Detailed information NTG0000416

Experimentally validated

Overview

• Name: comD/comD1
• Type: Regulator
• Locus tag: SGO_RS10505
• Genome accession: NC_009785
• Coordinates: 2192114..2193475 (-)
• Length: 453 a.a.
• NCBI ID: WP_012131078.1
• Uniprot ID: P95767
• Organism: Streptococcus gordonii str. Challis substr. CH1
• Function: phosphorylation of ComE Competence regulation

Function

In S. gordonii, pre-CSP is a 50 aa polypeptide that is cleaved at a double glycine to generate the mature 19 aa residue CSP. This peptide is then exported out of the cell via an ABC-binding cassette transporter encoded by comA and comB. Once a critical concentration of environmental CSP is reached, it is detected by the two-component system ComDE, comprising a membrane-bound histidine kinase (ComD), which phosphorylates the intracellular response regulator ComE. ComE activates a signalling cascade that includes upregulation of the master regulator SigX (designated ComR in S. gordonii), an alternate sigma factor that controls expression of late competence genes encoding DNA uptake and recombination machinery.

Genomic Context

Location: 2187114..2198475

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
SGO_RS10480 (SGO_2141)	pth	2189270..2189839 (-)	570	WP_012131076.1	aminoacyl-tRNA hydrolase	-
SGO_RS10485 (SGO_2142)	ychF	2189913..2191028 (-)	1116	WP_012131077.1	redox-regulated ATPase YchF	-
SGO_RS10500 (SGO_2145)	comE/comE1	2191350..2192117 (-)	768	WP_008808031.1	competence system response regulator transcription factor ComE	Regulator
SGO_RS10505 (SGO_2146)	comD/comD1	2192114..2193475 (-)	1362	WP_012131078.1	competence system sensor histidine kinase ComD	Regulator
SGO_RS10510 (SGO_2147)	comC/comC1	2193491..2193643 (-)	153	WP_012131079.1	bacteriocin	Regulator
SGO_RS10520 (SGO_2149)	rlmH	2193929..2194408 (-)	480	WP_012131080.1	23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH	-
SGO_RS10525 (SGO_2150)	htrA	2194602..2195795 (+)	1194	WP_012131081.1	S1C family serine protease	Regulator
SGO_RS10530 (SGO_2151)	spo0J	2195861..2196625 (+)	765	WP_012131082.1	ParB/RepB/Spo0J family partition protein	Regulator

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
comD/comD1	comE/comE1	positive effect
comE/comE1	comA	positive effect
comA	comC/comC1	positive effect
comC/comC1	comD/comD1	positive effect
comE/comE1	comB	positive effect
comB	comC/comC1	positive effect
comE/comE1	comR/comR2	positive effect
comR/comR2	late competence genes	positive effect
comE/comE1	comE/comE1	positive effect
comE/comE1	comC/comC1	positive effect
comE/comE1	comR/comR1	positive effect
comE/comE1	comD/comD1	positive effect
comR/comR1	late competence genes	positive effect
comR/comR2	late competence genes	positive effect
comR/comR1	late competence genes	positive effect

Sequence

Protein

• Length: 453 a.a.
• Molecular weight: 53636.59 Da
• Isoelectric Point: 6.4089

>NTDB_id=416 SGO_RS10505 WP_012131078.1 2192114..2193475(-) (comD/comD1) [Streptococcus gordonii str. Challis substr. CH1]
MIFTIILSLFPVIIQVFSYDFFYNKINRKKKINIKLIILFWGLIMVISFLYSLFLLLPDYWKIFRDIFHYLFLLIQPLIF
YKYFLIKRKEYENYLNLFLSFVIYLSVETSETFLSVIISSITGDSFVKQHYDIFYIIINLLSLFIILKVVDFFDFYFEYY
KEPIYKNDLYNVNKSYIVIHILLNISHWFSENAHLNSFASMIATIGFIMFLSTLFYLKSAREQYEKAKEIQQKKEEQRQL
QLYTDEIVGLYNEIRGFRHDYAGMLTSLQTGINSGDMKEVERIFHNVLSQANISLRSDDYTFFELNNVQDTALRSVLIQT
IFKARECGVEIVFEMKDVIETLPMKLLDLVRVASVLLNNAVEGAAESPSKTMNVSLVKLDKEIVFVIQNSRQSRYINLEE
IYEVGFSTKGENRGLGLNNVKEIIDKYDEVILETDIETNYFIQVVRFKRKEKI

