Detailed information NTG0000377

Experimentally validated

Overview

• Name: clpC
• Type: Regulator
• Locus tag: SMU_RS09275
• Genome accession: NC_004350
• Coordinates: 1899203..1901644 (-)
• Length: 813 a.a.
• NCBI ID: WP_002262344.1
• Uniprot ID: Q8DS14
• Organism: Streptococcus mutans UA159
• Function: degradation of ComX Competence regulation

Function

MecA interacts with both SigX and ClpC, forming a ternary SigX-MecA-ClpC complex. MecA mediates the formation of a ternary SigX-MecA-ClpC complex that sequesters SigX and thereby negatively regulates genetic competence in S. mutans.

Genomic Context

Location: 1894203..1906644

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
SMU_RS09260	rpsJ	1895024..1895332 (-)	309	WP_002262341.1	30S ribosomal protein S10	-
SMU_RS09265 (SMU.2027)	-	1895652..1896338 (+)	687	WP_002262342.1	helix-turn-helix domain-containing protein	-
SMU_RS09270 (SMU.2028)	-	1896529..1898916 (-)	2388	WP_002262343.1	glycoside hydrolase family 68 protein	-
SMU_RS09275 (SMU.2029)	clpC	1899203..1901644 (-)	2442	WP_002262344.1	ATP-dependent Clp protease ATP-binding subunit	Regulator
SMU_RS09280 (SMU.2030)	ctsR	1901641..1902105 (-)	465	WP_002262345.1	transcriptional regulator CtsR	-
SMU_RS09285 (SMU.2031)	tsf	1902386..1903432 (-)	1047	WP_002262346.1	translation elongation factor Ts	-
SMU_RS09290 (SMU.2032)	rpsB	1903499..1904284 (-)	786	WP_002262347.1	30S ribosomal protein S2	-
SMU_RS09295 (SMU.2033c)	-	1904475..1906328 (-)	1854	WP_002262348.1	hypothetical protein	-

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
clpC	comX/sigX	negative effect
comX/sigX	late competence genes	positive effect
comX/sigX	late competence genes	positive effect
scnR	comX/sigX	positive effect
hdrR	comX/sigX	positive effect
hdrR	comR	positive effect
hdrM	hdrR	negative effect
mecA	comX/sigX	negative effect
comR	comX/sigX	positive effect
comR	comS	positive effect
cipB	comR	positive effect
XrpA	comR	negative effect
clpP	comX/sigX	negative effect
XrpA	comX/sigX	negative effect
XrpA	comS	negative effect
scnK	comX/sigX	positive effect
comS	comX/sigX	positive effect
comS	comS	positive effect
oppD	comS	positive effect
cipB	comS	positive effect
comD/blpH	comX/sigX	positive effect
comD/blpH	comE/blpR	positive effect
vicR	comD/blpH	negative effect
comE/blpR	comD/blpH	positive effect
vicK	comD/blpH	negative effect
comC/blpC	comD/blpH	positive effect
vicK	comX/sigX	negative effect
vicK	comC/blpC	negative effect
vicK	comE/blpR	negative effect
comE/blpR	comX/sigX	positive effect
comE/blpR	comC/blpC	positive effect
comE/blpR	comA/nlmT	positive effect
comE/blpR	comE/blpR	positive effect
comE/blpR	comB/nlmE	positive effect
vicR	comE/blpR	negative effect
scnC	comX/sigX	positive effect
brsR	comX/sigX	positive effect
brsM	brsR	negative effect
cipB	comX/sigX	positive effect
vicR	comX/sigX	negative effect
vicR	comC/blpC	negative effect
comC/blpC	comX/sigX	positive effect
comA/nlmT	comC/blpC	positive effect
comB/nlmE	comC/blpC	positive effect
ciaH	comC/blpC	positive effect
sepM	comC/blpC	positive effect

