Detailed information NTG0000243

Experimentally validated

Overview

• Name: clpE
• Type: Regulator
• Locus tag: SPR_RS03635
• Genome accession: NC_003098
• Coordinates: 723946..726204 (-)
• Length: 752 a.a.
• NCBI ID: WP_000882517.1
• Uniprot ID: A0A0D6J9M7
• Organism: Streptococcus pneumoniae R6
• Function: degradation of ComX Competence regulation

Function

Degradation of the ComX protein depends largely on a ClpEP protease complex.

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type	MGE coordinates	Gene coordinates	Relative position	Distance (bp)
IScluster/Tn	720316..723221	723946..726204	flank	725

Gene organization within MGE regions

Location: 720316..726204

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
SPR_RS03615 (spr0719)	tnpB	721347..721526 (-)	180	WP_000376911.1	IS66 family insertion sequence element accessory protein TnpB	-
SPR_RS03620 (spr0720)	-	721895..722194 (-)	300	WP_000767195.1	DUF1827 family protein	-
SPR_RS03625 (spr0721)	-	722359..722781 (-)	423	WP_001814211.1	NUDIX hydrolase	-
SPR_RS03630	-	722892..723739 (+)	848	Protein_721	IS630 family transposase	-
SPR_RS03635 (spr0725)	clpE	723946..726204 (-)	2259	WP_000882517.1	ATP-dependent Clp protease ATP-binding subunit	Regulator

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
clpE	comX/comX1	negative effect
comX/comX1	late competence genes	positive effect
comX/comX2	late competence genes	positive effect
comX/comX1	late competence genes	positive effect
comX/comX2	late competence genes	positive effect
clpE	comX/comX2	negative effect
clpP	comX/comX2	negative effect
clpP	comX/comX1	negative effect
clpP	comW	negative effect
comW	comX/comX2	positive effect
comW	comX/comX1	positive effect
mecA	comW	negative effect
clpC	comW	negative effect
comE	comW	positive effect
comE	comX/comX2	positive effect
comE	comB	positive effect
comE	comC/comC1	positive effect
comE	comX/comX1	positive effect
comE	comA	positive effect
comE	comD/comD1	positive effect
comE	comM	positive effect
comE	comE	positive effect
comD/comD1	comE	positive effect
stkP	comE	positive effect
comB	comC/comC1	positive effect
comC/comC1	comD/comD1	positive effect
comA	comC/comC1	positive effect
ciaH	comC/comC1	negative effect
ciaR	comC/comC1	negative effect
htrA	comC/comC1	negative effect
comM	cbpD	negative effect
ciaH	htrA	positive effect
ciaR	htrA	positive effect
htrA	comEA/celA/cilE	negative effect
htrA	comEC/celB	negative effect
cbpD	lytC	positive effect
cbpD	lytA	positive effect

Sequence

Protein

• Length: 752 a.a.
• Molecular weight: 83840.26 Da
• Isoelectric Point: 5.3713

>NTDB_id=243 SPR_RS03635 WP_000882517.1 723946..726204(-) (clpE) [Streptococcus pneumoniae R6]
MLCQNCKINDSTIHLYTNLNGKQKQIDLCQNCYKIIKTDPNNSLFKGMTDLNNRDFDPFGDFFNDLNNFRPSSNTPPIPP
TQSGGGYGGNGGYGSQNRGSAQTPPPSQEKGLLEEFGINVTEIARRGDIDPVIGRDDEIIRVIEILNRRTKNNPVLIGEP
GVGKTAVVEGLAQKIVDGDVPHKLQGKQVIRLDVVSLVQGTGIRGQFEERMQKLMEEIRKREDIILFIDEIHEIVGAGSA
SDGNMDAGNILKPALARGELQLVGATTLNEYRIIEKDAALERRMQPVKVDEPTVDETITILKGIQKKYEDYHHVQYTDAA
IEAAATLSNRYIQDRFLPDKAIDLLDEAGSKMNLTLNFVDPKVIDQRLIEAENLKSQATREEDFEKAAYFRDQIAKYKEM
QKKKITDQDTPIISEKTIEHIIEQKTNIPVGDLKEKEQSQLIHLAEDLKSHVIGQDDAVDKIAKAIRRNRVGLGTPNRPI
GSFLFVGPTGVGKTELSKQLAIELFGSADSMIRFDMSEYMEKHSVAKLVGAPPGYVGYDEAGQLTEKVRHNPYSLILLDE
VEKAHPDVMHMFLQVLDDGRLTDGQGRTVSFKDAIIIMTSNAGTGKTEASVGFGAAREGRTNSVLGELGNFFSPEFMNRF
DGIIEFKALSKDNLLQIVELMLADVNKRLSSNNIRLDVTDKVKEKLVDLGYDPKMGARPLRRTIQDYIEDTITDYYLENP
SEKDLKAVMTSKGNIQIKSAKKAEVKSSEKEK

