1F1U

CRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS (NATIVE, LOW TEMPERATURE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases.

Vetting, M.W.Wackett, L.P.Que Jr., L.Lipscomb, J.D.Ohlendorf, D.H.

(2004) J Bacteriol 186: 1945-1958

  • DOI: 10.1128/jb.186.7.1945-1958.2004
  • Primary Citation of Related Structures:  
    1F1R, 1F1X, 1F1V, 1F1U, 1Q0C, 1Q0O

  • PubMed Abstract: 
  • The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on ...

    The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+ and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four betaalphabetabetabeta modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.


    Related Citations: 
    • Manganese(II)-dependent Extradiol-cleaving Catechol Dioxygenase from Arthrobacter globiformis CM-2
      Whiting, A.K., Boldt, Y.R., Hendrich, M.P., Wackett, L.P., Que Jr, L.
      (1996) Biochemistry 35: 160
    • A Manganese-dependent Dioxygenase from Arthrobacter globiformis CM-2 belongs to the Major Extradiol Dioxygenase Family
      Boldt, Y.R., Sadowsky, M.J., Ellis, L.B., Que Jr, L., Wackett, L.P.
      (1995) J Bacteriol 177: 1225
    • Manganese(II) Active Site Mutants of 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis Strain CM-2.
      Boldt, Y.R., Whiting, A.K., Wagner, M.L., Sadowsky, M.J., Que Jr, L., Wackett, L.P.
      (1997) Biochemistry 36: 2147
    • 3,4-Dihydroxyphenylacetate 2,3-dioxygenase. A Manganese(II) Dioxygenase from Bacillus brevis.
      Que Jr, L., Widom, J., Crawford, R.L.
      (1981) J Biol Chem 256: 10941

    Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Biophysics, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HOMOPROTOCATECHUATE 2,3-DIOXYGENASEAB323Arthrobacter globiformisMutation(s): 0 
Gene Names: mndD
EC: 1.13.11.15
Find proteins for Q44048 (Arthrobacter globiformis)
Explore Q44048 
Go to UniProtKB:  Q44048
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.8α = 90
b = 59.04β = 119
c = 102.25γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Data collection