Detailed information NTG0000610

Experimentally validated

Overview

• Name: clpC
• Type: Regulator
• Locus tag: V4T04_RS10165
• Genome accession: NZ_JAZICS010000009
• Coordinates: 2149..4599 (-)
• Length: 816 a.a.
• NCBI ID: WP_012897346.1
• Uniprot ID: S6FJR3
• Organism: Lactococcus lactis subsp. lactis strain DGCC12653
• Function: degradation of ComX Competence regulation

Function

The Clp degradation machinery plays a central role in competence repression.

Genomic Context

Location: 1..9599

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
V4T04_RS10155	eno	1..1272 (-)	1272	WP_260377620.1	phosphopyruvate hydratase	-
V4T04_RS10160	raiA	1457..2014 (-)	558	WP_003129564.1	ribosome hibernation-promoting factor, HPF/YfiA family	-
V4T04_RS10165	clpC	2149..4599 (-)	2451	WP_012897346.1	ATP-dependent Clp protease ATP-binding subunit	Regulator
V4T04_RS10170	-	4589..5044 (-)	456	WP_010905471.1	CtsR family transcriptional regulator	-
V4T04_RS10175	greA	5221..5694 (-)	474	WP_033899645.1	transcription elongation factor GreA	-
V4T04_RS10180	mltG	5754..7406 (-)	1653	WP_058203216.1	endolytic transglycosylase MltG	-
V4T04_RS10185	rpoE	7543..8106 (-)	564	WP_012897344.1	DNA-directed RNA polymerase subunit delta	-
V4T04_RS10190	-	8323..8835 (-)	513	WP_012897343.1	adenine phosphoribosyltransferase	-

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
clpC	comX	negative effect
clpP	comX	negative effect
mecA	comX	negative effect
ccpA	comX	negative effect
codY	comX	negative effect
covR	comX	negative effect
covS	comX	negative effect

Sequence

Protein

• Length: 816 a.a.
• Molecular weight: 90425.82 Da
• Isoelectric Point: 6.5300

>NTDB_id=610 V4T04_RS10165 WP_012897346.1 2149..4599(-) (clpC) [Lactococcus lactis subsp. lactis strain DGCC12653]
MKFENIKYTPTLDRILEKAEEYAHQYQYGTIESAHLLAAMATTSGSIAYSLLAGMNVDSSDLLIDLEDLSSHVKVKRSTL
RFSPRAEEVMTAASFLAIHNNSEAVGTEHLLYALLQVEDGFGLQLLKLQKINIVSLRKELEKRTGLKVPESKKAVTPMSK
RKMAKGVAENSTTPTLDSVSSDLTEEARLGKLDPMIGREAEIDRLIHILSRRTKNNPVLVGEPGVGKSAIIEGLAQRIVN
GQVPIGLMNSRIMALNMATVVAGTKFRGEFEDRLTAIVEEVSSDPDVIIFIDELHTIIGAGGGMDSVNDAANILKPALAR
GDFQMVGATTYHEYQKYIEKDEALERRLARINVDEPSPDEAIAILQGLREKFEDYHQVKFTDQAIKSAVMLSVRYMTSRK
LPDKAIDLLDEAAAAVKISVKNQQTKRLDLEKELAEAQEELSEAVIKLDIKASRTKEKAVEKIADKIYKFSVKEDKRQEV
TDQAVVAVASTLTGVPITQMTKSESDRLINLEKELHKRVVGQEEAISAVSRAIRRARSGVADSRRPMGSFMFLGPTGVGK
TELAKALADSVFGSEDNMIRVDMSEFMEKHSTSRLIGAPPGYVGYDEGGQLTERVRNKPYSVVLLDEVEKAHPDVFNIML
QILDDGFVTDTKGRKVDFRNTIIIMTSNLGATALRDDKTVGFGAKNITADYSAMKSRILEELKRHYRPEFLNRIDENIVF
HSLESQEIEQIVKIMSKSLIKRLAEQDIHVKLTPSAVKLIAEVGFDPEYGARPLRKALQKEVEDLLSEQLLSGEIKAGNH
VSIGASNKKIKIAQIV

