Detailed information NTG0000150

Experimentally validated

Overview

• Name: lytA
• Type: Auxiliary factor
• Locus tag: SP_RS09740
• Genome accession: NC_003028
• Coordinates: 1840405..1841361 (-)
• Length: 318 a.a.
• NCBI ID: WP_000405234.1
• Uniprot ID: B9W4U9
• Organism: Streptococcus pneumoniae TIGR4
• Function: increase the efficiency of the cell lysis Cell lysis

Function

The two peptidoglycan-hydrolyzing enzymes LytA and LytC, which are present in non-competent target cells, contribute to enhanced lysis during fratricide. Studies have shown that the muralytic activity of CbpD activates LytA and LytC in target cells, thereby accelerating and increasing the efficiency of the lysis reaction

Genomic Context

Location: 1835405..1846361

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
SP_RS09700 (SP_1930)	-	1836471..1836731 (-)	261	WP_001209211.1	hypothetical protein	-
SP_RS09705 (SP_1931)	-	1836790..1837341 (-)	552	WP_001111249.1	hypothetical protein	-
SP_RS09710	-	1837331..1837528 (-)	198	WP_000890144.1	hypothetical protein	-
SP_RS09715 (SP_1933)	-	1837532..1838326 (-)	795	WP_001101210.1	hypothetical protein	-
SP_RS09720 (SP_1934)	-	1838734..1839159 (-)	426	WP_000204063.1	hypothetical protein	-
SP_RS09725 (SP_1935)	-	1839288..1839647 (-)	360	WP_000749819.1	ImmA/IrrE family metallo-endopeptidase	-
SP_RS09730	-	1839693..1839899 (-)	207	WP_000366093.1	hypothetical protein	-
SP_RS09735 (SP_1936)	-	1839886..1840047 (-)	162	WP_000289348.1	helix-turn-helix domain-containing protein	-
SP_RS09740 (SP_1937)	lytA	1840405..1841361 (-)	957	WP_000405234.1	N-acetylmuramoyl-L-alanine amidase LytA	Auxiliary factor
SP_RS09745 (SP_1939)	-	1841737..1843107 (-)	1371	WP_001036271.1	MATE family efflux transporter	-
SP_RS09750 (SP_1940)	recA	1843413..1844579 (-)	1167	WP_001085462.1	recombinase RecA	Machinery gene
SP_RS09755 (SP_1941)	cinA	1844634..1845890 (-)	1257	WP_000642718.1	competence/damage-inducible protein A	Machinery gene

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
cbpD	lytA	positive effect
cbpD	lytC	positive effect
comM	cbpD	negative effect
comE	comM	positive effect
comE	comE	positive effect
comE	comX/comX1	positive effect
comE	comW	positive effect
comE	comA	positive effect
comE	comB	positive effect
comE	comX/comX2	positive effect
comE	comD/comD2	positive effect
comE	comC/comC2	positive effect
comD/comD2	comE	positive effect
stkP	comE	positive effect
comX/comX1	late competence genes	positive effect
clpP	comX/comX1	negative effect
comW	comX/comX1	positive effect
clpE	comX/comX1	negative effect
comW	comX/comX2	positive effect
clpP	comW	negative effect
mecA	comW	negative effect
clpC	comW	negative effect
comA	comC/comC2	positive effect
comB	comC/comC2	positive effect
comX/comX2	late competence genes	positive effect
clpP	comX/comX2	negative effect
clpE	comX/comX2	negative effect
comC/comC2	comD/comD2	positive effect
ciaH	comC/comC2	negative effect
htrA	comC/comC2	negative effect
ciaR	comC/comC2	negative effect
comX/comX2	late competence genes	positive effect
comX/comX1	late competence genes	positive effect
ciaH	htrA	positive effect
htrA	comEC/celB	negative effect
htrA	comEA/celA/cilE	negative effect
ciaR	htrA	positive effect

