Annotations: 6BYW

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	LodA_1st	e6bywB1	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 [auth B]	LodA_2nd	e6bywB2	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 [auth A]	LodA_1st	e6bywA2	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 [auth A]	LodA_2nd	e6bywA1	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)
C	LodA_1st	e6bywC1	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)
C	LodA_2nd	e6bywC2	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)
D	LodA_1st	e6bywD2	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)
D	LodA_2nd	e6bywD1	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 [auth B], B [auth A], C, D	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 [auth B], B [auth A], C, D	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C, D	IPR041168	L-Lysine epsilon oxidase, N-terminal	Domain
A [auth B], B [auth A], C, D	IPR041173	L-lysine epsilon oxidase, C-terminal	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth B], B [auth A], C, D	TRQ	Parent Component: TRP RESID: AA0148 PSI-MOD : oxidation of tryptophan to L-tryptophyl quinone MOD:00157

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.