Detailed information NTG0000214

Experimentally validated

Overview

• Name: cbpD
• Type: Auxiliary factor
• Locus tag: SPD_RS10730
• Genome accession: NC_008533
• Coordinates: 2006513..2007859 (-)
• Length: 448 a.a.
• NCBI ID: WP_000698544.1
• Uniprot ID: A0A0H2ZP12
• Organism: Streptococcus pneumoniae D39
• Function: fratricide process; lyse non-competent cells Cell lysis

Function

CbpD is a murein hydrolase that is involved in the fratricide process during competence. It is responsible for degrading the cell wall of non-competent cells, releasing DNA into the environment for uptake by competent cells.

Genomic Context

Location: 2001513..2012859

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
SPD_RS10705 (SPD_2023)	-	2002896..2003354 (-)	459	WP_001211279.1	CtsR family transcriptional regulator	-
SPD_RS10710 (SPD_2024)	-	2003473..2004201 (-)	729	WP_000136224.1	ABC transporter ATP-binding protein	-
SPD_RS10715 (SPD_2025)	-	2004201..2005208 (-)	1008	WP_000754546.1	ABC transporter substrate-binding protein	-
SPD_RS10720 (SPD_2026)	-	2005246..2006004 (-)	759	WP_001245132.1	ABC transporter permease	-
SPD_RS10725 (SPD_2027)	-	2005967..2006257 (-)	291	WP_000647661.1	thiamine-binding protein	-
SPD_RS10730 (SPD_2028)	cbpD	2006513..2007859 (-)	1347	WP_000698544.1	choline binding-anchored murein hydrolase CbpD	Auxiliary factor
SPD_RS10735 (SPD_2029)	-	2007948..2008214 (-)	267	WP_001278167.1	Veg family protein	-
SPD_RS10740 (SPD_2030)	dnaB	2008216..2009568 (-)	1353	WP_000852486.1	replicative DNA helicase	-
SPD_RS10745 (SPD_2031)	rplI	2009612..2010064 (-)	453	WP_000864220.1	50S ribosomal protein L9	-
SPD_RS10750 (SPD_2032)	-	2010061..2012034 (-)	1974	WP_000715109.1	DHH family phosphoesterase	-
SPD_RS10755 (SPD_2033)	hpf	2012170..2012718 (-)	549	WP_000599104.1	ribosome hibernation-promoting factor, HPF/YfiA family	-

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	comW	positive effect
comE	comA	positive effect
comE	comB	positive effect
comE	comE	positive effect
comE	comX/comX1	positive effect
comE	comD/comD1	positive effect
comE	comX/comX2	positive effect
comE	comC/comC1	positive effect
comD/comD1	comE	positive effect
stkP	comE	positive effect
ccpA	comE	positive effect
comW	comX/comX1	positive effect
comX/comX1	late competence genes	positive effect
clpE	comX/comX1	negative effect
clpP	comX/comX1	negative effect
comW	comX/comX2	positive effect
comX/comX2	late competence genes	positive effect
clpE	comX/comX2	negative effect
clpP	comX/comX2	negative effect
mecA	comW	negative effect
clpC	comW	negative effect
clpP	comW	negative effect
comA	comC/comC1	positive effect
comC/comC1	comD/comD1	positive effect
ccpA	comC/comC1	positive effect
comB	comC/comC1	positive effect
htrA	comC/comC1	negative effect
ciaR	comC/comC1	negative effect
ciaH	comC/comC1	negative effect
ccpA	comD/comD1	positive effect
comX/comX2	late competence genes	positive effect
comX/comX1	late competence genes	positive effect
htrA	comEA/celA/cilE	negative effect
htrA	comEC/celB	negative effect
ciaR	htrA	positive effect
ciaH	htrA	positive effect

Sequence

Protein

• Length: 448 a.a.
• Molecular weight: 50369.89 Da
• Isoelectric Point: 9.2357

>NTDB_id=214 SPD_RS10730 WP_000698544.1 2006513..2007859(-) (cbpD) [Streptococcus pneumoniae D39]
MKILPFIARGTSYYLKMSVKKLVPFLVVGLMLAAGDSVHAYSRGNGSIARGDDYPAYYKNGSQEIDQWRMYSRQCTSFVA
FRLSNVNGFEIPAAYGNANEWGHRARREGYRVDNTPTIGSITWSTAGTYGHVAWVSNVMGDQIEIEEYNYGYTESYNKRV
IKANTMTGFIHFKDLDSGSVGNSQSSASTGGTHYFKTKSAIKTEPLVSATVIDYYYPGEKVHYDQILEKDGYKWLSYTAY
NGSYRYVQLEAVNKNPLGNSVLSSTGGTHYFKIKSAIKTEPLVSATVIDYYYPGEKVHYDQILEKDGYKWLSYTAYNGSR
RYIQLEGVTSSQNYQNQSGNISSYGSNNSSTVGWKKINGSWYHFKSNGSKSTGWLKDGSSWYYLKLSGEMQTGWLKENGS
WYYLGSSGAMKTGWYQVSGEWYYSYSSGALAINTTVDGYRVNSDGERV