Sequence

Protein

• Length: 813 a.a.
• Molecular weight: 90330.13 Da
• Isoelectric Point: 6.9065

>NTDB_id=377 SMU_RS09275 WP_002262344.1 1899203..1901644(-) (clpC) [Streptococcus mutans UA159]
MTDYSLKMQEVFRLAQFEAARFESSYLESWHVLLAMVEIDSSVAGLSFAEFEADVRFEDYQAAAILAIGKKPKSSSNDIM
LLEQSHALKRTLAEAAAISQVTHAKEVGTEHVLFAMLLNPNLLATRILELVGFHAKDDGESIRLLDLRKVIERYAGFSKE
DIKAIFEMRKPKKVKNSSSFSDLMKPPSVTGELADFTRDLTELARQGRLEPVIGREQEISRMVQILSRKTKNNPVLVGDA
GVGKTALAYGLAQRIVDSAVPFELADMKVLELDMMSVVAGTRFRGDFEERMNQIIADIEADGHIVLFIDELHTIMGSGSG
IDSTLDAANILKPALARGSLRTIGATTQEEYQKHIEKDAALSRRFAKVTIEEPSEEEAYQILLGLKKSYETYHHVIISDA
AVMAAVKGAHRYLSGKNLPDSAIDLLDEASATVQGLVKKKAPAYLTDLDHALITNDYQLAKRLLKKEKKPLLKKRAEVKE
EDILATLSKLSGIPVKKLTQADSKKYLNLERELHKRVIGQDDAVSSISRAIRRNQSGIRVGKRPIGSFMFLGPTGVGKTE
LAKALAEVLFDDESALIRFDMSEYMEKFAASRLNGAPPGYVGYEEGGELTEKVRNKPYSVLLFDEVEKAHPDIFNILLQV
LDDGVLTDSRGRKVDFSNTIIIMTSNLGATALRDDKTVGFGAKSFSQDYKAMESRILEELKKVYRPEFINRIDEKVVFHN
LGQEDIRHIVKIMVAPLIAHLADQGITLKFQPSALKHLALAGYDAEMGARPLRRTLQTEVEDKLAELILSGKLASGQTLK
IGIQKEKLKFDIV

Nucleotide

• Length: 2442 bp

>NTDB_id=377 SMU_RS09275 WP_002262344.1 1899203..1901644(-) (clpC) [Streptococcus mutans UA159]
ATGACCGATTACTCATTAAAAATGCAGGAAGTCTTTCGATTGGCGCAGTTTGAAGCAGCTCGTTTTGAAAGTTCCTATTT
AGAAAGCTGGCATGTCCTTCTTGCAATGGTAGAGATTGATTCCTCAGTGGCTGGTTTAAGTTTTGCGGAGTTTGAAGCAG
ATGTCCGTTTTGAGGATTATCAGGCTGCTGCTATTTTGGCGATTGGTAAAAAGCCTAAGTCCTCGAGTAATGATATTATG
CTTTTAGAGCAATCACATGCTTTAAAACGAACCCTAGCAGAGGCCGCTGCTATTAGTCAGGTGACACACGCTAAAGAAGT
CGGCACAGAACATGTTCTCTTTGCTATGTTACTGAATCCTAATCTTTTGGCGACTCGCATTTTAGAATTAGTTGGTTTTC
ACGCCAAAGATGATGGAGAGTCCATCCGTCTTTTGGATCTGCGAAAAGTGATTGAACGTTATGCTGGCTTTTCCAAAGAG
GACATTAAGGCCATCTTTGAAATGCGTAAACCTAAAAAGGTCAAAAATAGCAGCAGCTTTTCTGATTTAATGAAGCCACC
TAGCGTTACAGGTGAACTAGCTGATTTTACACGGGATTTGACGGAGTTGGCAAGACAAGGTCGTTTAGAACCTGTTATTG
GCCGTGAACAAGAAATTTCACGGATGGTTCAAATTTTAAGCCGTAAGACAAAAAATAACCCTGTTTTAGTTGGCGATGCT
GGTGTTGGGAAGACGGCCTTGGCTTACGGCCTTGCTCAACGTATTGTGGATAGTGCCGTTCCTTTTGAATTGGCAGATAT
GAAAGTACTAGAGCTCGATATGATGAGTGTTGTTGCAGGGACTCGTTTTCGTGGCGATTTTGAGGAACGAATGAATCAAA
TTATTGCAGACATTGAAGCAGATGGTCACATTGTCCTCTTCATTGATGAGCTGCATACCATTATGGGTTCAGGAAGTGGT
ATTGATAGTACGCTGGATGCTGCTAATATTCTTAAACCAGCTTTAGCGCGCGGCAGTCTTAGAACGATTGGAGCGACTAC
TCAAGAGGAGTATCAAAAGCATATTGAAAAAGATGCTGCTCTTTCTCGCCGTTTTGCTAAGGTAACTATTGAAGAACCAA
GTGAAGAAGAAGCTTATCAGATCTTGCTTGGTTTAAAGAAAAGTTATGAAACTTATCATCATGTTATTATTTCTGATGCA
GCCGTAATGGCGGCAGTCAAAGGAGCACATCGTTATTTAAGTGGTAAAAATTTACCTGATTCGGCTATCGATCTTTTAGA
TGAAGCTAGTGCAACTGTTCAAGGCTTAGTGAAAAAAAAGGCACCAGCTTATTTGACAGATTTAGATCATGCTCTTATCA
CTAACGATTACCAATTAGCTAAGCGTTTGCTGAAAAAGGAGAAGAAGCCTCTACTTAAAAAACGAGCTGAAGTCAAGGAA
GAAGATATCCTAGCTACTCTCAGCAAACTTTCAGGCATCCCTGTCAAAAAATTAACACAGGCTGACAGTAAAAAGTACCT
TAATCTCGAAAGGGAATTACATAAGCGTGTAATTGGTCAAGACGATGCGGTGTCCAGTATCAGCCGTGCTATTCGCCGCA
ATCAATCCGGAATTCGGGTTGGCAAACGTCCCATTGGCTCTTTCATGTTTTTGGGGCCGACAGGTGTTGGTAAAACAGAG
CTTGCTAAGGCTTTGGCAGAAGTGCTTTTTGATGATGAGTCAGCTCTTATTCGTTTTGACATGAGCGAATATATGGAAAA
ATTTGCAGCTTCTCGCCTTAATGGAGCTCCTCCGGGCTATGTGGGGTATGAAGAAGGCGGTGAGTTGACGGAAAAGGTTC
GTAACAAACCTTACTCTGTTCTTCTTTTTGATGAGGTGGAAAAAGCTCATCCAGATATTTTCAATATCTTACTTCAAGTA
CTTGATGATGGTGTTTTGACAGATAGCCGTGGTCGCAAAGTTGATTTTTCAAATACGATTATTATCATGACCTCTAATTT
GGGTGCGACTGCGCTTCGTGATGATAAAACCGTTGGTTTTGGAGCTAAAAGCTTTTCCCAGGATTATAAGGCCATGGAAA
GTCGTATTTTAGAGGAATTAAAAAAGGTTTACCGACCTGAATTTATTAATCGTATTGATGAAAAAGTTGTCTTTCATAAC
CTTGGTCAAGAAGACATACGCCATATTGTTAAAATTATGGTTGCTCCATTGATTGCCCATTTGGCTGATCAGGGGATTAC
ACTTAAGTTTCAGCCTTCAGCTTTGAAACATTTAGCTCTGGCAGGTTATGATGCTGAAATGGGGGCACGTCCTTTGCGTC
GGACACTTCAGACAGAAGTGGAAGATAAGTTAGCAGAGCTTATTCTTTCGGGAAAACTAGCCAGTGGACAGACTCTGAAA
ATAGGTATTCAAAAAGAAAAATTAAAATTTGATATTGTATAA

