NTDB

Overview

Name	clpC	Type	Regulator
Locus tag	BSU_00860	Genome accession	NC_000964
Coordinates	103572..106004 (+)	Length	810 a.a.
NCBI ID	NP_387967.1	Uniprot ID	P37571
Organism	Bacillus subtilis subsp. subtilis str. 168
Function	degradation of ComK; degradation of DegU Competence regulation

Function

ComK is targeted by the adaptor protein MecA and degraded in a complex with ClpC and ClpP. Preferential degradation of DegU-P by ClpCP, but not of unphosphorylated DegU, was reported.

Genomic Context

Location: 98572..111004

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
BSU_00830 (BSU00830)	ctsR	101449..101913 (+)	465	NP_387964.1	transcriptional regulator of class III stress genes	-
BSU_00840 (BSU00840)	mcsA	101927..102484 (+)	558	NP_387965.1	activator of protein kinase McsB	-
BSU_00850 (BSU00850)	mcsB	102484..103575 (+)	1092	NP_387966.1	protein arginine kinase	-
BSU_00860 (BSU00860)	clpC	103572..106004 (+)	2433	NP_387967.1	class III stress response-related ATPase, AAA+ superfamily	Regulator
BSU_00870 (BSU00870)	radA	106096..107472 (+)	1377	NP_387968.1	DNA repair protein; 6-O-methylguanine-DNA methyltransferase	Machinery gene
BSU_00880 (BSU00880)	disA	107476..108558 (+)	1083	NP_387969.1	diadenylate cyclase; DNA integrity scanning protein; cell cycle checkpoint DNA scanning protein	-
BSU_00890 (BSU00890)	yacL	108674..109774 (+)	1101	NP_387970.1	putative membrane protein possibly involved in RNA binding	-
BSU_00900 (BSU00900)	ispD	109789..110487 (+)	699	NP_387971.1	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, nonmevalonate isoprenoid pathway	-
BSU_00910 (BSU00910)	ispF	110480..110956 (+)	477	NP_387972.1	2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase	-

Regulatory network

Positive effect

Negative effect

Regulator	Target	Regulation
clpC	degU	negative effect
degU	comK	positive effect
comK	comK	positive effect
comK	late competence genes	positive effect
codY	comK	negative effect
clpP	comK	negative effect
mecA	comK	negative effect
kre	comK	negative effect
abrB	comK	negative effect
comS	comK	positive effect
spo0A	comK	positive effect
rok	comK	negative effect
clpC	comK	negative effect
med	comK	positive effect
spo0A	comK	negative effect
comK	late competence genes	positive effect
clpP	degU	negative effect
abrB	rok	negative effect
spo0A	abrB	negative effect
comA	comS	positive effect
spo0A	rok	negative effect
sinR	spo0A	negative effect
sinR	rok	negative effect
sinR	degU	negative effect
degQ	degU	positive effect
degS	degU	positive effect
rapC	comA	negative effect
rapF	comA	negative effect
comP	comA	positive effect
sinI	sinR	negative effect
phrC	rapC	negative effect
phrF	rapF	negative effect
comX	comP	positive effect
comQ	comX	positive effect

Sequence

Protein

Download Length: 810 a.a. Molecular weight: 90118.60 Da Isoelectric Point: 6.0257

                                >NTDB_id=85 BSU_00860 NP_387967.1 103572..106004(+) (clpC) [Bacillus subtilis subsp. subtilis str. 168]

MMFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLIGRGQEMSQTIHY

TPRAKKVIELSMDEARKLGHSYVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLGSNETGSSAAGTNSNANT

PTLDSLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVM

TLDMGTVVAGTKYRGEFEDRLKKVMDEIRQAGNIILFIDELHTLIGAGGAEGAIDASNILKPSLARGELQCIGATTLDEY

RKYIEKDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGS

KVRLRSFTTPPNLKELEQKLDEVRKEKDAAVQSQEFEKAASLRDTEQRLREQVEDTKKSWKEKQGQENSEVTVDDIAMVV

SSWTGVPVSKIAQTETDKLLNMENILHSRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAE

SIFGDEESMIRIDMSEYMEKHSTSRLVGSPPGYVGYDEGGQLTEKVRRKPYSVVLLDEIEKAHPDVFNILLQVLEDGRLT

DSKGRTVDFRNTILIMTSNVGASELKRNKYVGFNVQDETQNHKDMKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLT

EIVSLMSDQLTKRLKEQDLSIELTDAAKAKVAEEGVDLEYGARPLRRAIQKHVEDRLSEELLRGNIHKGQHIVLDVEDGE

FVVKTTAKTN

Nucleotide

Download Length: 2433 bp

                                >NTDB_id=85 BSU_00860 NP_387967.1 103572..106004(+) (clpC) [Bacillus subtilis subsp. subtilis str. 168]

ATGATGTTTGGAAGATTTACAGAACGAGCTCAAAAAGTACTGGCGCTAGCACAGGAAGAAGCACTTCGGTTAGGTCATAA

TAACATTGGCACTGAGCATATTTTATTAGGACTGGTAAGAGAAGGAGAGGGCATTGCTGCTAAAGCTCTTCAAGCGCTTG

GACTCGGTTCAGAAAAAATTCAGAAAGAAGTAGAAAGTTTGATCGGGCGCGGGCAGGAAATGTCTCAAACGATTCATTAT

ACTCCTAGAGCTAAAAAAGTCATTGAGCTTTCAATGGATGAGGCAAGAAAACTCGGTCATTCTTATGTGGGAACAGAACA

TATTCTTCTTGGTCTGATTCGTGAAGGAGAAGGTGTTGCTGCGAGAGTTCTGAATAATCTCGGTGTCAGCTTAAATAAAG

CAAGACAGCAGGTGCTCCAGCTTCTAGGAAGTAATGAAACAGGATCATCAGCGGCAGGAACAAACAGCAATGCGAATACG

CCTACGCTTGACAGCTTGGCAAGAGACTTAACTGCTATTGCGAAGGAAGACAGCCTTGACCCTGTAATCGGCAGAAGCAA

GGAGATCCAGCGTGTCATTGAAGTGTTAAGCCGCAGAACGAAAAACAACCCTGTTCTCATTGGGGAACCAGGTGTAGGTA

AAACGGCTATCGCAGAAGGTTTGGCACAGCAAATTATCAATAATGAAGTACCCGAAATTTTGCGTGATAAACGTGTGATG

ACATTAGACATGGGAACAGTTGTTGCCGGCACAAAATACCGCGGAGAATTTGAGGATCGCCTGAAGAAGGTCATGGATGA

AATTCGCCAGGCAGGAAATATCATTCTATTCATCGATGAGCTCCATACATTAATCGGGGCAGGCGGAGCAGAAGGTGCTA

TTGATGCATCTAATATTTTAAAACCTTCACTTGCTCGTGGCGAACTCCAATGTATTGGTGCAACGACTCTTGATGAGTAC

CGTAAATATATTGAAAAAGATGCAGCACTGGAACGCCGTTTTCAGCCGATTCAGGTTGATCAGCCATCTGTAGATGAAAG

TATTCAAATTTTACAAGGTCTGCGTGACAGATACGAAGCCCACCACCGCGTTTCTATCACTGATGATGCCATTGAAGCTG

CGGTTAAGCTTTCTGACAGATATATTTCTGACCGCTTCCTTCCGGATAAAGCAATTGACTTGATCGATGAAGCGGGTTCA

AAGGTGAGACTGCGCTCATTTACAACGCCTCCTAACTTAAAAGAGCTTGAGCAGAAGCTTGATGAGGTTCGTAAAGAGAA

GGATGCGGCAGTGCAAAGCCAAGAGTTTGAAAAAGCTGCTTCCTTGCGTGATACTGAACAACGCCTGCGCGAGCAAGTAG

AGGATACGAAGAAATCATGGAAAGAGAAGCAAGGGCAGGAAAACTCAGAGGTTACTGTGGATGATATTGCGATGGTTGTA

TCCAGCTGGACCGGTGTGCCTGTATCTAAAATCGCCCAAACTGAAACTGATAAGCTTCTCAATATGGAAAACATTCTTCA

CTCCCGTGTCATCGGCCAGGATGAAGCAGTTGTAGCGGTTGCAAAAGCCGTCAGACGTGCAAGAGCAGGATTGAAAGATC

CTAAACGCCCAATCGGCTCATTCATTTTCTTAGGCCCTACAGGTGTAGGTAAAACAGAACTTGCACGAGCACTTGCTGAA

TCCATTTTTGGCGATGAAGAATCCATGATCAGAATTGATATGTCTGAATACATGGAAAAACATTCAACTTCAAGACTTGT

TGGTTCACCTCCGGGTTATGTGGGATATGATGAAGGCGGTCAATTGACAGAGAAAGTCAGAAGAAAACCTTACTCTGTCG

TGCTTCTTGATGAGATCGAGAAAGCGCACCCTGATGTCTTCAATATCCTTCTGCAAGTTCTTGAAGACGGACGATTGACT

GATTCTAAAGGACGCACAGTCGATTTCCGCAATACCATTCTGATCATGACATCAAACGTCGGAGCAAGTGAGCTAAAACG

CAATAAATATGTCGGCTTTAACGTTCAGGATGAAACTCAAAATCATAAAGACATGAAAGATAAAGTGATGGGTGAATTAA

AACGAGCGTTCAGACCTGAGTTCATCAACCGTATTGATGAAATCATTGTCTTCCATTCACTTGAGAAAAAACATCTCACT

GAGATTGTGTCATTAATGTCTGATCAATTAACGAAACGCCTGAAAGAACAAGATCTTTCTATCGAATTGACAGATGCTGC

AAAAGCGAAAGTCGCGGAAGAGGGCGTTGACCTGGAATACGGTGCCCGTCCGTTAAGAAGAGCGATCCAAAAACATGTCG

AGGATCGTTTATCTGAAGAACTCCTCAGAGGAAATATTCATAAAGGACAGCATATTGTTCTTGATGTAGAAGATGGCGAA

TTTGTCGTAAAAACGACTGCTAAAACGAATTAA

Domains

Predicted by InterproScan.

Clp amino terminal domain, pathogenicity island component (Clp_N)

(93-143)

Clp amino terminal domain, pathogenicity island component (Clp_N)

(17-69)

AAA lid domain (AAA_lid_9)

(343-444)

ATPase family associated with various cellular activities (AAA) (AAA)

