AMPDB_700 | Endolysin

1 General Description

AMPDB ID: AMPDB_700

Protein Names: Endolysin (EC 3.2.1.17) (Beta-1;4-N-acetylmuramidase) (Lysozyme) (Lytic enzyme) (Muramidase) (Protein P15)

Protein Family: Glycosyl hydrolase 24 family

Gene Name: XV

Source Organism: Enterobacteria phage PRD1 (Bacteriophage PRD1)

Protein Length: 149 AA

Protein Existence: Evidence at protein level

2 Protein Sequence & Composition

MQYTLWDIISRVESNGNLKALRFEPEYYQRRMERGDWDNSIIQNIRAANKCSLGTARMIYCSSWGAVQIMGFNLYLNGAFNLSVAHFMENEAYQVNEFRRFLLKNGLTEYTPERLASDKAARVKFAKVYNGAESYADLILQACQFYGVK

FASTA format

Counts of Amino Acids

'A': 15, 'R': 11, 'N': 12, 'D': 5, 'C': 3, 'Q': 7, 'E': 10, 'G': 9, 'H': 1, 'I': 8, 'L': 13, 'K': 7, 'M': 5, 'F': 8, 'P': 2, 'S': 9, 'T': 4, 'W': 3, 'Y': 10, 'V': 7

Frequencies of Amino Acids

'A': 10.07%, 'R': 7.38%, 'N': 8.05%, 'D': 3.36%, 'C': 2.01%, 'Q': 4.7%, 'E': 6.71%, 'G': 6.04%, 'H': 0.67%, 'I': 5.37%, 'L': 8.72%, 'K': 4.7%, 'M': 3.36%, 'F': 5.37%, 'P': 1.34%, 'S': 6.04%, 'T': 2.68%, 'W': 2.01%, 'Y': 6.71%, 'V': 4.7%

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

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	17268.7 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	78.658	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	28.769	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.338	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.582	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	8.753	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	2.912	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.329, 0.215, 0.289 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.141	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	31400, 31525	Computed by ProtParam module (biopython 1.79)

4.1 Target Organism(s)

Gram Negative Bacteria

4.2 Antimicrobial Activity

Antimicrobial, Bacteriolytic enzyme, Anti-gram-negative

4.3 Enzymatic Activity

Glycosidase, Hydrolase

4.4 Inhibitory Effect

4.5 Other Biological Activity

Cytolysis, Non-hemolytic, Non-ribosomal

Activity data manually curated from Literature and UniProt

5 Database Cross-references

5.1 Literature Database

Citation 1: Pakula TM, Savilahti H, Bamford DH, et al. Comparison of the amino acid sequence of the lytic enzyme from broad-host-range bacteriophage PRD1 with sequences of other cell-wall-peptidoglycan lytic enzymes. Eur J Biochem. 1989;180(1):149-52. Published 1989 Mar 1. doi:10.1111/j.1432-1033.1989.tb14625.x

PMID: 2651121

Citation 2: Savilahti H, Bamford DH, Bamford DH. The complete nucleotide sequence of the left very early region of Escherichia coli bacteriophage PRD1 coding for the terminal protein and the DNA polymerase. Gene. 1987;57(1):121-30. Published 1987. doi:10.1016/0378-1119(87)90183-1

PMID: 3322943

Citation 3: Bamford JK, HÃ¤nninen AL, Pakula TM, et al. Genome organization of membrane-containing bacteriophage PRD1. Virology. 1991;183(2):658-76. Published 1991 Aug. doi:10.1016/0042-6822(91)90995-n

PMID: 1853567

Citation 4: Saren AM, Ravantti JJ, Benson SD, et al. A snapshot of viral evolution from genome analysis of the tectiviridae family. J Mol Biol. 2005;350(3):427-40. Published 2005 Jul 15. doi:10.1016/j.jmb.2005.04.059

PMID: 15946683

Citation 5: Caldentey J, HÃ¤nninen AL, Bamford DH, et al. Gene XV of bacteriophage PRD1 encodes a lytic enzyme with muramidase activity. Eur J Biochem. 1994;225(1):341-6. Published 1994 Oct 1. doi:10.1111/j.1432-1033.1994.00341.x

PMID: 7925454

Citation 6: Rydman PS, Bamford DH, Bamford DH. The lytic enzyme of bacteriophage PRD1 is associated with the viral membrane. J Bacteriol. 2002;184(1):104-10. Published 2002 Jan. doi:10.1128/JB.184.1.104-110.2002

PMID: 11741849

5.2 Protein Sequence Databases

5.3 3D Structure Databases

AlphaFoldDB: P13559

5.4 Nucleotide Sequence Databases

Sl. no.	Accession(s)	Access Link(s)
1.	X14980	GenBank \|\| EMBL
2.	M22161	GenBank \|\| EMBL
3.	AY848689	GenBank \|\| EMBL

RefSeq: NP_040683.1

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: IPR024408, IPR016284

PANTHER: Not found

PROSITE: Not found

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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