Detailed information    

experimental Experimentally validated

Overview

Name   cbpD   Type   Auxiliary factor
Locus tag   SP_RS11240 Genome accession   NC_003028
Coordinates   2121460..2122806 (-) Length   448 a.a.
NCBI ID   WP_000698569.1    Uniprot ID   Q9KGZ2
Organism   Streptococcus pneumoniae TIGR4     
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: 2116460..2127806
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SP_RS11215 (SP_2195) - 2117842..2118300 (-) 459 WP_001211273.1 CtsR family transcriptional regulator -
  SP_RS11220 (SP_2196) - 2118419..2119147 (-) 729 WP_000136224.1 ABC transporter ATP-binding protein -
  SP_RS11225 (SP_2197) - 2119147..2120154 (-) 1008 WP_000754546.1 ABC transporter substrate-binding protein -
  SP_RS11230 (SP_2198) - 2120193..2120951 (-) 759 WP_001813866.1 ABC transporter permease -
  SP_RS11235 (SP_2199) - 2120914..2121204 (-) 291 WP_000647692.1 thiamine-binding protein -
  SP_RS11240 (SP_2201) cbpD 2121460..2122806 (-) 1347 WP_000698569.1 choline binding-anchored murein hydrolase CbpD Auxiliary factor
  SP_RS11245 (SP_2202) - 2122895..2123161 (-) 267 WP_001278167.1 Veg family protein -
  SP_RS11250 (SP_2203) dnaB 2123163..2124515 (-) 1353 WP_000852486.1 replicative DNA helicase -
  SP_RS11255 (SP_2204) rplI 2124559..2125011 (-) 453 WP_000864220.1 50S ribosomal protein L9 -
  SP_RS11260 (SP_2205) - 2125008..2126981 (-) 1974 WP_000715115.1 DHH family phosphoesterase -
  SP_RS11265 (SP_2206) hpf 2127117..2127665 (-) 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 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


Download         Length: 448 a.a.        Molecular weight: 50348.92 Da        Isoelectric Point: 9.3602

>NTDB_id=144 SP_RS11240 WP_000698569.1 2121460..2122806(-) (cbpD) [Streptococcus pneumoniae TIGR4]
MKILPFIARGTSYYLKMSVKKLVPFLVVGLMLAAGDSVYAYSRGNGSIARGDDYPAYYKNGSQEIDQWRMYSRQCTSFVA
FRLSNVNGFEIPAAYGNANEWGHRARREGYRVDNTPTIGSITWSTAGTYGHVAWVSNVMGDQIEIEEYNYGYTESYNKRV
IKANTMTGFIHFKDLDGGSVGNSQSSTSTGGTHYFKTKSAIKTEPLASGTVIDYYYPGEKVHYDQILEKDGYKWLSYTAY
NGSYRYVQLEAVNKNPLGNSVLSSTGGTHYFKTKSAIKTEPLVSATVIDYYYPGEKVHYDQILEKDGYKWLSYTAYNGSR
RYIQLEGVTSSQNYQNQSGNISSYGSHSSSTVGWKKINGSWYHFKSNGSKSTGWLKDGSSWYYLKLSGEMQTGWLKENGL
WYYLGSSGAMKTGWYQVSGKWYYSYSSGALAVNTTVDGYRVNSDGERV

Nucleotide


Download         Length: 1347 bp        

>NTDB_id=144 SP_RS11240 WP_000698569.1 2121460..2122806(-) (cbpD) [Streptococcus pneumoniae TIGR4]
ATGAAAATTTTACCGTTTATAGCAAGAGGAACAAGTTATTACTTGAAGATGTCAGTTAAAAAGCTTGTTCCTTTTTTAGT
AGTAGGATTGATGCTAGCAGCTGGTGATAGTGTCTATGCCTATTCCAGAGGAAATGGATCGATTGCGCGTGGGGATGATT
ATCCTGCTTATTATAAAAATGGGAGCCAGGAGATTGATCAGTGGCGCATGTATTCTCGTCAGTGTACTTCTTTTGTAGCC
TTTCGTTTGAGTAATGTCAATGGTTTTGAAATTCCGGCAGCTTATGGAAATGCGAATGAATGGGGACATCGTGCTCGTCG
GGAAGGTTATCGTGTAGATAATACACCGACGATTGGTTCCATTACTTGGTCTACTGCAGGAACTTATGGTCATGTTGCCT
GGGTGTCAAATGTAATGGGAGATCAGATTGAGATTGAGGAATATAACTATGGTTATACAGAATCCTATAATAAACGAGTT
ATAAAAGCAAACACGATGACAGGATTTATTCATTTTAAAGATTTGGATGGTGGCAGTGTTGGGAATAGTCAATCCTCAAC
TTCAACAGGCGGAACTCATTATTTTAAGACCAAGTCTGCTATTAAAACTGAACCTCTAGCTAGCGGAACTGTGATTGATT
ACTATTATCCTGGGGAGAAGGTTCATTATGATCAGATACTTGAAAAAGACGGCTATAAGTGGTTGAGTTATACTGCCTAT
AATGGAAGCTATCGTTATGTTCAATTGGAGGCTGTGAATAAAAATCCTCTAGGTAATTCTGTTCTTTCTTCAACAGGTGG
AACTCATTATTTTAAGACCAAGTCTGCTATCAAAACTGAACCCCTAGTTAGTGCAACTGTGATTGATTACTATTATCCTG
GAGAGAAGGTTCATTATGATCAAATTCTCGAAAAAGACGGCTACAAGTGGTTGAGTTATACGGCTTATAACGGAAGTCGT
CGCTATATACAGCTAGAGGGAGTGACTTCTTCACAAAATTATCAGAATCAATCAGGAAACATCTCTAGCTATGGATCCCA
TAGTAGTTCAACTGTCGGTTGGAAGAAAATAAATGGTAGTTGGTATCATTTCAAATCAAATGGTTCTAAATCAACAGGAT
GGCTGAAAGACGGTTCTAGCTGGTATTATTTGAAATTATCTGGTGAAATGCAGACAGGATGGTTAAAGGAAAATGGTTTG
TGGTATTATCTGGGTAGTTCAGGGGCAATGAAAACAGGCTGGTACCAGGTCTCTGGTAAGTGGTATTATTCTTACTCTTC
AGGCGCCTTAGCTGTTAATACGACGGTGGATGGCTACAGAGTAAACAGTGATGGAGAACGAGTATAG

Domains

Predicted by InterproScan.

CHAP domain (CHAP)

(68-149)

Choline-binding repeat (Choline_bind_3)

(352-390)

Choline-binding repeat (Choline_bind_3)

(392-434)

Bacterial SH3 domain (SH3_5)

(186-249)

Bacterial SH3 domain (SH3_5)

(264-325)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q9KGZ2

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

97.768

100

0.978
  cbpD Streptococcus pneumoniae R6

97.768

100

0.978
  cbpD Streptococcus pneumoniae D39

97.545

100

0.975
  cbpD Streptococcus mitis SK321

60.706

100

0.739
  cbpD Streptococcus mitis NCTC 12261

82.061

71.003

0.583
  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]