Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 169325.98 
• Atom Count: 11891 
• Residue Count: 1460 
• Unique protein chains: 1

5BWG

Structure of H200C variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.75 Ang resolution

• DOI: 10.2210/pdb5BWG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Brevibacterium fuscum
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2015-06-08 Released: 2015-10-28 
• Deposition Author(s): Kovaleva, E.G., Lipscomb, J.D.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council; National Institutes of Health/National Institute of General Medical Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.179 
• R-Value Work: 0.145 

Literature

A Long-Lived Fe(III)-(Hydroperoxo) Intermediate in the Active H200C Variant of Homoprotocatechuate 2,3-Dioxygenase: Characterization by Mossbauer, Electron Paramagnetic Resonance, and Density Functional Theory Methods.

Meier, K.K., Rogers, M.S., Kovaleva, E.G., Mbughuni, M.M., Bominaar, E.L., Lipscomb, J.D., Munck, E.

(2015) Inorg.Chem. 54: 10269-10280

• PubMed: 26485328 
• DOI: 10.1021/acs.inorgchem.5b01576
• Primary Citation of Related Structures:  
  5BWH


• PubMed Abstract: 
  

The extradiol-cleaving dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) binds substrate homoprotocatechuate (HPCA) and O2 sequentially in adjacent ligand sites of the active site Fe(II). Kinetic and spectroscopic studies of HPCD have elucidated catalytic roles of several active site residues, including the crucial acid-base chemistry of His200. In the present study, reaction of the His200Cys (H200C) variant with native substrate HPCA resulted in a decrease in both kcat and the rate constants for the activation steps following O2 binding by >400 fold. The reaction proceeds to form the correct extradiol product. This slow reaction allowed a long-lived (t1/2 = 1.5 min) intermediate, H200C-HPCAInt1 (Int1), to be trapped. Mössbauer and parallel mode electron paramagnetic resonance (EPR) studies show that Int1 contains an S1 = 5/2 Fe(III) center coupled to an SR = 1/2 radical to give a ground state with total spin S = 2 (J > 40 cm(-1)) in Hexch = JŜ1·ŜR. Density functional theory (DFT) property calculations for structural models suggest that Int1 is a (HPCA semiquinone(•))Fe(III)(OOH) complex, in which OOH is protonated at the distal O and the substrate hydroxyls are deprotonated. By combining Mössbauer and EPR data of Int1 with DFT calculations, the orientations of the principal axes of the (57)Fe electric field gradient and the zero-field splitting tensors (D = 1.6 cm(-1), E/D = 0.05) were determined. This information was used to predict hyperfine splittings from bound (17)OOH. DFT reactivity analysis suggests that Int1 can evolve from a ferromagnetically coupled Fe(III)-superoxo precursor by an inner-sphere proton-coupled-electron-transfer process. Our spectroscopic and DFT results suggest that a ferric hydroperoxo species is capable of extradiol catalysis.

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Organizational Affiliation: 

Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A, B, C, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CA	B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MPO	A, B	3[N-MORPHOLINO]PROPANE SULFONIC ACID C7 H15 N O4 S DVLFYONBTKHTER-UHFFFAOYSA-N
P6G	A, B, C, D	HEXAETHYLENE GLYCOL POLYETHYLENE GLYCOL PEG400 C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
FE2	A, B, C, D	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.179 
• R-Value Work: 0.145 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 110.748	α = 90.00
b = 150.627	β = 90.00
c = 96.269	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-06-08 
• Released Date: 2015-10-28 
• Deposition Author(s): Kovaleva, E.G., Lipscomb, J.D.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/H001905/1
National Institutes of Health/National Institute of General Medical Sciences	United States	GM 24689

Revision History 

• Version 1.0: 2015-10-28
  Type: Initial release
• Version 1.1: 2015-11-11
  Type: Database references
• Version 1.2: 2017-09-06
  Type: Author supporting evidence, Database references, Derived calculations, Structure summary
• Version 1.3: 2017-11-22
  Type: Database references