CCP4phasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance