AMPDB_367 | Invertebrate-type lysozyme

1 General Description

AMPDB ID: AMPDB_367

Protein Names: Invertebrate-type lysozyme (EC 3.2.1.17) (1;4-beta-N-acetylmuramidase) (Destabilase)

Protein Family: Glycosyl hydrolase 22 family; Type-I lysozyme subfamily

Gene Name: Nil

Source Organism: Ruditapes philippinarum (Japanese littleneck clam) (Venerupis philippinarum)

Protein Length: 136 AA

Protein Existence: Evidence at protein level

2 Protein Sequence & Composition

METVSVEEGLDFAPGMVSQKCLLCMCKLESGGCKPIGCRMDVGSLSCGYFQIKQPYWIDCGKPGKDWKSCSNDINCSSKCVQQYMKRYATHYRCPLNCEGFAREHNGGPNGCHSSRTLKYWELLQKIPGCKGVKFS

FASTA format

Counts of Amino Acids

'A': 3, 'R': 5, 'N': 5, 'D': 5, 'C': 14, 'Q': 6, 'E': 7, 'G': 15, 'H': 3, 'I': 5, 'L': 9, 'K': 13, 'M': 5, 'F': 4, 'P': 7, 'S': 12, 'T': 3, 'W': 3, 'Y': 6, 'V': 6

Frequencies of Amino Acids

'A': 2.21%, 'R': 3.68%, 'N': 3.68%, 'D': 3.68%, 'C': 10.29%, 'Q': 4.41%, 'E': 5.15%, 'G': 11.03%, 'H': 2.21%, 'I': 3.68%, 'L': 6.62%, 'K': 9.56%, 'M': 3.68%, 'F': 2.94%, 'P': 5.15%, 'S': 8.82%, 'T': 2.21%, 'W': 2.21%, 'Y': 4.41%, 'V': 4.41%

Missing Amino Acid(s)

No Amino Acid(s) are missing in this protein

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

A, H, T, W

Hydrophobic Amino Acid(s) Count

Hydrophilic Amino Acid(s) Count

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	15197.6 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	55.147	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	39.043	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.439	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.618	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	8.319	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	5.409	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.243, 0.287, 0.176 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.096	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	25440, 26315	Computed by ProtParam module (biopython 1.79)

4.1 Target Organism(s)

M.luteus (Gram-negative)

4.2 Antimicrobial Activity

Antibiotic, Antimicrobial, Bacteriolytic enzyme, Anti-gram-negative

4.3 Enzymatic Activity

Glycosidase, Hydrolase

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: Takeshita K, Hashimoto Y, Thujihata Y, et al. Determination of the complete cDNA sequence, construction of expression systems, and elucidation of fibrinolytic activity for Tapes japonica lysozyme. Protein Expr Purif. 2004;36(2):254-62. Published 2004 Aug. doi:10.1016/j.pep.2004.05.001

PMID: 15249048

Citation 2: Ito Y, Yoshikawa A, Hotani T, et al. Amino acid sequences of lysozymes newly purified from invertebrates imply wide distribution of a novel class in the lysozyme family. Eur J Biochem. 1999;259(1-2):456-61. Published 1999 Jan. doi:10.1046/j.1432-1327.1999.00064.x

PMID: 9914527

Citation 3: Takeshita K, Hashimoto Y, Ueda T, et al. A small chimerically bifunctional monomeric protein: Tapes japonica lysozyme. Cell Mol Life Sci. 2003;60(9):1944-51. Published 2003 Sep. doi:10.1007/s00018-003-3082-z

PMID: 14523554

Citation 4: Goto T, Abe Y, Kakuta Y, et al. Crystal structure of Tapes japonica Lysozyme with substrate analogue: structural basis of the catalytic mechanism and manifestation of its chitinase activity accompanied by quaternary structural change. J Biol Chem. 2007;282(37):27459-27467. Published 2007 Sep 14. doi:10.1074/jbc.M704555200

PMID: 17631496

5.2 Protein Sequence Databases

5.3 3D Structure Databases

	Sl. no.	PDB ID	Method	Resolution	Access Links	3D View

AlphaFoldDB: Q8IU26

5.4 Nucleotide Sequence Databases

Sl. no.	Accession(s)	Access Link(s)
1.	AB091383	GenBank \|\| EMBL
2.	AB055701	GenBank \|\| EMBL

RefSeq: Not found

5.5 Protein-Protein Interaction Databases

STRING: Not found

IntAct: Not found

BioGRID: Not found

5.6 Ligand Databases

BindingDB: Not found

DrugBank: Not found

ChEMBL: Not found

5.7 Family & Domain Databases

InterPro: IPR008597, IPR023346

PANTHER: PTHR11195

PROSITE: PS51909

5.8 Genome Annotation Databases

Ensembl: Not found

5.9 Phylogenomic Databases

GeneTree: Not found

5.10 Enzyme & Pathway Databases

BRENDA: Not found

BioCyc: Not found

5.11 Protein-RNA Interaction Databases

RNAct: Not found

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