Nucleotide

• Length: 2259 bp

>NTDB_id=243 SPR_RS03635 WP_000882517.1 723946..726204(-) (clpE) [Streptococcus pneumoniae R6]
ATGCTTTGTCAAAACTGTAAAATTAACGACTCAACAATTCATCTTTACACCAATCTCAATGGAAAACAAAAACAAATTGA
CCTCTGTCAAAACTGCTATAAGATTATCAAAACAGATCCTAACAATAGCCTCTTCAAAGGTATGACGGATCTGAACAATC
GTGACTTCGATCCCTTTGGTGATTTCTTCAATGATCTAAACAATTTCAGACCTTCTAGCAATACTCCTCCTATTCCCCCA
ACCCAATCAGGTGGAGGTTACGGTGGAAACGGCGGTTATGGTTCCCAAAATCGTGGATCTGCTCAAACTCCGCCACCTAG
CCAAGAAAAAGGCCTGCTGGAAGAATTTGGTATTAATGTAACTGAAATTGCCCGTCGTGGAGACATTGACCCCGTTATTG
GGCGCGACGATGAGATTATCCGTGTCATCGAGATTCTCAATCGTAGAACCAAGAATAATCCTGTCCTTATCGGTGAACCT
GGTGTCGGAAAAACGGCCGTTGTCGAAGGTCTAGCTCAGAAAATTGTCGATGGCGATGTGCCACATAAACTCCAAGGTAA
ACAAGTCATCCGTCTGGATGTGGTTAGCTTAGTTCAAGGAACGGGGATTCGAGGACAATTTGAAGAACGCATGCAAAAAC
TCATGGAAGAAATTCGCAAACGTGAAGACATCATCCTCTTTATCGATGAAATCCATGAAATTGTTGGTGCTGGTTCTGCG
AGTGATGGTAATATGGACGCAGGAAATATCCTCAAGCCAGCCCTTGCTCGTGGAGAACTGCAACTAGTCGGTGCTACTAC
CCTCAATGAATACCGTATCATTGAAAAGGATGCTGCCCTCGAGCGTCGTATGCAGCCTGTTAAAGTCGATGAACCAACGG
TGGACGAAACAATCACTATTCTCAAAGGGATTCAAAAGAAATACGAAGATTACCACCACGTTCAATATACAGATGCTGCG
ATTGAAGCAGCTGCAACTCTTTCCAATCGCTACATCCAAGATCGCTTCTTGCCTGACAAGGCCATTGACCTCCTAGATGA
AGCTGGTTCTAAGATGAACTTGACCTTGAATTTTGTGGATCCTAAAGTAATTGATCAGCGCTTGATTGAGGCTGAAAATC
TCAAGTCTCAAGCTACACGAGAAGAAGATTTTGAGAAGGCGGCCTACTTCCGCGACCAGATTGCCAAGTATAAGGAAATG
CAAAAGAAAAAGATCACAGACCAGGATACTCCTATCATCAGCGAGAAAACTATTGAGCACATTATCGAGCAGAAAACCAA
TATCCCTGTTGGTGATTTGAAAGAGAAAGAACAATCTCAACTCATCCATCTAGCCGAAGATCTCAAGTCTCATGTTATTG
GCCAAGATGATGCAGTCGATAAGATTGCCAAGGCTATTCGCCGTAATCGTGTCGGACTTGGTACCCCTAACCGCCCAATC
GGAAGCTTCCTCTTCGTTGGGCCAACTGGTGTCGGTAAGACAGAACTTTCCAAACAACTGGCTATCGAACTTTTTGGTTC
TGCTGATAGTATGATTCGCTTTGATATGAGTGAATACATGGAAAAACATAGTGTGGCTAAGTTGGTCGGCGCCCCTCCAG
GTTATGTTGGCTATGATGAGGCTGGTCAATTAACTGAAAAAGTTCGCCACAATCCATATTCTCTCATCCTTCTCGATGAA
GTGGAAAAAGCTCACCCAGATGTTATGCACATGTTTCTTCAAGTCTTGGACGATGGTCGTTTGACAGACGGGCAAGGACG
CACCGTTAGCTTCAAGGATGCCATCATTATCATGACCTCAAATGCAGGTACAGGAAAGACCGAAGCTAGCGTTGGATTTG
GTGCTGCTAGAGAAGGACGTACCAATTCTGTCCTCGGTGAACTCGGTAACTTCTTTAGCCCAGAGTTTATGAACCGTTTT
GATGGCATTATCGAATTTAAGGCTCTCAGCAAGGATAACCTCCTTCAGATTGTCGAGCTCATGCTAGCAGATGTTAACAA
GCGCCTCTCTAGTAACAACATTCGTTTGGATGTAACTGATAAGGTCAAGGAAAAGTTGGTTGACCTAGGTTATGATCCAA
AAATGGGAGCACGCCCACTTCGTCGGACTATTCAAGACTATATTGAGGACACAATCACTGACTACTACCTTGAAAATCCA
AGCGAAAAAGATCTCAAAGCAGTTATGACTAGCAAGGGAAACATTCAGATTAAATCTGCCAAAAAAGCTGAAGTTAAAAG
TTCTGAAAAAGAAAAATAA