Nucleotide

• Length: 2451 bp

>NTDB_id=610 V4T04_RS10165 WP_012897346.1 2149..4599(-) (clpC) [Lactococcus lactis subsp. lactis strain DGCC12653]
ATGAAATTTGAAAATATAAAATATACACCAACGCTTGACCGAATTTTAGAAAAAGCGGAAGAGTATGCTCACCAATATCA
ATATGGCACCATTGAAAGTGCTCATTTACTAGCTGCAATGGCAACGACCTCAGGCTCAATTGCTTACAGCCTTCTTGCAG
GAATGAATGTTGATTCTTCTGACTTACTGATTGATTTAGAGGATTTATCAAGTCATGTTAAGGTCAAACGTTCAACTTTA
CGTTTTTCACCTCGTGCAGAAGAAGTGATGACTGCGGCAAGTTTTTTAGCAATTCATAATAACTCAGAAGCCGTTGGAAC
AGAACACCTGCTTTATGCCCTACTTCAAGTAGAAGATGGATTTGGTCTTCAACTTCTAAAATTACAAAAAATCAATATTG
TATCTTTGCGAAAAGAGCTTGAGAAAAGAACTGGACTCAAAGTTCCAGAAAGTAAAAAAGCTGTGACTCCAATGTCAAAA
CGTAAGATGGCAAAGGGAGTTGCAGAAAACTCAACGACGCCAACGTTAGACTCTGTATCCTCAGATTTAACCGAAGAAGC
TCGCTTGGGTAAACTTGACCCAATGATTGGACGAGAAGCTGAAATTGACCGTTTGATTCATATTCTCAGCCGCAGAACAA
AAAATAATCCTGTCTTAGTTGGAGAGCCCGGTGTTGGGAAATCAGCAATTATTGAAGGTTTGGCCCAAAGAATTGTCAAT
GGTCAAGTTCCAATTGGTTTGATGAATAGTCGAATTATGGCCTTGAATATGGCGACTGTTGTTGCTGGGACAAAATTTAG
AGGTGAATTTGAGGATCGTTTGACAGCTATTGTTGAAGAAGTTAGCAGTGATCCAGATGTCATTATTTTCATTGATGAAT
TACACACAATCATCGGTGCTGGTGGCGGTATGGATTCTGTCAATGATGCCGCAAATATTTTGAAACCAGCGCTTGCTCGT
GGTGATTTTCAAATGGTCGGAGCAACAACCTATCATGAATATCAAAAATATATTGAAAAAGATGAAGCTTTAGAACGCCG
TTTGGCGAGAATAAATGTTGATGAGCCAAGTCCAGATGAAGCGATTGCTATTTTGCAAGGCTTACGTGAAAAATTTGAAG
ACTATCATCAAGTGAAATTTACTGACCAAGCCATTAAAAGTGCTGTAATGCTCAGTGTTCGTTATATGACTAGCCGAAAA
TTGCCTGACAAAGCCATTGATTTACTTGATGAAGCTGCAGCAGCAGTGAAAATTTCTGTCAAAAATCAACAAACAAAACG
TCTTGATTTAGAAAAAGAATTAGCGGAAGCTCAAGAAGAATTATCAGAAGCTGTCATTAAACTTGATATCAAAGCGTCTC
GTACAAAAGAAAAAGCAGTTGAAAAAATTGCTGACAAGATTTATAAATTCTCAGTAAAAGAAGATAAACGTCAAGAAGTT
ACTGACCAAGCTGTTGTTGCTGTTGCCTCAACACTGACAGGTGTTCCAATCACACAAATGACTAAGTCTGAAAGTGATCG
TTTAATCAATCTTGAAAAAGAATTACACAAACGAGTTGTTGGACAAGAAGAAGCTATTTCTGCCGTTTCAAGAGCCATTC
GTCGGGCACGTTCCGGTGTTGCTGACAGCCGTCGTCCAATGGGTTCTTTCATGTTCCTTGGACCAACAGGGGTCGGTAAA
ACCGAACTTGCTAAAGCACTGGCTGACAGTGTGTTTGGTAGTGAAGATAATATGATTCGTGTTGACATGAGTGAATTCAT
GGAAAAACATTCGACTTCACGCTTGATTGGAGCTCCTCCAGGGTATGTAGGTTATGATGAGGGTGGTCAATTGACAGAAC
GCGTTCGTAATAAACCTTATTCTGTTGTTCTTTTAGATGAAGTCGAAAAAGCTCATCCTGACGTTTTCAACATCATGTTG
CAAATTCTAGATGATGGCTTTGTGACTGATACTAAAGGTCGTAAAGTTGATTTCAGAAATACAATTATTATCATGACTTC
AAACTTGGGAGCGACTGCTCTTCGTGATGATAAGACAGTTGGTTTTGGCGCTAAAAATATCACAGCTGATTATTCAGCCA
TGAAATCAAGAATATTAGAAGAGCTTAAACGTCATTATCGTCCTGAGTTTCTTAATCGAATTGATGAAAATATTGTTTTC
CACTCATTGGAAAGTCAAGAGATTGAACAAATTGTTAAAATTATGAGTAAATCTTTGATTAAACGTCTGGCAGAACAAGA
TATTCATGTTAAACTCACACCGTCAGCGGTGAAATTAATTGCTGAGGTAGGTTTTGACCCAGAATATGGTGCACGTCCGC
TCCGCAAGGCTCTTCAAAAAGAAGTTGAAGACCTTTTAAGTGAACAATTGCTCTCTGGTGAAATCAAAGCAGGTAATCAT
GTTTCAATTGGGGCATCTAATAAAAAAATTAAAATCGCTCAAATTGTTTGA

Domains

Predicted by InterproScan.

• C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small) (723-802)

• Clp amino terminal domain, pathogenicity island component (Clp_N) (19-69)

• Clp amino terminal domain, pathogenicity island component (Clp_N) (96-144)

• ATPase family associated with various cellular activities (AAA) (AAA) (218-334)

• AAA domain (Cdc48 subfamily) (AAA_2) (545-716)

• AAA lid domain (AAA_lid_9) (357-453)

3D structure

• AlphaFold DB: S6FJR3

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
clpC	Streptococcus thermophilus LMD-9	50.542	100	0.515
clpC	Streptococcus thermophilus LMG 18311	50.421	100	0.513
clpC	Streptococcus mutans UA159	49.1	100	0.503
clpC	Streptococcus pneumoniae D39	48.798	100	0.501
clpC	Streptococcus pneumoniae Rx1	48.798	100	0.501
clpC	Bacillus subtilis subsp. subtilis str. 168	50.499	99.012	0.5
clpC	Streptococcus pneumoniae TIGR4	48.678	100	0.5
clpE	Streptococcus mutans UA159	47.846	86.321	0.413
clpC	Lactococcus lactis subsp. cremoris KW2	47.023	87.567	0.412
clpE	Streptococcus pneumoniae R6	47.687	83.378	0.398
clpE	Streptococcus pneumoniae D39	47.687	83.378	0.398
clpE	Streptococcus pneumoniae Rx1	47.687	83.378	0.398
clpE	Streptococcus pneumoniae TIGR4	47.687	83.378	0.398
clpA	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	34.555	100	0.372

References

• [1]: Frédéric Toussaint et al. (2024) Unveiling the regulatory network controlling natural transformation in lactococci. PLoS Genetics 20(7):e1011340. [PMID: 38950059]