Detailed information NTG0000329

Experimentally validated

Overview

• Name: clpC
• Type: Regulator
• Locus tag: STU_RS10020
• Genome accession: NC_006448
• Coordinates: 86146..88596 (+)
• Length: 816 a.a.
• NCBI ID: WP_011225298.1
• Uniprot ID: Q5M6G1
• Organism: Streptococcus thermophilus LMG 18311
• Function: degradation of ComX Competence regulation

Function

σX degradation is performed by the MecA–ClpCP complex.

Genomic Context

Location: 81146..93596

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
STU_RS19010	-	81472..82424 (-)	953	Protein_59	S66 family peptidase	-
STU_RS10000 (stu0073)	rpsB	82947..83714 (+)	768	WP_002944541.1	30S ribosomal protein S2	-
STU_RS10005 (stu0074)	tsf	83825..84865 (+)	1041	WP_002949105.1	translation elongation factor Ts	-
STU_RS10010 (stu0075)	-	84976..85446 (-)	471	WP_011225296.1	COG2426 family protein	-
STU_RS10015 (stu0076)	-	85690..86145 (+)	456	WP_011225297.1	CtsR family transcriptional regulator	-
STU_RS10020 (stu0077)	clpC	86146..88596 (+)	2451	WP_011225298.1	ATP-dependent Clp protease ATP-binding subunit	Regulator
STU_RS10025 (stu0078)	pbp3	88724..89957 (-)	1234	Protein_65	D-alanyl-D-alanine carboxypeptidase PBP3	-
STU_RS10030 (stu0080)	pbp3	90127..91374 (-)	1248	WP_041828096.1	D-alanyl-D-alanine carboxypeptidase PBP3	-

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
clpC	comX	negative effect
comX	ssbA	positive effect
comX	comGE	positive effect
comX	comGB	positive effect
comX	comGD	positive effect
comX	comGF	positive effect
comX	comGG	positive effect
comX	radA	positive effect
comX	comEC	positive effect
comX	comFC	positive effect
comX	recA	positive effect
comX	comEA	positive effect
comX	comGC	positive effect
comX	cinA	positive effect
comX	coiA	positive effect
comX	comGA	positive effect
comX	comFA	positive effect
comX	dprA	positive effect
comR	comX	positive effect
comR	comS	positive effect
comS	comX	positive effect
comS	comS	positive effect
amiC	comS	positive effect
eeP	comS	positive effect
amiD	comS	positive effect
amiF	comS	positive effect
amiA3	comS	positive effect
amiE	comS	positive effect
clpP	comX	negative effect
mecA	comX	negative effect

Sequence

Protein

• Length: 816 a.a.
• Molecular weight: 90284.49 Da
• Isoelectric Point: 5.7956

>NTDB_id=329 STU_RS10020 WP_011225298.1 86146..88596(+) (clpC) [Streptococcus thermophilus LMG 18311]
MTIYSRKMQAIFHRAQLEAERFESPFLETWHVLLAMVEVPGSVAYLTFTDFEDRIHSEEIETAAVLAMEKRPKDLSESDI
IDLRAQSPALEAMLQEAQGIASVTGAVEVGSEHVLMAFLLHKDLMVCRLLEVAGFQYKDDSDKPRIIDLRRSLERNAGLS
KQDLKAIHDLRKPKKSKASANFANMMQPPQSSTGELADYTKDLTALAESGNLDPIIGRDEEISRMIQVLSRKTKNNPVLV
GEAGVGKTALALGLAQRIASGEVPFELADMRILELDMMSVVAGTRFRGDFEERMNQIIDEIEADGKIILFIDELHTIIGS
GSGIDSTLDAANILKPALARGTLHMVGATTQAEYQKHIEKDAALSRRFAKITIEEPSVSEAIDILNGLRSSYEDYHRVTI
TDAAVETAVKAAHRYLTSKNLPDSAIDLLDEASATVQVRIKKEAKREITPLDEALISGDIGAAVKQYKANQKAKFPKPAL
VDADQIMQTLSRLSGIPVEKMTQTDSKRYLNLESELHKRVIGQDEAVSAISRAIRRNQSGIRTGKRPIGSFMFLGPTGVG
KTELAKALAEVLFDDESALLRFDMSEYMEKFAASRLNGAPPGYVGYDEGGELTEKVRNKPYSVLLFDEIEKAHPDIFNVL
LQVLDDGVLTDSRGRKVDFSNTIIIMTSNLGATALRDDKTVGFGAQTISHNHQAMQARIMEELKKSYRPEFINRIDEKVV
FHSLEEEQLHDIVKIMVKPLISALADKGISLKFQPAALKHLAKDGYDIEMGARPLRRTIQTQVEDKLSELLLGGQVVSGQ
TLKIGCSKDKLTFTVV