Domains

Predicted by InterproScan.

• ATPase family associated with various cellular activities (AAA) (AAA) (155-276)

• C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small) (649-723)

• AAA lid domain (AAA_lid_9) (293-390)

• AAA domain (Cdc48 subfamily) (AAA_2) (478-641)

3D structure

• AlphaFold DB: A0A0D6J9M7

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
clpE	Streptococcus pneumoniae Rx1	100	100	1
clpE	Streptococcus pneumoniae D39	100	100	1
clpE	Streptococcus pneumoniae TIGR4	99.867	100	0.999
clpE	Streptococcus mutans UA159	82.754	99.336	0.822
clpC	Lactococcus lactis subsp. cremoris KW2	76.839	97.606	0.75
clpC	Bacillus subtilis subsp. subtilis str. 168	52.308	86.436	0.452
clpC	Lactococcus lactis subsp. lactis strain DGCC12653	47.687	83.378	0.398
clpC	Streptococcus pneumoniae Rx1	46.91	83.91	0.394
clpC	Streptococcus pneumoniae D39	46.91	83.91	0.394
clpC	Streptococcus pneumoniae TIGR4	46.91	83.91	0.394
clpC	Streptococcus thermophilus LMD-9	46.795	82.979	0.388
clpC	Streptococcus mutans UA159	46.571	83.378	0.388
clpC	Streptococcus thermophilus LMG 18311	46.4	83.112	0.386

References

• [1]: Andrew Piotrowski et al. (2009) Competence for genetic transformation in Streptococcus pneumoniae: termination of activity of the alternative sigma factor ComX is independent of proteolysis of ComX and ComW. Journal of Bacteriology 191(10):3359-66. [PMID: 19286798]