AMPDB_55 | L-lysine 6-oxidase

1 General Description

AMPDB ID: AMPDB_55

Protein Names: L-lysine 6-oxidase (EC 1.4.3.20) (L-lysine-epsilon-oxidase) (Marinocine)

Protein Family: Nil

Gene Name: lodA Marme_2662

Source Organism: Marinomonas mediterranea (strain ATCC 700492 JCM 21426 NBRC 103028 MMB-1)

Protein Length: 726 AA

Protein Existence: Evidence at protein level

2 Protein Sequence & Composition

MALSVHPSIGVARLGNANTDNFVLNPMEIGGLPYEHDVDLKPTTTVVNFKDEAGCIRRQGQVFKVFGASNEELTLDSPNVKNIEWTVHLANKKAAWYEFRELNGNLLYGRDNSYSARGVPWRNASKTASSERQSLIIDLGPRSVSGVMATVEISINNIPETYLHPSYPSGELLQGSKHFESLGTLRTDSQGRLIVLGGYGFAGGNTDLSGYGGGDDWYDDISDGSVTCVVTYSDDSSETSTAWMVVGSPDFAPEIVNISTLSDTCFDVGVRNFDLVPDMYDSATGHYKSDYVANFDRDILPIIQRISQYQWVSNVQSMSGFFSFQFDYRDGSAANKANRMKYYNYFRQLDNKVIGDYDQPQQVLMSSEVEGDILPLMPMNSGSNSVSSSNFYDLTDNVVEKFLALDATQLFLLGQWAEGEFTAGPADDYPVSDMDTASIGNCVGLPMCPGIEMTWSLQNPVIYKDAYQIKHYQDKAYFDVNGLTPERDECEEETGCEPGDLTKRMACPWQADFFNCTIQTVNFSEPSVNKASQTETVTSRTHYEWGNLPAGVSVPDQSSVSATKNVDEKVPLPPAYYSYWWPPQSPWDVLTGELDTEGQLHSHLPAGQQINYARGINSYSQMVEHWSALAFIRDRNQNNDGFPFFTETERNHELFDFKEVLVGQVTGNSEDNETSLPVFFINANKESLEGKGTKKGKLMASYFEERAFSKVRSSNIRPRSGTRMRG

FASTA format

Counts of Amino Acids

'A': 41, 'R': 30, 'N': 47, 'D': 52, 'C': 9, 'Q': 30, 'E': 44, 'G': 57, 'H': 12, 'I': 29, 'L': 50, 'K': 27, 'M': 17, 'F': 34, 'P': 38, 'S': 69, 'T': 42, 'W': 14, 'Y': 32, 'V': 52

Frequencies of Amino Acids

'A': 5.65%, 'R': 4.13%, 'N': 6.47%, 'D': 7.16%, 'C': 1.24%, 'Q': 4.13%, 'E': 6.06%, 'G': 7.85%, 'H': 1.65%, 'I': 3.99%, 'L': 6.89%, 'K': 3.72%, 'M': 2.34%, 'F': 4.68%, 'P': 5.23%, 'S': 9.5%, 'T': 5.79%, 'W': 1.93%, 'Y': 4.41%, 'V': 7.16%

Missing Amino Acid(s)

No Amino Acid(s) are missing in this protein

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

Hydrophobic Amino Acid(s) Count

332

Hydrophilic Amino Acid(s) Count

394

Basic Amino Acid(s) Count

Acidic Amino Acid(s) Count

Modified Amino Acid(s) Count

Modified Amino Acid(s) Frequencies

Computed by biopython (version 1.79) & proteinAnalysis (version 1)

3 Physicochemical Properties

Sl. No.	Properties	Values	Reference
1.	Molecular Mass	80879.6 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	68.857	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	43.234	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.474	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.792	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	4.405	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	-38.403	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.291, 0.291, 0.209 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.11	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	124680, 125180	Computed by ProtParam module (biopython 1.79)

4.1 Target Organism(s)

Pseudomonas sp. (Gram-negative), S.aureus (Gram-positive)

4.2 Antimicrobial Activity

Antibiotic, Antimicrobial, Anti-biofilm, Anti-gram-negative, Anti-gram-Positive

4.3 Enzymatic Activity

4.4 Inhibitory Effect

4.5 Other Biological Activity

Non-hemolytic, Non-ribosomal

Activity data manually curated from Literature and UniProt

5 Database Cross-references

5.1 Literature Database

Citation 1: Lucas-ElÃo P, GÃ³mez D, Solano F, et al. The antimicrobial activity of marinocine, synthesized by Marinomonas mediterranea, is due to hydrogen peroxide generated by its lysine oxidase activity. J Bacteriol. 2006;188(7):2493-501. Published 2006 Apr. doi:10.1128/JB.188.7.2493-2501.2006

PMID: 16547036

Citation 2: Lucas-ElÃo P, Goodwin L, Woyke T, et al. Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1(T)). Stand Genomic Sci. 2012;6(1):63-73. Published 2012 Mar 19. doi:10.4056/sigs.2545743

PMID: 22675599

Citation 3: Lucas-Elio P, Hernandez P, Sanchez-Amat A, et al. Purification and partial characterization of marinocine, a new broad-spectrum antibacterial protein produced by Marinomonas mediterranea. Biochim Biophys Acta. 2005;1721(1-3):193-203. Published 2005 Jan 18. doi:10.1016/j.bbagen.2004.11.002

PMID: 15652194

Citation 4: GÃ³mez D, Lucas-ElÃo P, Sanchez-Amat A, et al. A novel type of lysine oxidase: L-lysine-epsilon-oxidase. Biochim Biophys Acta. 2006;1764(10):1577-85. Published 2006 Oct. doi:10.1016/j.bbapap.2006.08.014

PMID: 17030025

Citation 5: Mai-Prochnow A, Lucas-Elio P, Egan S, et al. Hydrogen peroxide linked to lysine oxidase activity facilitates biofilm differentiation and dispersal in several gram-negative bacteria. J Bacteriol. 2008;190(15):5493-501. Published 2008 Aug. doi:10.1128/JB.00549-08

PMID: 18502869

Citation 6: GÃ³mez D, Lucas-ElÃo P, Solano F, et al. Both genes in the Marinomonas mediterranea lodAB operon are required for the expression of the antimicrobial protein lysine oxidase. Mol Microbiol. 2010;75(2):462-73. Published 2010 Jan. doi:10.1111/j.1365-2958.2009.07000.x

PMID: 20025674

Citation 7: Okazaki S, Nakano S, Matsui D, et al. X-ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine Îµ-oxidase from Marinomonas mediterranea. J Biochem. 2013;154(3):233-6. Published 2013 Sep. doi:10.1093/jb/mvt070

PMID: 23908359

5.2 Protein Sequence Databases

5.3 3D Structure Databases