Nucleotide

• Length: 1362 bp

>NTDB_id=416 SGO_RS10505 WP_012131078.1 2192114..2193475(-) (comD/comD1) [Streptococcus gordonii str. Challis substr. CH1]
ATGATATTTACAATAATACTGTCTTTATTTCCAGTTATAATACAAGTTTTTTCCTATGATTTTTTTTACAATAAAATTAA
TAGAAAAAAGAAAATTAATATTAAACTCATTATTCTATTTTGGGGTTTAATAATGGTAATATCATTTCTTTATTCTCTAT
TCTTATTATTACCAGATTATTGGAAAATTTTTCGAGATATTTTTCATTATTTATTTTTACTTATTCAGCCTCTTATTTTC
TACAAATATTTTCTTATTAAAAGAAAAGAGTATGAAAATTACTTGAATTTGTTTTTATCGTTTGTTATCTATTTATCTGT
GGAGACTTCTGAAACTTTTTTATCTGTCATTATTTCTTCAATAACAGGAGATTCTTTTGTAAAACAACATTATGATATTT
TTTACATTATAATTAATCTTTTATCTTTGTTTATTATTTTAAAGGTTGTTGATTTTTTTGACTTTTATTTTGAGTACTAT
AAAGAACCAATTTATAAAAATGATCTATATAATGTTAATAAGTCATATATAGTAATCCATATCCTATTAAATATTTCTCA
TTGGTTCAGCGAAAATGCACATCTTAATAGCTTTGCTAGTATGATTGCAACTATAGGATTTATTATGTTTTTGTCGACTT
TATTTTATCTGAAGTCTGCTCGTGAACAATATGAAAAAGCTAAAGAAATTCAGCAAAAAAAGGAAGAACAAAGACAACTA
CAACTTTATACAGATGAAATTGTAGGTCTTTATAACGAAATTCGAGGTTTTCGTCACGATTATGCTGGTATGTTAACAAG
TTTGCAAACCGGAATTAACTCAGGTGATATGAAAGAAGTAGAGCGAATCTTTCATAATGTTTTAAGTCAAGCTAATATTT
CCCTTCGATCAGATGACTATACTTTTTTTGAGTTAAATAATGTTCAAGACACTGCCTTGAGAAGTGTGTTAATTCAAACT
ATATTTAAGGCTCGAGAGTGTGGAGTAGAGATCGTATTTGAAATGAAGGATGTTATTGAGACATTACCTATGAAACTTTT
AGATTTAGTTCGAGTAGCTAGTGTATTGCTCAATAATGCAGTTGAAGGGGCAGCTGAAAGTCCCTCAAAAACAATGAACG
TGTCTTTAGTAAAGCTAGATAAAGAAATTGTTTTTGTAATTCAGAATTCTCGTCAAAGCCGTTACATTAATTTAGAAGAA
ATTTATGAAGTAGGCTTCTCAACAAAAGGAGAAAATCGAGGATTAGGTTTAAATAATGTCAAAGAAATTATTGACAAATA
TGATGAAGTTATTCTGGAAACAGATATAGAAACAAATTATTTTATACAAGTTGTAAGATTTAAAAGAAAGGAAAAAATAT
GA

Domains

Predicted by InterproScan.

• GHKL domain (HATPase_c_5) (344-445)

3D structure

• AlphaFold DB: P95767

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
comD/comD2	Streptococcus gordonii strain NCTC7865	89.845	100	0.9
comD/comD1	Streptococcus pneumoniae D39	47.17	93.598	0.442
comD/comD1	Streptococcus pneumoniae R6	47.17	93.598	0.442
comD/comD1	Streptococcus pneumoniae Rx1	47.17	93.598	0.442
comD/comD2	Streptococcus pneumoniae TIGR4	47.17	93.598	0.442
comD	Streptococcus mitis SK321	46.682	93.157	0.435
comD	Streptococcus mitis NCTC 12261	45.647	93.819	0.428

References

• [1]: Alison A Jack et al. (2015) Streptococcus gordonii comCDE (competence) operon modulates biofilm formation with Candida albicans. Microbiology (Reading, England) 161(Pt 2):411-421. [PMID: 25505189]
• [2]: Nicholas C K Heng et al. (2007) Competence-dependent bacteriocin production by Streptococcus gordonii DL1 (Challis). Journal of Bacteriology 189(4):1468-72. [PMID: 17012395]
• [3]: R D Lunsford et al. (1996) Natural genetic transformation in Streptococcus gordonii: comX imparts spontaneous competence on strain wicky. Journal of Bacteriology 178(19):5831-5. [PMID: 8824638]
• [4]: L S Håvarstein et al. (1996) Identification of the streptococcal competence-pheromone receptor. Molecular Microbiology 21(4):863-9. [PMID: 8878047]