4WHR

Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase.

Knoot, C.J.Purpero, V.M.Lipscomb, J.D.

(2015) Proc.Natl.Acad.Sci.USA 112: 388-393

  • DOI: 10.1073/pnas.1419118112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe(3+) to activate O2 and catecholic substrates for reaction. The inability of Fe(3+) to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatec ...

    Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe(3+) to activate O2 and catecholic substrates for reaction. The inability of Fe(3+) to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe(3+) species, and the anhydride-Fe(3+) intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe(2+)-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe(2+) intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.


    Organizational Affiliation

    Department of Biochemistry Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455 lipsc001@umn.edu.,Department of Biochemistry Molecular Biology and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protocatechuate 3,4-dioxygenase alpha chain
A, E, C
200Pseudomonas putidaMutation(s): 0 
Gene Names: pcaG
EC: 1.13.11.3
Find proteins for P00436 (Pseudomonas putida)
Go to UniProtKB:  P00436
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protocatechuate 3,4-dioxygenase beta chain
D, B
238Pseudomonas putidaMutation(s): 0 
Gene Names: pcaH
EC: 1.13.11.3
Find proteins for P00437 (Pseudomonas putida)
Go to UniProtKB:  P00437
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protocatechuate 3,4-dioxygenase beta chain
F
238Pseudomonas putidaMutation(s): 0 
Gene Names: pcaH
EC: 1.13.11.3
Find proteins for P00437 (Pseudomonas putida)
Go to UniProtKB:  P00437
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3N8
Query on 3N8

Download SDF File 
Download CCD File 
A, B, C, D, E, F
4-fluorobenzene-1,2-diol
C6 H5 F O2
NFWGQJUHSAGJBE-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BME
Query on BME

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Download CCD File 
A, B, F
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
B, D, F
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
3NJ
Query on 3NJ

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Download CCD File 
B
4-fluorooxepine-2,7-dione
C6 H3 F O3
MARYQJLDFKFFCO-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
B, D, F
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
MHO
Query on MHO
F
L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.148 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 128.437α = 90.00
b = 140.644β = 90.00
c = 168.291γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data reduction
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM24689
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM08700

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2015-01-28
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy