Detailed information    

experimental Experimentally validated

Overview

Name   cbpD   Type   Auxiliary factor
Locus tag   SPR_RS10215 Genome accession   NC_003098
Coordinates   1999012..2000358 (-) Length   448 a.a.
NCBI ID   WP_000698573.1    Uniprot ID   A0A2U3RWM9
Organism   Streptococcus pneumoniae R6     
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: 1994012..2005358
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SPR_RS10190 (spr2001) - 1995395..1995853 (-) 459 WP_001211279.1 CtsR family transcriptional regulator -
  SPR_RS10195 (spr2002) - 1995972..1996700 (-) 729 WP_000136224.1 ABC transporter ATP-binding protein -
  SPR_RS10200 (spr2003) - 1996700..1997707 (-) 1008 WP_000754546.1 ABC transporter substrate-binding protein -
  SPR_RS10205 (spr2004) - 1997745..1998503 (-) 759 WP_001245132.1 ABC transporter permease -
  SPR_RS10210 (spr2005) - 1998466..1998756 (-) 291 WP_000647661.1 thiamine-binding protein -
  SPR_RS10215 (spr2006) cbpD 1999012..2000358 (-) 1347 WP_000698573.1 choline binding-anchored murein hydrolase CbpD Auxiliary factor
  SPR_RS10220 (spr2007) - 2000447..2000713 (-) 267 WP_001278167.1 Veg family protein -
  SPR_RS10225 (spr2008) dnaB 2000715..2002067 (-) 1353 WP_000852486.1 replicative DNA helicase -
  SPR_RS10230 (spr2009) rplI 2002111..2002563 (-) 453 WP_000864220.1 50S ribosomal protein L9 -
  SPR_RS10235 (spr2010) - 2002560..2004533 (-) 1974 WP_000715109.1 DHH family phosphoesterase -
  SPR_RS10240 (spr2011) hpf 2004669..2005217 (-) 549 WP_000599104.1 ribosome hibernation-promoting factor, HPF/YfiA family -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  cbpD lytC positive effect
  cbpD lytA positive effect
  comM cbpD negative effect
  comE comM positive effect
  comE comB positive effect
  comE comW positive effect
  comE comC/comC1 positive effect
  comE comX/comX1 positive effect
  comE comA positive effect
  comE comD/comD1 positive effect
  comE comX/comX2 positive effect
  comE comE positive effect
  comD/comD1 comE positive effect
  stkP comE positive effect
  comB 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
  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
  clpP comW negative effect
  mecA comW negative effect
  clpC comW negative 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


Download         Length: 448 a.a.        Molecular weight: 50395.93 Da        Isoelectric Point: 9.2265

>NTDB_id=180 SPR_RS10215 WP_000698573.1 1999012..2000358(-) (cbpD) [Streptococcus pneumoniae R6]
MKILPFIARGTSYYLKMSVKKLVPFLVVGLMLAAGDSVYAYSRGNGSIARGDDYPAYYKNGSQEIDQWRMYSRQCTSFVA
FRLSNVNGFEIPAAYGNANEWGHRARREGYRVDNTPTIGSITWSTAGTYGHVAWVSNVMGDQIEIEEYNYGYTESYNKRV
IKANTMTGFIHFKDLDSGSVGNSQSSASTGGTHYFKTKSAIKTEPLVSATVIDYYYPGEKVHYDQILEKDGYKWLSYTAY
NGSYRYVQLEAVNKNPLGNSVLSSTGGTHYFKIKSAIKTEPLVSATVIDYYYPGEKVHYDQILEKDGYKWLSYTAYNGSR
RYIQLEGVTSSQNYQNQSGNISSYGSNNSSTVGWKKINGSWYHFKSNGSKSTGWLKDGSSWYYLKLSGEMQTGWLKENGS
WYYLGSSGAMKTGWYQVSGEWYYSYSSGALAINTTVDGYRVNSDGERV

Nucleotide


Download         Length: 1347 bp        

>NTDB_id=180 SPR_RS10215 WP_000698573.1 1999012..2000358(-) (cbpD) [Streptococcus pneumoniae R6]
ATGAAAATTTTACCGTTTATAGCAAGAGGAACAAGTTATTACTTGAAGATGTCAGTTAAAAAGCTTGTTCCTTTTTTAGT
AGTAGGATTGATGCTAGCAGCTGGTGATAGTGTCTATGCCTATTCCAGAGGAAATGGATCGATTGCGCGTGGGGATGATT
ATCCTGCTTATTATAAAAATGGGAGCCAGGAGATTGATCAGTGGCGCATGTATTCTCGTCAGTGTACTTCTTTTGTAGCC
TTTCGTTTGAGTAATGTCAATGGTTTTGAAATTCCGGCAGCTTATGGAAATGCGAATGAATGGGGACATCGTGCTCGTCG
GGAAGGTTATCGTGTAGATAATACACCGACGATTGGTTCCATTACTTGGTCTACTGCAGGAACTTATGGTCATGTTGCCT
GGGTGTCAAATGTAATGGGAGATCAGATTGAGATTGAGGAATATAACTATGGTTATACAGAATCCTATAATAAACGAGTT
ATAAAAGCAAACACGATGACAGGATTTATTCATTTTAAAGATTTGGATAGTGGCAGTGTTGGGAATAGTCAATCCTCAGC
TTCAACAGGCGGAACTCATTATTTTAAGACCAAGTCTGCTATTAAAACTGAACCCCTAGTTAGTGCAACTGTGATTGATT
ACTATTATCCTGGGGAGAAGGTTCATTATGATCAGATACTTGAAAAAGACGGCTATAAGTGGTTGAGTTATACTGCCTAT
AATGGAAGCTATCGTTATGTTCAATTGGAGGCTGTGAATAAAAATCCTCTAGGTAATTCTGTTCTTTCTTCAACAGGAGG
AACTCATTATTTTAAGATCAAGTCTGCTATTAAAACTGAACCCCTAGTTAGTGCAACTGTGATTGATTACTATTATCCTG
GAGAGAAGGTTCATTATGATCAGATACTTGAAAAAGACGGCTATAAGTGGTTGAGTTATACGGCTTATAACGGAAGTCGT
CGCTATATACAGCTAGAGGGAGTGACTTCTTCACAAAATTATCAGAATCAATCAGGAAATATCTCTAGCTATGGATCCAA
TAATAGTTCAACTGTCGGTTGGAAGAAAATAAATGGTAGTTGGTATCATTTCAAATCAAATGGTTCTAAATCAACAGGAT
GGCTGAAAGACGGTTCTAGCTGGTATTATTTGAAATTATCTGGTGAAATGCAGACAGGATGGTTAAAGGAGAATGGCTCG
TGGTATTATCTGGGTAGTTCAGGGGCAATGAAAACAGGCTGGTACCAGGTCTCTGGTGAGTGGTATTATTCTTACTCTTC
AGGCGCCTTAGCTATTAATACGACGGTGGATGGCTACAGAGTAAACAGTGATGGAGAACGAGTATAG

Domains

Predicted by InterproScan.

Choline-binding repeat (Choline_bind_3)

(352-390)

Choline-binding repeat (Choline_bind_3)

(392-434)

CHAP domain (CHAP)

(68-149)

Bacterial SH3 domain (SH3_5)

(264-325)

Bacterial SH3 domain (SH3_5)

(186-249)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A2U3RWM9

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  cbpD Streptococcus pneumoniae Rx1

100

100

1
  cbpD Streptococcus pneumoniae D39

99.777

100

0.998
  cbpD Streptococcus pneumoniae TIGR4

97.768

100

0.978
  cbpD Streptococcus mitis NCTC 12261

60.889

100

0.743
  cbpD Streptococcus mitis SK321

60.265

100

0.734
  cbpD/crfP Streptococcus suis strain ZY05719

43.689

100

0.444

Multiple sequence alignment    



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] 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]
[3] 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]
[4] 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]
[5] 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]
[6] 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]
[7] 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]