2BUR

Crystal Structure Of Wild-Type Protocatechuate 3,4-Dioxygenase from Acinetobacter Sp. ADP1 in Complex with 4-hydroxybenzoate

• PDB DOI: https://doi.org/10.2210/pdb2BUR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter baylyi ADP1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-17 Released: 2006-09-05 
• Deposition Author(s): Vetting, M.W., Valley, M.P., D'Argenio, D.A., Ornston, L.N., Lipscomb, J.D., Ohlendorf, D.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.193 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 

Starting Model: experimental

Literature

Biophysical Analyses of Designed and Selected Mutants of Protocatechuate 3,4-Dioxygenase

Brown, C.K., Vetting, M.W., Earhart, C.A., Ohlendorf, D.H.

(2004) Annu Rev Microbiol 58: 555-585

• PubMed: 15487948 
• DOI: https://doi.org/10.1146/annurev.micro.57.030502.090927
• Primary Citation of Related Structures:  
  2BUM, 2BUQ, 2BUR, 2BUT, 2BUV


• PubMed Abstract: 
  

  The catechol dioxygenases allow a wide variety of bacteria to use aromatic compounds as carbon sources by catalyzing the key ring-opening step. These enzymes use specifically either catechol or protocatechuate (2,3-dihydroxybenozate) as their substrates; they use a bare metal ion as the sole cofactor. To learn how this family of metalloenzymes functions, a structural analysis of designed and selected mutants of these enzymes has been undertaken. Here we review the results of this analysis on the nonheme ferric iron intradiol dioxygenase protocatechuate 3,4-dioxygenase.

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Organizational Affiliation: 

Center for Metals in Biocatalysis and Department of Biochemistry, Molecular Biology, and Biophysics , Minneapolis, Minnesota 55455, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12 Pseudo Symmetry: Tetrahedral - T  (Explore in 3D)
Pseudo Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 51.29 kDa 
• Atom Count: 3,818 
• Modelled Residue Count: 440 
• Deposited Residue Count: 450 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN	A	209	Acinetobacter baylyi ADP1	Mutation(s): 0  EC: 1.13.11.3
UniProt
Find proteins for P20371 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P20371  Go to UniProtKB:  P20371

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN	B	241	Acinetobacter baylyi ADP1	Mutation(s): 0  EC: 1.13.11.3
UniProt
Find proteins for P20372 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P20372  Go to UniProtKB:  P20372

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHB	D [auth B]	P-HYDROXYBENZOIC ACID C7 H6 O3 FJKROLUGYXJWQN-UHFFFAOYSA-N
FE	C [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.193 
• R-Value Work: 0.163 
• R-Value Observed: 0.163 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.9	α = 90
b = 144.9	β = 90
c = 144.9	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-05 
Deposition Author(s): Vetting, M.W., Valley, M.P., D'Argenio, D.A., Ornston, L.N., Lipscomb, J.D., Ohlendorf, D.H.

Revision History  

• Version 1.0: 2006-09-05
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-06-20
  Changes: Data collection, Database references
• Version 1.4: 2019-05-22
  Changes: Data collection, Refinement description
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description