Nucleotide

• Length: 1347 bp

>NTDB_id=214 SPD_RS10730 WP_000698544.1 2006513..2007859(-) (cbpD) [Streptococcus pneumoniae D39]
ATGAAAATTTTACCGTTTATAGCAAGAGGAACAAGTTATTACTTGAAGATGTCAGTTAAAAAGCTTGTTCCTTTTTTAGT
AGTAGGATTGATGCTAGCAGCTGGTGATAGTGTCCATGCCTATTCCAGAGGAAATGGATCGATTGCGCGTGGGGATGATT
ATCCTGCTTATTATAAAAATGGGAGCCAGGAGATTGATCAGTGGCGCATGTATTCTCGTCAGTGTACTTCTTTTGTAGCC
TTTCGTTTGAGTAATGTCAATGGTTTTGAAATTCCGGCAGCTTATGGAAATGCGAATGAATGGGGACATCGTGCTCGTCG
GGAAGGTTATCGTGTAGATAATACACCGACGATTGGTTCCATTACTTGGTCTACTGCAGGAACTTATGGTCATGTTGCCT
GGGTGTCAAATGTAATGGGAGATCAGATTGAGATTGAGGAATATAACTATGGTTATACAGAATCCTATAATAAACGAGTT
ATAAAAGCAAACACGATGACAGGATTTATTCATTTTAAAGATTTGGATAGTGGCAGTGTTGGGAATAGTCAATCCTCAGC
TTCAACAGGCGGAACTCATTATTTTAAGACCAAGTCTGCTATTAAAACTGAACCCCTAGTTAGTGCAACTGTGATTGATT
ACTATTATCCTGGGGAGAAGGTTCATTATGATCAGATACTTGAAAAAGACGGCTATAAGTGGTTGAGTTATACTGCCTAT
AATGGAAGCTATCGTTATGTTCAATTGGAGGCTGTGAATAAAAATCCTCTAGGTAATTCTGTTCTTTCTTCAACAGGAGG
AACTCATTATTTTAAGATCAAGTCTGCTATTAAAACTGAACCCCTAGTTAGTGCAACTGTGATTGATTACTATTATCCTG
GAGAGAAGGTTCATTATGATCAGATACTTGAAAAAGACGGCTATAAGTGGTTGAGTTATACGGCTTATAACGGAAGTCGT
CGCTATATACAGCTAGAGGGAGTGACTTCTTCACAAAATTATCAGAATCAATCAGGAAATATCTCTAGCTATGGATCCAA
TAATAGTTCAACTGTCGGTTGGAAGAAAATAAATGGTAGTTGGTATCATTTCAAATCAAATGGTTCTAAATCAACAGGAT
GGCTGAAAGACGGTTCTAGCTGGTATTATTTGAAATTATCTGGTGAAATGCAGACAGGATGGTTAAAGGAGAATGGCTCG
TGGTATTATCTGGGTAGTTCAGGGGCAATGAAAACAGGCTGGTACCAGGTCTCTGGTGAGTGGTATTATTCTTACTCTTC
AGGCGCCTTAGCTATTAATACGACGGTGGATGGCTACAGAGTAAACAGTGATGGAGAACGAGTATAG

Domains

Predicted by InterproScan.

• CHAP domain (CHAP) (68-149)

• Bacterial SH3 domain (SH3_5) (264-325)

• Bacterial SH3 domain (SH3_5) (186-249)

• Choline-binding repeat (Choline_bind_3) (352-390)

• Choline-binding repeat (Choline_bind_3) (392-434)

3D structure

• AlphaFold DB: A0A0H2ZP12

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
cbpD	Streptococcus pneumoniae R6	99.777	100	0.998
cbpD	Streptococcus pneumoniae Rx1	99.777	100	0.998
cbpD	Streptococcus pneumoniae TIGR4	97.545	100	0.975
cbpD	Streptococcus mitis NCTC 12261	60.667	100	0.74
cbpD	Streptococcus mitis SK321	60.044	100	0.731
cbpD/crfP	Streptococcus suis strain ZY05719	43.689	100	0.444

References

• [1]: Hongsheng Ji et al. (2023) Function analysis of choline binding domains (CBDs) of LytA, LytC and CbpD in biofilm formation of Streptococcus pneumoniae. Microbial Pathogenesis 174:105939. [PMID: 36521655]
• [2]: Vikrant Minhas et al. (2023) Competence remodels the pneumococcal cell wall exposing key surface virulence factors that mediate increased host adherence. PLoS Biology 21(1):e3001990. [PMID: 36716340]
• [3]: Truls Johan Biørnstad et al. (2012) Deletion of the murein hydrolase CbpD reduces transformation efficiency in Streptococcus thermophilus. Microbiology (Reading, England) 158(Pt 4):877-885. [PMID: 22241050]
• [4]: Vegard Eldholm et al. (2010) Pneumococcal CbpD is a murein hydrolase that requires a dual cell envelope binding specificity to kill target cells during fratricide. Molecular Microbiology 76(4):905-17. [PMID: 20384696]
• [5]: 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]
• [6]: Leiv Sigve Håvarstein et al. (2006) New insights into the pneumococcal fratricide: relationship to clumping and identification of a novel immunity factor. Molecular Microbiology 59(4):1297-307. [PMID: 16430701]
• [7]: Sébastien Guiral et al. (2005) Competence-programmed predation of noncompetent cells in the human pathogen Streptococcus pneumoniae: genetic requirements. Proceedings of The National Academy of Sciences of The United States of America 102(24):8710-5. [PMID: 15928084]
• [8]: Louise Kausmally et al. (2005) Choline-binding protein D (CbpD) in Streptococcus pneumoniae is essential for competence-induced cell lysis. Journal of Bacteriology 187(13):4338-45. [PMID: 15968042]