Detailed information    

experimental Experimentally validated

Overview

Name   comD/comD1   Type   Regulator
Locus tag   SPR_RS10405 Genome accession   NC_003098
Coordinates   2033991..2035316 (-) Length   441 a.a.
NCBI ID   WP_000362880.1    Uniprot ID   Q79CK8
Organism   Streptococcus pneumoniae R6     
Function   phosphorylation of ComE   
Competence regulation

Function

ComD, a membrane-bound histidine kinase, is the receptor of the competence-stimulating peptide (CSP). Binding of CSP to its associated ComD receptor will result in autophosphorylation of ComD and subsequent transfer of the phosphoryl group to ComE. This activation initiates the transcription of early competence genes.


Genomic Context

Location: 2028991..2040316
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SPR_RS11165 - 2030675..2032278 (-) 1604 Protein_2011 YhgE/Pip family protein -
  SPR_RS10385 (spr2040) - 2032457..2032999 (+) 543 WP_001158266.1 TetR/AcrR family transcriptional regulator -
  SPR_RS10400 (spr2041) comE 2033242..2033994 (-) 753 WP_000866065.1 competence system response regulator transcription factor ComE Regulator
  SPR_RS10405 (spr2042) comD/comD1 2033991..2035316 (-) 1326 WP_000362880.1 competence system sensor histidine kinase ComD Regulator
  SPR_RS10410 (spr2043) comC/comC1 2035337..2035462 (-) 126 WP_000799689.1 competence-stimulating peptide ComC Regulator
  SPR_RS10420 (spr2044) rlmH 2035744..2036223 (-) 480 WP_000695929.1 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH -
  SPR_RS10425 (spr2045) htrA 2036406..2037587 (+) 1182 WP_000681597.1 S1C family serine protease Regulator
  SPR_RS10430 (spr2046) spo0J 2037645..2038403 (+) 759 WP_000410378.1 ParB/RepB/Spo0J family partition protein Regulator

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  comD/comD1 comE positive effect
  comE comB positive effect
  comB comC/comC1 positive effect
  comC/comC1 comD/comD1 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
  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
  comE comX/comX2 positive effect
  comX/comX2 late competence genes positive effect
  clpE comX/comX2 negative effect
  clpP comX/comX2 negative effect
  comE comM positive effect
  comM cbpD 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
  cbpD lytC positive effect
  cbpD lytA positive effect

Sequence

Protein


Download         Length: 441 a.a.        Molecular weight: 51353.78 Da        Isoelectric Point: 6.6400

>NTDB_id=174 SPR_RS10405 WP_000362880.1 2033991..2035316(-) (comD/comD1) [Streptococcus pneumoniae R6]
MDLFGFGTVIVHFLIISHSYHFICKGQINRKELFVFGAYTLLTEIVFDFPLYILYLDGLGIERFLFPLGLYSYFRWMKQY
ERDRGLFLSLLLSLLYESTHNFLSVTFSSITGDNFVLQYHFPFFFVVTVLTYFVTLKIIYYFHLELAYFDEDYLYPFLKK
VFFALLLLHIVSFVSDMVSTIKHLNSFGSILSSIVFISLLLTFFAMNSHKVQMEKEIALKQKKFEQKHLQNYTDEIVGLY
NEIRGFRHDYAGMLVSMQMAIDSGNLQEIDRIYNEVLVKANHKLRSDKYTYFDLNNIEDSALRSLVAQSIVYARNNGVEF
TLEVKDTITKLPIELLDLVRIMSVLLNNAVEGSADSYKKQMEVAVIKMETETVIVIQNSCKMTMTPSGDLFALGFSTKGR
NRGVGLNNVKELLDKYNNIILETEMEGSTFRQIIRFKREFE

