3WEV | pdb_00003wev

Crystal structure of the Schiff base intermediate of L-Lys epsilon-oxidase from Marinomonas mediterranea with L-Lys

• PDB DOI: https://doi.org/10.2210/pdb3WEV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Marinomonas mediterranea MMB-1
• Expression System: Marinomonas mediterranea MMB-1
• Mutation(s): No 


• Deposited: 2013-07-12 Released: 2013-09-04 
• Deposition Author(s): Okazaki, S., Nakano, S., Matsui, D., Akaji, S., Inagaki, K., Asano, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.189 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

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

• PubMed: 23908359 
• DOI: https://doi.org/10.1093/jb/mvt070
• Primary Citation Related Structures: 
  3WEU, 3WEV


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 163.56 kDa 
• Atom Count: 12,181 
• Modeled Residue Count: 1,361 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lysine 6-oxidase	A, B	726	Marinomonas mediterranea MMB-1	Mutation(s): 0  Gene Names: lodA EC: 1.4.3.20
UniProt
Find proteins for F2JXJ3 (Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1)) Explore F2JXJ3  Go to UniProtKB:  F2JXJ3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	C [auth A], M [auth B]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
SO4	D [auth A], E [auth A], F [auth A], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DIO	P [auth B]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TRQ	A, B	L-PEPTIDE LINKING	C11 H10 N2 O4		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.189 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.992	α = 90
b = 126.164	β = 99.03
c = 70.865	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Okazaki, S., Nakano, S., Matsui, D., Akaji, S., Inagaki, K., Asano, Y.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description