(205-317)

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

(714-793)

AAA domain (Cdc48 subfamily) (AAA_2)

(536-708)

Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.

3D structure

Source	ID	Structure
PDB	2K77
PDB	2Y1Q
PDB	2Y1R
PDB	3J3R
PDB	3J3S
PDB	3J3T
PDB	3J3U
PDB	3PXG
PDB	3PXI
PDB	5HBN
PDB	7ABR
PDB	8B3S
PDB	8OTK

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 (%)	H_a-value
clpC	Lactococcus lactis subsp. lactis strain DGCC12653	50.499	99.012	0.5
clpC	Streptococcus thermophilus LMD-9	46.65	100	0.473
clpC	Streptococcus thermophilus LMG 18311	46.407	100	0.47
clpC	Lactococcus lactis subsp. cremoris KW2	48.664	95.053	0.463
clpE	Streptococcus mutans UA159	53.313	86.189	0.459
clpE	Streptococcus pneumoniae TIGR4	52.308	86.436	0.452
clpE	Streptococcus pneumoniae Rx1	52.308	86.436	0.452
clpE	Streptococcus pneumoniae D39	52.308	86.436	0.452
clpE	Streptococcus pneumoniae R6	52.308	86.436	0.452
clpC	Streptococcus pneumoniae D39	45.241	99.877	0.452
clpC	Streptococcus pneumoniae Rx1	45.241	99.877	0.452
clpC	Streptococcus pneumoniae TIGR4	45.117	99.877	0.451
clpC	Streptococcus mutans UA159	43.826	100	0.445
clpA	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	36.237	100	0.405

Multiple sequence alignment

References

[1]	Andrew W Tanner et al. (2018) ClpC and MecA, components of a proteolytic machine, prevent Spo0A-P-dependent transcription without degradation. Molecular Microbiology 108(2):178-186. [PMID: 29446505]
[2]	Mitsuo Ogura et al. (2010) Autoregulation of the Bacillus subtilis response regulator gene degU is coupled with the proteolysis of DegU-P by ClpCP. Molecular Microbiology 75(5):1244-59. [PMID: 20070525]
[3]	Tilman Schlothauer et al. (2003) MecA, an adaptor protein necessary for ClpC chaperone activity. Proceedings of The National Academy of Sciences of The United States of America 100(5):2306-11. [PMID: 12598648]
[4]	K Turgay et al. (2001) Roles of the two ClpC ATP binding sites in the regulation of competence and the stress response. Molecular Microbiology 42(3):717-27. [PMID: 11722737]
[5]	K Turgay et al. (1997) Biochemical characterization of a molecular switch involving the heat shock protein ClpC, which controls the activity of ComK, the competence transcription factor of Bacillus subtilis. Genes & Development 11(1):119-28. [PMID: 9000055]
[6]	EIke Krüger et al. (1997) The Bacillus subtilis clpC operon encodes DNA repair and competence proteins. Microbiology (Reading, England) 143 ( Pt 4):1309-1316. [PMID: 9141693]
[7]	L Kong et al. (1994) Regulation of competence-specific gene expression by Mec-mediated protein-protein interaction in Bacillus subtilis. Proceedings of The National Academy of Sciences of The United States of America 91(13):5793-7. [PMID: 8016067]

Detailed information NTG0000085