3ZDS

Structure of homogentisate 1,2-dioxygenase in complex with reaction intermediates of homogentisate with oxygen.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Visualizing the Substrate-, Superoxo-, Alkylperoxo- and Product-Bound States at the Non-Heme Fe(II) Site of Homogentisate Dioxygenase

Jeoung, J.-H.Bommer, M.Lin, T.-Y.Dobbek, H.

(2013) Proc Natl Acad Sci U S A 110: 12625

  • DOI: 10.1073/pnas.1302144110
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Homogentisate 1,2-dioxygenase (HGDO) uses a mononuclear nonheme Fe(2+) to catalyze the oxidative ring cleavage in the degradation of Tyr and Phe by producing maleylacetoacetate from homogentisate (2,5-dihydroxyphenylacetate). Here, we report three cr ...

    Homogentisate 1,2-dioxygenase (HGDO) uses a mononuclear nonheme Fe(2+) to catalyze the oxidative ring cleavage in the degradation of Tyr and Phe by producing maleylacetoacetate from homogentisate (2,5-dihydroxyphenylacetate). Here, we report three crystal structures of HGDO, revealing five different steps in its reaction cycle at 1.7-1.98 Å resolution. The resting state structure displays an octahedral coordination for Fe(2+) with two histidine residues (His331 and His367), a bidentate carboxylate ligand (Glu337), and two water molecules. Homogentisate binds as a monodentate ligand to Fe(2+), and its interaction with Tyr346 invokes the folding of a loop over the active site, effectively shielding it from solvent. Binding of homogentisate is driven by enthalpy and is entropically disfavored as shown by anoxic isothermal titration calorimetry. Three different reaction cycle intermediates have been trapped in different HGDO subunits of a single crystal showing the influence of crystal packing interactions on the course of enzymatic reactions. The observed superoxo:semiquinone-, alkylperoxo-, and product-bound intermediates have been resolved in a crystal grown anoxically with homogentisate, which was subsequently incubated with dioxygen. We demonstrate that, despite different folds, active site architectures, and Fe(2+) coordination, extradiol dioxygenases can proceed through the same principal reaction intermediates to catalyze the O2-dependent cleavage of aromatic rings. Thus, convergent evolution of nonhomologous enzymes using the 2-His-1-carboxylate facial triad motif developed different solutions to stabilize closely related intermediates in unlike environments.


    Organizational Affiliation

    Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HOMOGENTISATE 1,2-DIOXYGENASEA, B, C, D, E, F, G, H, I, J, K, L433Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: hmgAPP_4621
EC: 1.13.11.5
Find proteins for Q88E47 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440))
Explore Q88E47 
Go to UniProtKB:  Q88E47
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M8O
Query on M8O

Download CCD File 
A
4-Maleylacetoacetic acid
C8 H8 O6
GACSIVHAIFQKTC-UHFFFAOYSA-N
 Ligand Interaction
HMQ
Query on HMQ

Download CCD File 
F, L
2-[(6R)-6-(dioxidanyl)-6-oxidanyl-3-oxidanylidene-cyclohexa-1,4-dien-1-yl]ethanoic acid
C8 H8 O6
WRLJTDRVSAMRQB-MRVPVSSYSA-N
 Ligand Interaction
OMD
Query on OMD

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B, D, E, G, H, I, J, K
2-(3,6-DIHYDROXYPHENYL)ACETIC ACID
C8 H8 O4
IGMNYECMUMZDDF-UHFFFAOYSA-N
 Ligand Interaction
HQ9
Query on HQ9

Download CCD File 
C
2-(6-oxidanyl-3-oxidanylidene-cyclohexa-1,4-dien-1-yl)ethanoic acid
C8 H8 O4
SORMFPBLGIOKJT-ZETCQYMHSA-N
 Ligand Interaction
PO4
Query on PO4

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E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FE
Query on FE

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A, B, C, D, E, F, G, H, I, J, K, L
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
OXY
Query on OXY

Download CCD File 
C
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.737α = 87.62
b = 93.857β = 80.39
c = 163.438γ = 68.29
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Atomic model, Derived calculations, Other
  • Version 1.2: 2013-08-14
    Changes: Database references
  • Version 1.3: 2019-03-06
    Changes: Advisory, Data collection, Experimental preparation, Other