Detailed information NTG0000185

Experimentally validated

Overview

• Name: lytA
• Type: Auxiliary factor
• Locus tag: SPR_RS08815
• Genome accession: NC_003098
• Coordinates: 1722069..1723025 (-)
• Length: 318 a.a.
• NCBI ID: WP_000405235.1
• Uniprot ID: Q7ZAK4
• Organism: Streptococcus pneumoniae R6
• 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: 1717069..1728025

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
SPR_RS08775 (spr1746)	-	1718122..1718382 (-)	261	WP_001209210.1	hypothetical protein	-
SPR_RS08780 (spr1747)	-	1718441..1718992 (-)	552	WP_001111255.1	hypothetical protein	-
SPR_RS08785 (spr1748)	-	1718982..1719179 (-)	198	WP_000890144.1	hypothetical protein	-
SPR_RS08790 (spr1749)	-	1719183..1719977 (-)	795	WP_001101210.1	hypothetical protein	-
SPR_RS08795 (spr1750)	-	1720385..1720810 (-)	426	WP_000204065.1	hypothetical protein	-
SPR_RS08800 (spr1751)	-	1720939..1721298 (-)	360	WP_000749822.1	ImmA/IrrE family metallo-endopeptidase	-
SPR_RS08805 (spr1752)	-	1721344..1721550 (-)	207	WP_000366091.1	hypothetical protein	-
SPR_RS08810 (spr1753)	-	1721537..1721710 (-)	174	WP_000289349.1	helix-turn-helix domain-containing protein	-
SPR_RS08815 (spr1754)	lytA	1722069..1723025 (-)	957	WP_000405235.1	N-acetylmuramoyl-L-alanine amidase LytA	Auxiliary factor
SPR_RS08820 (spr1756)	-	1723401..1724771 (-)	1371	WP_001036271.1	MATE family efflux transporter	-
SPR_RS08825 (spr1757)	recA	1725078..1726244 (-)	1167	WP_001085462.1	recombinase RecA	Machinery gene
SPR_RS08830 (spr1758)	cinA	1726299..1727555 (-)	1257	WP_000642700.1	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	comB	positive effect
comB	comC/comC1	positive effect
comE	comW	positive effect
comW	comX/comX1	positive effect
comW	comX/comX2	positive effect
clpP	comW	negative effect
mecA	comW	negative effect
clpC	comW	negative effect
comE	comC/comC1	positive effect
comC/comC1	comD/comD1	positive effect
comA	comC/comC1	positive effect
ciaH	comC/comC1	negative effect
ciaR	comC/comC1	negative effect
htrA	comC/comC1	negative effect
comE	comX/comX1	positive effect
comX/comX1	late competence genes	positive effect
clpE	comX/comX1	negative effect
clpP	comX/comX1	negative effect
comE	comA	positive effect
comE	comD/comD1	positive effect
comD/comD1	comE	positive effect
comE	comX/comX2	positive effect
comX/comX2	late competence genes	positive effect
clpE	comX/comX2	negative effect
clpP	comX/comX2	negative effect
comE	comE	positive effect
stkP	comE	positive effect
ciaH	htrA	positive effect
ciaR	htrA	positive effect
htrA	comEA/celA/cilE	negative effect
htrA	comEC/celB	negative effect
comX/comX2	late competence genes	positive effect
comX/comX1	late competence genes	positive effect

Sequence

Protein

• Length: 318 a.a.
• Molecular weight: 36572.40 Da
• Isoelectric Point: 4.9850

>NTDB_id=185 SPR_RS08815 WP_000405235.1 1722069..1723025(-) (lytA) [Streptococcus pneumoniae R6]
MEINVSKLRTDLPQVGVQPYRQVHAHSTGNPHSTVQNEADYHWRKDPELGFFSHIVGNGCIMQVGPVDNGAWDVGGGWNA
ETYAAVELIESHSTKEEFMTDYRLYIELLRNLADEAGLPKTLDTGSLAGIKTHEYCTNNQPNNHSDHVDPYPYLAKWGIS
REQFKHDIENGLTIETGWQKNDTGYWYVHSDGSYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATG
WKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADRPEFTVEPDGLITVK

Nucleotide

• Length: 957 bp

>NTDB_id=185 SPR_RS08815 WP_000405235.1 1722069..1723025(-) (lytA) [Streptococcus pneumoniae R6]
ATGGAAATTAATGTGAGTAAATTAAGAACAGATTTGCCTCAAGTCGGCGTGCAACCATATAGGCAAGTACACGCACACTC
AACTGGGAATCCGCATTCAACCGTACAGAATGAAGCGGATTATCACTGGCGGAAAGACCCAGAATTAGGTTTTTTCTCGC
ACATTGTTGGGAACGGTTGCATCATGCAGGTAGGACCTGTTGATAATGGTGCCTGGGACGTTGGGGGCGGTTGGAATGCT
GAGACCTATGCAGCGGTTGAACTGATTGAAAGCCATTCAACCAAAGAAGAGTTCATGACGGACTACCGCCTTTATATCGA
ACTCTTACGCAATCTAGCAGATGAAGCAGGTTTGCCGAAAACGCTTGATACAGGGAGTTTAGCTGGAATTAAAACGCACG
AGTATTGCACGAATAACCAACCAAACAACCACTCAGACCACGTTGACCCTTATCCATATCTTGCTAAATGGGGCATTAGC
CGTGAGCAGTTTAAGCATGATATTGAGAACGGCTTGACGATTGAAACAGGCTGGCAGAAGAATGACACTGGCTACTGGTA
CGTACATTCAGACGGCTCTTATCCAAAAGACAAGTTTGAGAAAATCAATGGCACTTGGTACTACTTTGACAGTTCAGGCT
ATATGCTTGCAGACCGCTGGAGGAAGCACACAGACGGCAACTGGTACTGGTTCGACAACTCAGGCGAAATGGCTACAGGC
TGGAAGAAAATCGCTGATAAGTGGTACTATTTCAACGAAGAAGGTGCCATGAAGACAGGCTGGGTCAAGTACAAGGACAC
TTGGTACTACTTAGACGCTAAAGAAGGCGCCATGGTATCAAATGCCTTTATCCAGTCAGCGGACGGAACAGGCTGGTACT
ACCTCAAACCAGACGGAACACTGGCAGACAGGCCAGAATTCACAGTAGAGCCAGATGGCTTGATTACAGTAAAATAA

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: Q7ZAK4

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
lytA	Streptococcus pneumoniae Rx1	100	100	1
lytA	Streptococcus pneumoniae D39	100	100	1
lytA	Streptococcus pneumoniae TIGR4	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]