AMPDB_796 | Lysozyme RrrD

PEPTIDE SUMMARY

Lysozyme RrrD

1 General Description

AMPDB ID: AMPDB_796

Protein Names: Lysozyme RrrD (EC 3.2.1.17) (Endolysin) (Lysis protein) (Muramidase)

Protein Family: Glycosyl hydrolase 24 family

Gene Name: rrrD arrD ybcS b0555 JW0544

Source Organism: Escherichia coli (strain K12)

Protein Length: 165 AA

Protein Existence: Evidence at protein level

2 Protein Sequence & Composition

2.1 Sequence

MPPSLRKAVAAAIGGGAIAIASVLITGPSGNDGLEGVSYIPYKDIVGVWTVCHGHTGKDIMLGKTYTKAECKALLNKDLATVARQINPYIKVDIPETTRGALYSFVYNVGAGNFRTSTLLRKINQGDIKGACDQLRRWTYAGGKQWKGLMTRREIEREVCLWGQQ

FASTA format

2.2 Composition

Counts of Amino Acids

'A': 15, 'R': 10, 'N': 6, 'D': 7, 'C': 4, 'Q': 6, 'E': 6, 'G': 20, 'H': 2, 'I': 13, 'L': 13, 'K': 12, 'M': 3, 'F': 2, 'P': 6, 'S': 6, 'T': 12, 'W': 4, 'Y': 7, 'V': 11

Frequencies of Amino Acids

'A': 9.09%, 'R': 6.06%, 'N': 3.64%, 'D': 4.24%, 'C': 2.42%, 'Q': 3.64%, 'E': 3.64%, 'G': 12.12%, 'H': 1.21%, 'I': 7.88%, 'L': 7.88%, 'K': 7.27%, 'M': 1.82%, 'F': 1.21%, 'P': 3.64%, 'S': 3.64%, 'T': 7.27%, 'W': 2.42%, 'Y': 4.24%, 'V': 6.67%

Missing Amino Acid(s)

No Amino Acid(s) are missing in this protein

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

F, H

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	17971.8 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	89.879	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	36.57	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.162	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.743	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	9.918	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	8.936	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.303, 0.23, 0.224 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.079	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	32430, 32680	Computed by ProtParam module (biopython 1.79)

4 Activity Details

4.1 Target Organism(s)

E.coli (Gram-negative), S.typhi

4.2 Antimicrobial Activity

Antimicrobial, Bacteriolytic enzyme, Anti-gram-negative

4.3 Enzymatic Activity

Glycosidase, Hydrolase

4.4 Inhibitory Effect

Not found

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

5.1.1 PubMed

Citation 1: Blattner FR, Plunkett G 3rd, Bloch CA, et al. The complete genome sequence of Escherichia coli K-12. Science. 1997;277(5331):1453-62. Published 1997 Sep 5. doi:10.1126/science.277.5331.1453

PMID: 9278503

Citation 2: Hayashi K, Morooka N, Yamamoto Y, et al. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006;2:2006.0007. Published 2006. doi:10.1038/msb4100049

PMID: 16738553

Citation 3: Srividhya KV, Krishnaswamy S, Krishnaswamy S. Subclassification and targeted characterization of prophage-encoded two-component cell lysis cassette. J Biosci. 2007;32(5):979-90. Published 2007 Aug. doi:10.1007/s12038-007-0097-x

PMID: 17914239

Citation 4: Toba FA, Thompson MG, Campbell BR, et al. Role of DLP12 lysis genes in Escherichia coli biofilm formation. Microbiology (Reading). 2011;157(Pt 6):1640-1650. Published 2011 Jun. doi:10.1099/mic.0.045161-0

PMID: 21415116

5.2 Protein Sequence Databases

UniProt: P78285

5.3 3D Structure Databases

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

AlphaFoldDB: P78285

5.4 Nucleotide Sequence Databases

Sl. no.	Accession(s)	Access Link(s)
1.	U82598	GenBank \|\| EMBL
2.	U00096	GenBank \|\| EMBL
3.	AP009048	GenBank \|\| EMBL

CCDS: Not found

RefSeq: NP_415087.1, WP_001135281.1

5.5 Protein-Protein Interaction Databases

STRING: 511145.b0555

IntAct: P78285

MINT: Not found

DIP: Not found

BioGRID: 4259885

5.6 Ligand Databases

BindingDB: Not found

DrugBank: Not found

ChEMBL: Not found

5.7 Family & Domain Databases

InterPro: IPR034690, IPR002196, IPR023346, IPR023347, IPR043688

PANTHER: Not found

PROSITE: Not found

5.8 Genome Annotation Databases

Ensembl: Not found

KEGG: ecj:JW0544, eco:b0555

5.9 Phylogenomic Databases

GeneTree: Not found

5.10 Enzyme & Pathway Databases

BRENDA: Not found

BioCyc: EcoCyc:G6310-MON, MetaCyc:G6310-MON

5.11 Protein-RNA Interaction Databases

RNAct: Not found

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