4YSB

Crystal structure of ETHE1 from Myxococcus xanthus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterizations of Two Bacterial Persulfide Dioxygenases of the Metallo-beta-lactamase Superfamily.

Sattler, S.A.Wang, X.Lewis, K.M.DeHan, P.J.Park, C.M.Xin, Y.Liu, H.Xian, M.Xun, L.Kang, C.

(2015) J Biol Chem 290: 18914-18923

  • DOI: 10.1074/jbc.M115.652537
  • Primary Citation of Related Structures:  
    4YSK, 4YSL, 4YSB

  • PubMed Abstract: 
  • Persulfide dioxygenases (PDOs), also known as sulfur dioxygenases (SDOs), oxidize glutathione persulfide (GSSH) to sulfite and GSH. PDOs belong to the metallo-β-lactamase superfamily and play critical roles in animals, plants, and microorganisms, including sulfide detoxification ...

    Persulfide dioxygenases (PDOs), also known as sulfur dioxygenases (SDOs), oxidize glutathione persulfide (GSSH) to sulfite and GSH. PDOs belong to the metallo-β-lactamase superfamily and play critical roles in animals, plants, and microorganisms, including sulfide detoxification. The structures of two PDOs from human and Arabidopsis thaliana have been reported; however, little is known about the substrate binding and catalytic mechanism. The crystal structures of two bacterial PDOs from Pseudomonas putida and Myxococcus xanthus were determined at 1.5- and 2.5-Å resolution, respectively. The structures of both PDOs were homodimers, and their metal centers and β-lactamase folds were superimposable with those of related enzymes, especially the glyoxalases II. The PDOs share similar Fe(II) coordination and a secondary coordination sphere-based hydrogen bond network that is absent in glyoxalases II, in which the corresponding residues are involved instead in coordinating a second metal ion. The crystal structure of the complex between the Pseudomonas PDO and GSH also reveals the similarity of substrate binding between it and glyoxalases II. Further analysis implicates an identical mode of substrate binding by known PDOs. Thus, the data not only reveal the differences in metal binding and coordination between the dioxygenases and the hydrolytic enzymes in the metallo-β-lactamase superfamily, but also provide detailed information on substrate binding by PDOs.


    Organizational Affiliation

    From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, the Department of Chemistry, Washington State University, Pullman, Washington 99164-4630 chkang@wsu.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metallo-beta-lactamase family proteinA, B233Myxococcus xanthus DK 1622Mutation(s): 0 
Gene Names: MXAN_4319
Find proteins for Q1D4C9 (Myxococcus xanthus (strain DK 1622))
Explore Q1D4C9 
Go to UniProtKB:  Q1D4C9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.180 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.603α = 90
b = 116.603β = 90
c = 65.061γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references
  • Version 1.2: 2015-08-12
    Changes: Database references