Detailed information    

experimental Experimentally validated

Overview

Name   comD/comD2   Type   Regulator
Locus tag   SP_RS11430 Genome accession   NC_003028
Coordinates   2156414..2157739 (-) Length   441 a.a.
NCBI ID   WP_000364845.1    Uniprot ID   Q9S1K4
Organism   Streptococcus pneumoniae TIGR4     
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: 2151414..2162739
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SP_RS13565 - 2153099..2154701 (-) 1603 Protein_2131 YhgE/Pip family protein -
  SP_RS11410 (SP_2234) - 2154880..2155422 (+) 543 WP_001158266.1 TetR/AcrR family transcriptional regulator -
  SP_RS11425 (SP_2235) comE 2155665..2156417 (-) 753 WP_000866065.1 competence system response regulator transcription factor ComE Regulator
  SP_RS11430 (SP_2236) comD/comD2 2156414..2157739 (-) 1326 WP_000364845.1 competence system sensor histidine kinase ComD Regulator
  SP_RS11435 (SP_2237) comC/comC2 2157760..2157885 (-) 126 WP_000799686.1 competence-stimulating peptide ComC Regulator
  SP_RS11445 (SP_2238) rlmH 2158167..2158646 (-) 480 WP_000695929.1 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH -
  SP_RS11450 (SP_2239) htrA 2158829..2160010 (+) 1182 WP_000681597.1 S1C family serine protease Regulator
  SP_RS11455 (SP_2240) spo0J 2160068..2160826 (+) 759 WP_000410378.1 ParB/RepB/Spo0J family partition protein Regulator

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  comD/comD2 comE positive effect
  comE comE positive effect
  comE comX/comX1 positive effect
  comE comW positive effect
  comE comA positive effect
  comE comB positive effect
  comE comM positive effect
  comE comX/comX2 positive effect
  comE comD/comD2 positive effect
  comE comC/comC2 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
  comM cbpD negative 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
  cbpD lytA positive effect
  cbpD lytC 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: 441 a.a.        Molecular weight: 51435.07 Da        Isoelectric Point: 7.5816

>NTDB_id=138 SP_RS11430 WP_000364845.1 2156414..2157739(-) (comD/comD2) [Streptococcus pneumoniae TIGR4]
MDLLGFGTVIVHFLIISHSYRLICKGRINRKELYVFGAYTLLTEIVLEFSFYLLYLDKIGIERFLFPLGLYSYFRWMKQY
ERDRGLFLSLLLSLLYESTHNFLSVIFSSITGDNFVLQYHFPFFFVVTVLTYFVTLKIIYYFHLELAYFDKDYLYPFLKK
VFFALLLLHIVSFVSDMVSTIKHLNSFGSILSSIVFISLLLTFFAMNSHKVQMEKEIALKQKKFEQKHLQNYTDEIVGLY
NEIRGFRHDYAGMLVSMQMAIDSGNLQEIDRIYNEVLVKANHKLRSDKYTYFDLNNIEDSALRSLVAQSIVYARNNGVEF
TLEVKDTITKLPIELLDLVRIMSVLLNNAVEGSADSYKKQMEVAVIKMETETVIVIQNSCKMTMTPSGDLFALGFSTKGR
NRGVGLNNVKELLDKYNNIILETEMEGSTFRQIIRFKREFE

Nucleotide


Download         Length: 1326 bp        

>NTDB_id=138 SP_RS11430 WP_000364845.1 2156414..2157739(-) (comD/comD2) [Streptococcus pneumoniae TIGR4]
ATGGATTTACTTGGATTTGGGACAGTTATTGTTCATTTTTTAATTATTAGTCACAGTTACCGTTTAATTTGTAAAGGTCG
AATAAATAGAAAAGAATTATACGTTTTTGGTGCTTATACATTACTAACTGAAATAGTACTTGAATTTTCCTTTTATCTTC
TATATTTAGATAAAATAGGGATTGAAAGATTTTTATTTCCTTTGGGCTTATATTCCTATTTTCGATGGATGAAACAGTAT
GAGAGGGATAGAGGACTATTCCTAAGTTTACTACTATCTCTTTTATATGAGAGCACTCATAACTTTCTGTCCGTAATTTT
CTCCTCTATAACAGGAGATAATTTTGTTTTACAATATCATTTCCCATTCTTTTTCGTTGTGACGGTGTTAACCTATTTTG
TTACATTAAAAATCATTTACTATTTCCATTTGGAACTAGCCTATTTTGACAAGGACTACCTTTATCCTTTCTTGAAAAAA
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 Q9S1K4

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

96.825

100

0.968
  comD/comD1 Streptococcus pneumoniae D39

96.825

100

0.968
  comD/comD1 Streptococcus pneumoniae R6

96.825

100

0.968
  comD Streptococcus mitis SK321

92.063

100

0.921
  comD Streptococcus mitis NCTC 12261

86.621

100

0.866
  comD/comD1 Streptococcus gordonii str. Challis substr. CH1

47.17

93.598

0.442
  comD/comD2 Streptococcus gordonii strain NCTC7865

49.468

85.261

0.422

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]