Nucleotide


Download         Length: 1326 bp        

>NTDB_id=174 SPR_RS10405 WP_000362880.1 2033991..2035316(-) (comD/comD1) [Streptococcus pneumoniae R6]
ATGGATTTATTTGGATTTGGGACGGTTATTGTTCATTTTTTAATTATTAGTCACAGTTACCATTTTATTTGTAAAGGTCA
AATAAATAGAAAAGAATTATTCGTTTTTGGTGCTTATACATTACTAACAGAAATAGTATTTGATTTTCCCTTATATATTC
TATATTTAGATGGGTTAGGGATTGAAAGATTTTTATTTCCTTTGGGATTATATTCCTATTTTCGATGGATGAAACAGTAT
GAGAGGGATAGAGGACTATTCCTAAGTTTACTACTATCTCTTTTATATGAGAGCACTCATAACTTTCTGTCCGTAACTTT
CTCCTCTATAACAGGAGATAATTTTGTTTTACAATATCATTTCCCATTCTTTTTCGTTGTGACGGTGTTAACCTATTTTG
TTACATTAAAAATCATTTACTATTTCCATTTGGAACTAGCCTATTTTGACGAGGACTACCTTTATCCTTTCTTGAAAAAA
GTATTTTTTGCTTTACTATTGCTACATATTGTATCTTTCGTTTCAGATATGGTAAGTACGATTAAACATTTGAATAGTTT
TGGAAGTATTTTGTCATCTATTGTCTTTATCTCTCTCCTTTTGACCTTCTTTGCAATGAATTCTCATAAAGTTCAAATGG
AGAAAGAGATTGCTTTGAAGCAGAAGAAATTTGAACAGAAACATTTACAGAATTACACAGATGAAATTGTTGGTCTGTAT
AATGAAATCCGTGGTTTTCGACATGATTATGCTGGAATGCTTGTCAGCATGCAGATGGCAATTGACAGTGGTAATTTACA
GGAAATTGACAGAATTTACAATGAAGTTTTAGTCAAAGCAAATCATAAATTGCGTTCAGATAAGTACACTTACTTTGATT
TGAACAACATAGAAGACTCAGCTTTACGAAGTTTGGTTGCTCAGTCAATTGTCTATGCTCGAAATAATGGTGTAGAGTTT
ACACTGGAAGTAAAAGATACGATTACCAAGCTTCCAATTGAACTATTGGATTTGGTTCGTATCATGAGCGTTTTATTGAA
TAATGCTGTCGAAGGATCGGCTGATAGCTATAAAAAGCAGATGGAAGTAGCAGTTATTAAGATGGAAACTGAAACAGTTA
TTGTGATTCAGAATTCATGTAAAATGACGATGACTCCTTCAGGAGATCTATTTGCCTTAGGATTCTCCACTAAGGGAAGA
AATCGCGGAGTCGGATTAAATAATGTGAAAGAACTACTAGATAAGTACAACAATATTATTTTAGAAACAGAGATGGAAGG
CAGTACATTTAGACAAATCATTAGATTTAAGAGGGAATTTGAATGA

Domains

Predicted by InterproScan.

GHKL domain (HATPase_c_5)

(334-434)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q79CK8

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
  comD/comD1 Streptococcus pneumoniae Rx1

100

100

1
  comD/comD1 Streptococcus pneumoniae D39

100

100

1
  comD/comD2 Streptococcus pneumoniae TIGR4

96.825

100

0.968
  comD Streptococcus mitis SK321

92.063

100

0.921
  comD Streptococcus mitis NCTC 12261

86.168

100

0.862
  comD/comD1 Streptococcus gordonii str. Challis substr. CH1

47.17

93.598

0.442
  comD/comD2 Streptococcus gordonii strain NCTC7865

47.42

90.044

0.427

Multiple sequence alignment    



References

[1] Bimal Koirala et al. (2019) Unveiling the Importance of Amide Protons in CSP:ComD Interactions in Streptococcus pneumoniae. ACS Medicinal Chemistry Letters 10(6):880-886. [PMID: 31223442]
[2] Bimal Koirala et al. (2018) Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae. Beilstein Journal of Organic Chemistry 14:1769-1777. [PMID: 30112082]
[3] Yifang Yang et al. (2017) Structure-Activity Relationships of the Competence Stimulating Peptides (CSPs) in Streptococcus pneumoniae Reveal Motifs Critical for Intra-group and Cross-group ComD Receptor Activation. ACS Chemical Biology 12(4):1141-1151. [PMID: 28221753]
[4] Bernard Martin et al. (2013) ComE/ComE~P interplay dictates activation or extinction status of pneumococcal X-state (competence). Molecular Microbiology 87(2):394-411. [PMID: 23216914]
[5] Bernard Martin et al. (2010) Expression and maintenance of ComD-ComE, the two-component signal-transduction system that controls competence of Streptococcus pneumoniae. Molecular Microbiology 75(6):1513-28. [PMID: 20180906]
[6] Francesco Iannelli et al. (2005) Sensor domain of histidine kinase ComD confers competence pherotype specificity in Streptoccoccus pneumoniae. FEMS Microbiology Letters 252(2):321-6. [PMID: 16209911]
[7] E V Pestova et al. (1996) Regulation of competence for genetic transformation in Streptococcus pneumoniae by an auto-induced peptide pheromone and a two-component regulatory system. Molecular Microbiology 21(4):853-62. [PMID: 8878046]
[8] L S Håvarstein et al. (1996) Identification of the streptococcal competence-pheromone receptor. Molecular Microbiology 21(4):863-9. [PMID: 8878047]