Detailed information NTG0000244

Experimentally validated

Overview

• Name: clpP
• Type: Regulator
• Locus tag: SPR_RS03300
• Genome accession: NC_003098
• Coordinates: 661436..662026 (+)
• Length: 196 a.a.
• NCBI ID: WP_000613477.1
• Uniprot ID: A0A064BX72
• Organism: Streptococcus pneumoniae R6
• 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	660077..671088	661436..662026	within	0

Gene organization within MGE regions

Location: 660077..671088

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
SPR_RS03290 (spr0654)	-	660077..660544 (+)	468	WP_000136976.1	deoxycytidylate deaminase	-
SPR_RS03295 (spr0655)	upp	660633..661262 (+)	630	WP_000515974.1	uracil phosphoribosyltransferase	-
SPR_RS03300 (spr0656)	clpP	661436..662026 (+)	591	WP_000613477.1	ATP-dependent Clp protease proteolytic subunit ClpP	Regulator
SPR_RS03305 (spr0657)	-	662105..662353 (+)	249	WP_000462126.1	YlbG family protein	-
SPR_RS03310 (spr0659)	-	662455..663615 (+)	1161	WP_000726149.1	ABC transporter substrate-binding protein	-
SPR_RS03315 (spr0660)	-	663883..664752 (+)	870	WP_000941426.1	branched-chain amino acid ABC transporter permease	-
SPR_RS03320 (spr0661)	-	664756..665712 (+)	957	WP_000662293.1	branched-chain amino acid ABC transporter permease	-
SPR_RS03325 (spr0662)	-	665712..666476 (+)	765	WP_001186003.1	ABC transporter ATP-binding protein	-
SPR_RS03330 (spr0663)	-	666476..667186 (+)	711	WP_000114808.1	ABC transporter ATP-binding protein	-
SPR_RS03335 (spr0664)	-	667600..668256 (+)	657	WP_000268654.1	CBS domain-containing protein	-
SPR_RS03340 (spr0665)	prfB	668364..669459 (+)	1096	WP_097556756.1	peptide chain release factor 2	-
SPR_RS03345 (spr0666)	ftsE	669477..670169 (+)	693	WP_000022268.1	cell division ATP-binding protein FtsE	-
SPR_RS03350 (spr0667)	ftsX	670162..671088 (+)	927	WP_000625532.1	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
clpE	comX/comX2	negative effect
clpE	comX/comX1	negative 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
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: 196 a.a.
• Molecular weight: 21358.36 Da
• Isoelectric Point: 4.4910

>NTDB_id=244 SPR_RS03300 WP_000613477.1 661436..662026(+) (clpP) [Streptococcus pneumoniae R6]
MIPVVIEQTSRGERSYDIYSRLLKDRIIMLTGPVEDNMANSVIAQLLFLDAQDSTKDIYLYVNTPGGSVSAGLAIVDTMN
FIKADVQTIVMGMAASMGTVIASSGAKGKRFMLPNAEYMIHQPMGGTGGGTQQTDMAIAAEHLLKTRNTLEKILAENSGQ
SMEKVHADAERDNWMSAQETLEYGFIDEIMANNSLN

Nucleotide

• Length: 591 bp

>NTDB_id=244 SPR_RS03300 WP_000613477.1 661436..662026(+) (clpP) [Streptococcus pneumoniae R6]
ATGATTCCTGTAGTTATTGAACAAACAAGCCGTGGAGAACGTTCTTACGATATTTACTCACGTCTTCTCAAAGACCGCAT
CATTATGCTGACAGGTCCGGTTGAAGACAATATGGCTAACTCTGTTATTGCCCAACTGCTTTTCTTGGATGCCCAAGATA
GTACAAAAGATATTTACCTTTATGTCAATACACCAGGTGGTTCTGTTTCAGCTGGTTTGGCAATCGTAGATACCATGAAC
TTTATCAAGGCAGATGTCCAAACCATTGTTATGGGAATGGCTGCATCTATGGGAACAGTCATCGCATCAAGTGGAGCAAA
AGGCAAACGTTTCATGCTTCCAAATGCTGAATACATGATTCACCAACCAATGGGCGGTACAGGTGGTGGTACCCAACAAA
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 D39	100	100	1
clpP	Streptococcus pneumoniae Rx1	100	100	1
clpP	Streptococcus pneumoniae TIGR4	100	100	1
clpP	Streptococcus thermophilus LMG 18311	92.821	99.49	0.923
clpP	Streptococcus thermophilus LMD-9	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]