Nucleotide

• Length: 2451 bp

>NTDB_id=329 STU_RS10020 WP_011225298.1 86146..88596(+) (clpC) [Streptococcus thermophilus LMG 18311]
ATGACGATATATTCAAGAAAAATGCAGGCCATTTTCCATCGTGCTCAGCTTGAAGCGGAGCGTTTTGAAAGTCCTTTCTT
GGAGACTTGGCATGTGCTTCTAGCTATGGTTGAGGTTCCGGGATCTGTAGCCTACTTAACATTTACTGATTTTGAGGACC
GTATTCATTCGGAAGAGATTGAGACAGCTGCTGTATTGGCTATGGAGAAGAGGCCAAAAGACTTGTCGGAATCAGATATT
ATCGATTTACGTGCACAGTCACCTGCGCTAGAGGCTATGTTGCAAGAGGCGCAAGGAATCGCTAGTGTGACTGGTGCTGT
AGAGGTGGGGTCTGAACATGTATTGATGGCCTTCCTTCTTCATAAGGATTTAATGGTTTGTCGCCTCCTTGAAGTGGCTG
GTTTTCAATATAAAGATGATAGCGATAAACCTCGCATCATAGATTTACGACGTTCTTTGGAGCGTAATGCTGGTCTTAGC
AAGCAAGATTTGAAGGCAATTCACGATCTTCGTAAACCTAAGAAATCAAAAGCATCTGCGAATTTTGCCAATATGATGCA
ACCTCCTCAATCATCTACTGGTGAACTGGCAGATTATACCAAAGACTTAACTGCATTAGCGGAGTCAGGAAATCTTGATC
CCATTATTGGACGCGATGAAGAAATTTCACGCATGATTCAGGTTTTGAGTCGTAAAACGAAGAATAATCCTGTCTTGGTA
GGTGAAGCTGGTGTCGGTAAGACAGCACTTGCTCTTGGTTTAGCGCAACGTATTGCTTCAGGCGAAGTACCATTTGAATT
GGCTGATATGCGTATCTTAGAGCTTGACATGATGAGCGTTGTTGCAGGGACACGTTTCCGTGGTGATTTCGAAGAGCGTA
TGAATCAGATCATTGATGAGATTGAAGCTGATGGGAAAATCATTCTCTTTATTGACGAACTACATACGATTATTGGATCT
GGTTCAGGTATTGATAGTACCTTGGATGCGGCTAATATTTTGAAACCGGCCCTTGCGCGCGGGACACTTCACATGGTTGG
AGCAACCACGCAAGCTGAATACCAAAAGCATATTGAGAAAGATGCAGCTTTATCCCGTCGTTTTGCTAAAATTACAATTG
AAGAACCAAGTGTATCTGAAGCAATCGATATTTTAAACGGTTTGCGTTCGTCTTATGAAGACTATCATCGTGTGACTATT
ACGGACGCGGCAGTTGAGACGGCAGTCAAGGCAGCGCATCGCTATTTGACGAGTAAGAATTTGCCTGATTCGGCAATTGA
CCTTTTAGATGAAGCGAGTGCAACTGTTCAAGTTCGTATCAAAAAAGAGGCCAAACGTGAGATAACGCCTTTGGATGAAG
CACTTATATCTGGGGATATTGGGGCTGCTGTTAAACAGTATAAGGCTAACCAAAAGGCAAAATTTCCTAAACCTGCTTTG
GTAGATGCGGATCAGATTATGCAAACTCTTAGTCGTTTATCAGGTATCCCTGTTGAGAAGATGACGCAGACTGACAGCAA
GCGTTACCTGAATCTTGAATCAGAACTCCACAAACGTGTTATTGGTCAAGATGAGGCGGTTTCGGCTATCAGCCGTGCTA
TTCGTCGTAATCAGTCAGGTATTCGTACTGGAAAACGTCCTATTGGCTCCTTCATGTTCCTTGGACCTACTGGTGTTGGT
AAGACAGAATTGGCCAAGGCTTTGGCGGAAGTTCTCTTTGATGATGAATCAGCTTTGCTTCGCTTTGATATGTCGGAGTA
TATGGAAAAATTTGCGGCTAGTCGCCTTAATGGTGCTCCTCCAGGATATGTCGGATATGATGAGGGTGGAGAGTTGACAG
AGAAAGTTCGAAATAAGCCCTACTCAGTTCTTCTCTTTGACGAGATTGAGAAAGCTCATCCAGATATCTTCAACGTTCTC
TTACAGGTTTTGGATGACGGTGTTTTAACAGATAGCCGTGGTCGTAAGGTTGATTTTTCAAACACTATCATCATTATGAC
CTCAAATTTGGGAGCTACAGCTCTTCGTGATGATAAAACTGTTGGTTTTGGTGCTCAAACTATTTCTCATAATCACCAAG
CCATGCAAGCACGCATTATGGAAGAGCTTAAGAAGTCCTATCGTCCAGAATTTATTAACCGTATTGATGAGAAGGTTGTC
TTCCACAGCTTAGAGGAAGAACAACTACATGACATTGTCAAGATTATGGTTAAACCATTAATTTCAGCTCTAGCCGATAA
AGGTATAAGCTTAAAATTCCAACCAGCTGCTCTTAAGCATTTGGCTAAGGATGGCTATGATATTGAGATGGGAGCTCGTC
CATTACGTCGTACGATTCAAACTCAAGTGGAGGACAAGTTGTCTGAGTTATTACTAGGTGGCCAAGTTGTTAGCGGACAG
ACCCTTAAGATTGGTTGCTCGAAAGATAAATTAACCTTTACAGTAGTGTAA

Domains

Predicted by InterproScan.

• C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small) (724-804)

• AAA domain (Cdc48 subfamily) (AAA_2) (546-717)

• ATPase family associated with various cellular activities (AAA) (AAA) (238-370)

• AAA lid domain (AAA_lid_9) (377-454)

• Clp amino terminal domain, pathogenicity island component (Clp_N) (107-135)

• Clp amino terminal domain, pathogenicity island component (Clp_N) (15-46)

3D structure

• AlphaFold DB: Q5M6G1

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
clpC	Streptococcus thermophilus LMD-9	99.387	100	0.994
clpC	Streptococcus mutans UA159	72.426	100	0.727
clpC	Streptococcus pneumoniae Rx1	65.971	100	0.663
clpC	Streptococcus pneumoniae TIGR4	65.971	100	0.663
clpC	Streptococcus pneumoniae D39	65.971	100	0.663
clpC	Lactococcus lactis subsp. lactis strain DGCC12653	50.421	100	0.513
clpC	Bacillus subtilis subsp. subtilis str. 168	46.407	100	0.47
clpE	Streptococcus mutans UA159	47.444	83.134	0.394
clpE	Streptococcus pneumoniae TIGR4	46.486	83.245	0.387
clpE	Streptococcus pneumoniae R6	46.4	83.112	0.386
clpE	Streptococcus pneumoniae D39	46.4	83.112	0.386
clpE	Streptococcus pneumoniae Rx1	46.4	83.112	0.386
clpA	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	42.072	89.845	0.378
clpC	Lactococcus lactis subsp. cremoris KW2	45.779	82.353	0.377

References

• [1]: Astrid Wahl et al. (2014) Control of natural transformation in salivarius Streptococci through specific degradation of σX by the MecA-ClpCP protease complex. Journal of Bacteriology 196(15):2807-16. [PMID: 24837292]
• [2]: Céline Boutry et al. (2012) Adaptor protein MecA is a negative regulator of the expression of late competence genes in Streptococcus thermophilus. Journal of Bacteriology 194(7):1777-88. [PMID: 22287513]
• [3]: Truls Johan Biørnstad et al. (2011) ClpC acts as a negative regulator of competence in Streptococcus thermophilus. Microbiology (Reading, England) 157(Pt 6):1676-1684. [PMID: 21436217]