3WEU

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

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	LodA_1st	e3weuA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LodA_1st	ECOD (1.6)
A	LodA_2nd	e3weuA2	A: a+b complex topology	X: L-Lys epsilon-oxidase C-terminal domain (From Topology)	H: L-Lys epsilon-oxidase C-terminal domain (From Topology)	T: L-Lys epsilon-oxidase C-terminal domain	F: LodA_2nd	ECOD (1.6)
B	LodA_1st	e3weuB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LodA_1st	ECOD (1.6)
B	LodA_2nd	e3weuB2	A: a+b complex topology	X: L-Lys epsilon-oxidase C-terminal domain (From Topology)	H: L-Lys epsilon-oxidase C-terminal domain (From Topology)	T: L-Lys epsilon-oxidase C-terminal domain	F: LodA_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF17990	L-Lysine epsilon oxidase N-terminal (LodA_N)	L-Lysine epsilon oxidase N-terminal	This is the N-terminal domain found in antimicrobial protein (LodA) with lysine-epsilon oxidase activity (EC 1.4.3.20) which is produced by gram-negative marine bacteria such as Marinomonas mediterranea [1]. The enzyme, previously named marinocine, c ...	This is the N-terminal domain found in antimicrobial protein (LodA) with lysine-epsilon oxidase activity (EC 1.4.3.20) which is produced by gram-negative marine bacteria such as Marinomonas mediterranea [1]. The enzyme, previously named marinocine, catalyzes the oxidative deamination of l-lysine into 6-semialdehyde 2-aminoadipic acid, ammonia, and hydrogen peroxide (H2O2). Orthologous proteins have been detected in other bacterial genera, where they participate in biofilm development and dispersal [2]. It has been shown that M. mediterranea LodA and its homologues induce cell death in the microcolonies formed in the process of biofilm development due to the hydrogen peroxide generated by their enzymatic activity. Moreover, cells dispersed from the biofilm by means of this mechanism show a phenotypic variation in growth and biofilm formation. The active form of LodA containing the quinonic cofactor is generated intracellularly only in the presence of LodB, suggesting that the latter protein is involved in this process [3].	Domain
A, B	PF18417	L-lysine epsilon oxidase C-terminal domain (LodA_C)	L-lysine epsilon oxidase C-terminal domain	This is the C-terminal domain of L-Lysine epsilon-oxidase (LodA, EC 1.4.3.20), an enzyme which catalyses the oxidative deamination of free L-lysine into L-2-aminoadipate 6-semialdehyde, ammonia and hydrogen peroxide [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	L-lysine 6-oxidase	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor L-lysine 6-oxidase activity primary methylamine oxidase activity catalytic activity L-amino-acid oxidase activity binding quinone binding small molecule binding	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus cell aggregation regulation of biological process biofilm formation biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus cell aggregation regulation of biological process biofilm formation regulation of cellular process biological process involved in intraspecies interaction between organisms biological regulation negative regulation of biological process single-species biofilm formation aggregation of unicellular organisms negative regulation of single-species biofilm formation regulation of single-species biofilm formation negative regulation of cellular process cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR041168	L-Lysine epsilon oxidase, N-terminal	Domain
A, B	IPR033797	L-lysine epsilon-oxidase	Family
A, B	IPR041173	L-lysine epsilon oxidase, C-terminal	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267
A, B	TRQ	Parent Component: TRP RESID: AA0262 , AA0148 PSI-MOD : L-cysteine sulfinic acid MOD:00267 , oxidation of tryptophan to L-tryptophyl quinone MOD:00157

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.