3WEU

Crystal structure of the L-Lys epsilon-oxidase from Marinomonas mediterranea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


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Literature

X-Ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine {varepsilon}-oxidase from Marinomonas mediterranea

Okazaki, S.Nakano, S.Matsui, D.Akaji, S.Inagaki, K.Asano, Y.

(2013) J.Biochem. 154: 233-236

  • DOI: 10.1093/jb/mvt070
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have determined the x-ray crystal structure of L-lysine ε-oxidase from Marinomonas mediterranea in its native and L-lysine-complex forms at 1.94- and 1.99-Å resolution, respectively. In the native enzyme, electron densities clearly indicate the pr ...

    We have determined the x-ray crystal structure of L-lysine ε-oxidase from Marinomonas mediterranea in its native and L-lysine-complex forms at 1.94- and 1.99-Å resolution, respectively. In the native enzyme, electron densities clearly indicate the presence of cysteine tryptophylquinone (CTQ) previously identified in quinohemoprotein amine dehydrogenase. In the L-lysine-complex, an electron density corresponding to the bound L-lysine shows that its ε-amino group is attached to the C6 carbonyl group of CTQ, suggesting the formation of a Schiff-base intermediate. Collectively, the present crystal structure provides the first example of an enzyme employing a tryptophylquinone cofactor in an amine oxidase.


    Organizational Affiliation

    Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-lysine 6-oxidase
A, B
726Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1)Mutation(s): 0 
Gene Names: lodA
EC: 1.4.3.20
Find proteins for F2JXJ3 (Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1))
Go to UniProtKB:  F2JXJ3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download SDF File 
Download CCD File 
A, B
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
TRQ
Query on TRQ
A, B
L-PEPTIDE LINKINGC11 H10 N2 O4TRP
CSD
Query on CSD
A, B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 194.089α = 90.00
b = 125.746β = 99.22
c = 70.591γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-04
    Type: Initial release