Domains

Predicted by InterproScan.

• Clp amino terminal domain, pathogenicity island component (Clp_N) (105-133)

• Clp amino terminal domain, pathogenicity island component (Clp_N) (15-55)

• AAA domain (Cdc48 subfamily) (AAA_2) (543-714)

• C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small) (721-801)

• AAA lid domain (AAA_lid_9) (374-461)

• ATPase family associated with various cellular activities (AAA) (AAA) (235-366)

3D structure

• AlphaFold DB: Q8DS14

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
clpC	Streptococcus thermophilus LMD-9	72.549	100	0.728
clpC	Streptococcus thermophilus LMG 18311	72.426	100	0.727
clpC	Streptococcus pneumoniae TIGR4	66.79	100	0.67
clpC	Streptococcus pneumoniae D39	66.79	100	0.67
clpC	Streptococcus pneumoniae Rx1	66.79	100	0.67
clpC	Lactococcus lactis subsp. lactis strain DGCC12653	49.1	100	0.503
clpC	Bacillus subtilis subsp. subtilis str. 168	43.826	100	0.445
clpA	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	38.089	100	0.41
clpE	Streptococcus pneumoniae TIGR4	47.36	83.112	0.394
clpE	Streptococcus pneumoniae R6	46.571	83.378	0.388
clpE	Streptococcus pneumoniae D39	46.571	83.378	0.388
clpE	Streptococcus pneumoniae Rx1	46.571	83.378	0.388
clpE	Streptococcus mutans UA159	47.011	82.205	0.386
clpC	Lactococcus lactis subsp. cremoris KW2	45.631	82.62	0.377

References

• [1]: Satya D Pandey et al. (2022) Clp ATPases differentially affect natural competence development in Streptococcus mutans. MicrobiologyOpen 11(3):e1288. [PMID: 35765180]
• [2]: M Son et al. (2018) Threshold regulation and stochasticity from the MecA/ClpCP proteolytic system in Streptococcus mutans competence. Molecular Microbiology 110(6):914-930. [PMID: 29873131]
• [3]: Gaofeng Dong et al. (2014) Regulated proteolysis of the alternative sigma factor SigX in Streptococcus mutans: implication in the escape from competence. BMC Microbiology 14:183. [PMID: 25005884]
• [4]: Xiao-Lin Tian et al. (2013) MecA protein acts as a negative regulator of genetic competence in Streptococcus mutans. Journal of Bacteriology 195(22):5196-206. [PMID: 24039267]