Sequence

Protein

• Length: 318 a.a.
• Molecular weight: 36544.38 Da
• Isoelectric Point: 4.9850

>NTDB_id=150 SP_RS09740 WP_000405234.1 1840405..1841361(-) (lytA) [Streptococcus pneumoniae TIGR4]
MEINVSKLRTDLPQVGVQPYRQVHAHSTGNPHSTVQNEADYHWRKDPELGFFSHIVGNGCIMQVGPVDNGAWDVGGGWNA
ETYAAVELIESHSTKEEFMTDYRLYIELLRNLADEAGLPKTLDTGSLAGIKTHEYCTNNQPNNHSDHVDPYPYLAKWGIS
REQFKHDIENGLTIETGWQKNDTGYWYVHSDGSYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATG
WKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADKPEFTVEPDGLITVK

Nucleotide

• Length: 957 bp

>NTDB_id=150 SP_RS09740 WP_000405234.1 1840405..1841361(-) (lytA) [Streptococcus pneumoniae TIGR4]
ATGGAAATTAATGTGAGTAAATTAAGAACAGATTTGCCTCAAGTCGGCGTGCAACCATATAGGCAAGTACACGCACACTC
AACTGGGAATCCGCATTCAACCGTACAGAATGAAGCGGATTATCACTGGCGGAAAGACCCAGAATTAGGTTTTTTCTCGC
ACATTGTTGGGAACGGTTGCATCATGCAGGTAGGACCTGTTGATAATGGTGCCTGGGACGTTGGGGGCGGTTGGAATGCT
GAGACCTATGCAGCGGTTGAACTGATTGAAAGCCATTCAACCAAAGAAGAGTTCATGACGGACTACCGCCTTTATATCGA
ACTCTTACGCAATCTAGCAGATGAAGCAGGTTTGCCGAAAACGCTTGATACAGGGAGTTTAGCTGGAATTAAAACGCACG
AGTATTGCACGAATAACCAACCAAACAACCACTCAGACCACGTTGACCCTTATCCATATCTTGCTAAATGGGGCATTAGC
CGTGAGCAGTTTAAGCATGATATTGAGAACGGCTTGACGATTGAAACAGGCTGGCAGAAGAATGACACTGGCTACTGGTA
CGTACATTCAGACGGCTCTTATCCAAAAGACAAGTTTGAGAAAATCAATGGCACTTGGTACTACTTTGACAGTTCAGGCT
ATATGCTTGCAGACCGCTGGAGGAAGCACACAGACGGCAACTGGTACTGGTTCGACAACTCAGGCGAAATGGCTACAGGC
TGGAAGAAAATCGCTGATAAGTGGTACTATTTCAACGAAGAAGGTGCCATGAAGACAGGCTGGGTCAAGTACAAGGACAC
TTGGTACTACTTAGACGCTAAAGAAGGCGCCATGGTATCAAATGCCTTTATCCAGTCAGCGGACGGAACAGGCTGGTACT
ACCTCAAACCAGACGGAACACTGGCAGACAAGCCAGAATTCACAGTAGAGCCAGATGGCTTGATTACAGTAAAATAA

Domains

Predicted by InterproScan.

• Putative cell wall binding repeat (Choline_bind_1) (198-215)

• Putative cell wall binding repeat (Choline_bind_1) (218-237)

• Choline-binding repeat (Choline_bind_3) (238-283)

3D structure

• AlphaFold DB: B9W4U9

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
lytA	Streptococcus pneumoniae Rx1	99.686	100	0.997
lytA	Streptococcus pneumoniae D39	99.686	100	0.997
lytA	Streptococcus pneumoniae R6	99.686	100	0.997

References

• [1]: Vegard Eldholm et al. (2009) Fratricide in Streptococcus pneumoniae: contributions and role of the cell wall hydrolases CbpD, LytA and LytC. Microbiology (Reading, England) 155(Pt 7):2223-2234. [PMID: 19389766]