Detailed information NTG0000242

Experimentally validated

Overview

• Name: clpP
• Type: Regulator
• Locus tag: SP_RS03655
• Genome accession: NC_003028
• Coordinates: 706882..707472 (+)
• Length: 196 a.a.
• NCBI ID: WP_000613477.1
• Uniprot ID: A0A064BX72
• Organism: Streptococcus pneumoniae TIGR4
• Function: degradation of ComX; degradation of ComW Competence regulation

Function

Degradation of the ComX protein depends largely on a ClpEP protease complex. ComW is also a target of the Clp machinery and was shown to be degraded by ClpCP.

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)
Prophage	705523..716427	706882..707472	within	0

Gene organization within MGE regions

Location: 705523..716427

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
SP_RS03645 (SP_0744)	-	705523..705990 (+)	468	WP_000136976.1	deoxycytidylate deaminase	-
SP_RS03650 (SP_0745)	upp	706079..706708 (+)	630	WP_000515972.1	uracil phosphoribosyltransferase	-
SP_RS03655 (SP_0746)	clpP	706882..707472 (+)	591	WP_000613477.1	ATP-dependent Clp protease proteolytic subunit ClpP	Regulator
SP_RS03660 (SP_0748)	-	707551..707799 (+)	249	WP_000462126.1	YlbG family protein	-
SP_RS03665 (SP_0749)	-	707900..709060 (+)	1161	WP_000726149.1	ABC transporter substrate-binding protein	-
SP_RS03670 (SP_0750)	-	709328..710197 (+)	870	WP_000941421.1	branched-chain amino acid ABC transporter permease	-
SP_RS03675 (SP_0751)	-	710201..711157 (+)	957	WP_000662293.1	branched-chain amino acid ABC transporter permease	-
SP_RS03680 (SP_0752)	-	711157..711921 (+)	765	WP_001186003.1	ABC transporter ATP-binding protein	-
SP_RS03685 (SP_0753)	-	711921..712631 (+)	711	WP_000062224.1	ABC transporter ATP-binding protein	-
SP_RS03690 (SP_0754)	-	712939..713595 (+)	657	WP_000268636.1	CBS domain-containing protein	-
SP_RS03695 (SP_0755)	prfB	713703..714798 (+)	1096	WP_010963246.1	peptide chain release factor 2	-
SP_RS03700 (SP_0756)	ftsE	714816..715508 (+)	693	WP_000022268.1	cell division ATP-binding protein FtsE	-
SP_RS03705 (SP_0757)	ftsX	715501..716427 (+)	927	WP_000625536.1	permease-like cell division protein FtsX	-

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
clpP	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
comE	comX/comX2	positive effect
comE	comE	positive effect
comE	comX/comX1	positive effect
comE	comW	positive effect
comE	comA	positive effect
comE	comB	positive effect
comE	comM	positive effect
comE	comD/comD2	positive effect
comE	comC/comC2	positive effect
comD/comD2	comE	positive effect
stkP	comE	positive effect
clpP	comX/comX2	negative effect
clpP	comW	negative effect
comW	comX/comX2	positive effect
comW	comX/comX1	positive effect
mecA	comW	negative effect
clpC	comW	negative effect
clpE	comX/comX2	negative effect
clpE	comX/comX1	negative effect
comA	comC/comC2	positive effect
comB	comC/comC2	positive effect
comM	cbpD	negative effect
comC/comC2	comD/comD2	positive effect
ciaH	comC/comC2	negative effect
htrA	comC/comC2	negative effect
ciaR	comC/comC2	negative effect
cbpD	lytA	positive effect
cbpD	lytC	positive effect
ciaH	htrA	positive effect
htrA	comEC/celB	negative effect
htrA	comEA/celA/cilE	negative effect
ciaR	htrA	positive effect

Sequence

Protein

• Length: 196 a.a.
• Molecular weight: 21358.36 Da
• Isoelectric Point: 4.4910

>NTDB_id=242 SP_RS03655 WP_000613477.1 706882..707472(+) (clpP) [Streptococcus pneumoniae TIGR4]
MIPVVIEQTSRGERSYDIYSRLLKDRIIMLTGPVEDNMANSVIAQLLFLDAQDSTKDIYLYVNTPGGSVSAGLAIVDTMN
FIKADVQTIVMGMAASMGTVIASSGAKGKRFMLPNAEYMIHQPMGGTGGGTQQTDMAIAAEHLLKTRNTLEKILAENSGQ
SMEKVHADAERDNWMSAQETLEYGFIDEIMANNSLN

Nucleotide

• Length: 591 bp

>NTDB_id=242 SP_RS03655 WP_000613477.1 706882..707472(+) (clpP) [Streptococcus pneumoniae TIGR4]
ATGATTCCTGTAGTTATTGAACAAACAAGCCGTGGAGAACGTTCTTACGATATTTACTCACGTCTTCTCAAAGACCGCAT
CATTATGCTGACAGGTCCGGTTGAAGACAATATGGCTAACTCTGTTATTGCCCAATTGCTTTTCTTGGATGCCCAAGATA
GTACAAAAGATATTTACCTTTATGTCAATACACCAGGTGGTTCTGTTTCAGCTGGTTTGGCAATCGTAGATACCATGAAC
TTTATCAAGGCAGATGTCCAAACCATTGTTATGGGAATGGCTGCATCTATGGGGACTGTCATCGCATCAAGTGGAGCAAA
AGGCAAACGTTTCATGCTTCCAAATGCTGAATACATGATTCACCAACCAATGGGTGGTACAGGTGGTGGTACCCAACAAA
CTGATATGGCTATCGCTGCAGAACACTTGCTCAAAACTCGTAATACCTTGGAAAAAATCTTGGCTGAAAATTCAGGTCAG
TCAATGGAAAAAGTCCATGCAGATGCAGAACGTGATAACTGGATGAGCGCCCAGGAAACACTTGAATATGGCTTTATTGA
TGAAATTATGGCCAACAATTCATTGAACTAA

Domains

Predicted by InterproScan.

• Clp protease (CLP_protease) (11-192)

3D structure

• AlphaFold DB: A0A064BX72

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
clpP	Streptococcus pneumoniae R6	100	100	1
clpP	Streptococcus pneumoniae D39	100	100	1
clpP	Streptococcus pneumoniae Rx1	100	100	1
clpP	Streptococcus thermophilus LMD-9	92.821	99.49	0.923
clpP	Streptococcus thermophilus LMG 18311	92.821	99.49	0.923
clpP	Streptococcus pyogenes JRS4	90.769	99.49	0.903
clpP	Streptococcus pyogenes MGAS315	90.769	99.49	0.903
clpP	Streptococcus mutans UA159	85.714	100	0.857
clpP	Lactococcus lactis subsp. lactis strain DGCC12653	85.128	99.49	0.847
clpP	Lactococcus lactis subsp. cremoris KW2	84.615	99.49	0.842
clpP	Bacillus subtilis subsp. subtilis str. 168	58.854	97.959	0.577
clpP	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	58.031	98.469	0.571

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]