Detailed information    

experimental Experimentally validated

Overview

Name   prx   Type   Regulator
Locus tag   SPYM3_RS04945 Genome accession   NC_004070
Coordinates   977437..977625 (-) Length   62 a.a.
NCBI ID   WP_011054546.1    Uniprot ID   A0A5S4TJS4
Organism   Streptococcus pyogenes MGAS315     
Function   Inhibit ComR activation   
Competence regulation

Function

In vitro experiments demonstrate that Prx binds ComR directly and prevents the ComR-XIP complex from interacting with DNA. Mutations of prx in vivo caused increased expression of the late competence gene ssb when induced with XIP as compared to wild-type, and Prx orthologues are able to inhibit ComR activation by XIP in a reporter strain which lacks an endogenous prx. An X-ray crystal structure of Prx reveals a unique fold that implies a novel molecular mechanism to inhibit ComR.


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 969849..1019176 977437..977625 within 0


Gene organization within MGE regions


Location: 969849..1019176
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SPYM3_RS04915 (SpyM3_0913) pfkA 969849..970862 (-) 1014 WP_011054544.1 6-phosphofructokinase -
  SPYM3_RS04920 (SpyM3_0914) - 970942..974052 (-) 3111 WP_011054545.1 DNA polymerase III subunit alpha -
  SPYM3_RS04925 (SpyM3_0915) - 974237..974608 (+) 372 WP_002989617.1 GntR family transcriptional regulator -
  SPYM3_RS04930 (SpyM3_0916) - 974608..975306 (+) 699 WP_002984437.1 ABC transporter ATP-binding protein -
  SPYM3_RS04935 (SpyM3_0917) - 975316..976101 (+) 786 WP_002984433.1 hypothetical protein -
  SPYM3_RS04940 (SpyM3_0918) - 976232..976846 (-) 615 WP_002989607.1 TVP38/TMEM64 family protein -
  SPYM3_RS04945 (SpyM3_0919) prx 977437..977625 (-) 189 WP_011054546.1 hypothetical protein Regulator
  SPYM3_RS04950 (SpyM3_0920) entC3 977738..978520 (-) 783 WP_002988472.1 enterotoxin type C3 EntC3 -
  SPYM3_RS04955 (SpyM3_0921) - 978733..979857 (-) 1125 WP_011054547.1 Fic family protein -
  SPYM3_RS04960 (SpyM3_0922) - 979995..981203 (-) 1209 WP_011054548.1 glucosaminidase domain-containing protein -
  SPYM3_RS04970 (SpyM3_0923) - 981319..981546 (-) 228 WP_000609113.1 phage holin -
  SPYM3_RS04975 (SpyM3_0924) - 981543..981818 (-) 276 WP_002987582.1 DUF7365 family protein -
  SPYM3_RS04980 (SpyM3_0925) - 981828..982445 (-) 618 WP_010922094.1 DUF1366 domain-containing protein -
  SPYM3_RS04985 (SpyM3_0926) - 982448..982879 (-) 432 WP_002983467.1 DUF1617 family protein -
  SPYM3_RS04990 (SpyM3_0927) - 982891..984774 (-) 1884 WP_011054549.1 gp58-like family protein -
  SPYM3_RS04995 (SpyM3_0929) hylP 984789..985803 (-) 1015 Protein_951 hyaluronidase HylP -
  SPYM3_RS05000 (SpyM3_0930) - 985800..987944 (-) 2145 WP_044557243.1 phage tail spike protein -
  SPYM3_RS05005 (SpyM3_0931) - 987941..988648 (-) 708 WP_011054553.1 distal tail protein Dit -
  SPYM3_RS05010 (SpyM3_0932) - 988648..992571 (-) 3924 WP_011054554.1 phage tail tape measure protein -
  SPYM3_RS10340 (SpyM3_0933) - 992584..992733 (-) 150 WP_023609816.1 hypothetical protein -
  SPYM3_RS05020 (SpyM3_0934) gpG 992781..993107 (-) 327 WP_011054556.1 phage tail assembly chaperone G -
  SPYM3_RS05025 (SpyM3_0935) - 993160..993771 (-) 612 WP_011054557.1 major tail protein -
  SPYM3_RS05030 (SpyM3_0936) - 993790..994215 (-) 426 WP_011054558.1 hypothetical protein -
  SPYM3_RS05035 (SpyM3_0937) - 994212..994589 (-) 378 WP_011054559.1 HK97-gp10 family putative phage morphogenesis protein -
  SPYM3_RS05040 (SpyM3_0938) - 994586..994924 (-) 339 WP_011054560.1 phage head closure protein -
  SPYM3_RS05045 (SpyM3_0939) - 994921..995223 (-) 303 WP_011054561.1 head-tail connector protein -
  SPYM3_RS10630 (SpyM3_0940) - 995226..995354 (-) 129 WP_011054562.1 hypothetical protein -
  SPYM3_RS05050 (SpyM3_0941) - 995368..996552 (-) 1185 WP_011054563.1 phage major capsid protein -
  SPYM3_RS05055 (SpyM3_0942) - 996578..997243 (-) 666 WP_011054564.1 head maturation protease, ClpP-related -
  SPYM3_RS05060 (SpyM3_0943) - 997221..998441 (-) 1221 WP_011054565.1 phage portal protein -
  SPYM3_RS05065 (SpyM3_0944) - 998475..998741 (-) 267 WP_011054566.1 hypothetical protein -
  SPYM3_RS10345 (SpyM3_0945) - 998734..998904 (-) 171 WP_011054567.1 hypothetical protein -
  SPYM3_RS05070 (SpyM3_0946) - 998901..1000655 (-) 1755 WP_011054568.1 terminase large subunit -
  SPYM3_RS05075 (SpyM3_0947) - 1000670..1001137 (-) 468 WP_011054569.1 phage terminase small subunit P27 family -
  SPYM3_RS05080 (SpyM3_0948) - 1001309..1001647 (-) 339 WP_002985375.1 HNH endonuclease -
  SPYM3_RS05090 (SpyM3_0950) - 1002233..1002673 (-) 441 WP_011054571.1 ArpU family phage packaging/lysis transcriptional regulator -
  SPYM3_RS05095 (SpyM3_0951) - 1002946..1003581 (-) 636 WP_011054572.1 N-6 DNA methylase -
  SPYM3_RS05100 (SpyM3_0952) - 1003581..1003982 (-) 402 WP_011054573.1 DUF7448 domain-containing protein -
  SPYM3_RS05105 (SpyM3_0953) - 1004173..1004547 (-) 375 WP_011054574.1 methyltransferase domain-containing protein -
  SPYM3_RS05110 - 1004572..1004856 (-) 285 WP_011106747.1 hypothetical protein -
  SPYM3_RS05115 (SpyM3_0954) - 1004853..1005056 (-) 204 WP_011054575.1 hypothetical protein -
  SPYM3_RS05120 (SpyM3_0955) - 1005040..1005360 (-) 321 WP_011054576.1 VRR-NUC domain-containing protein -
  SPYM3_RS05125 (SpyM3_0956) - 1005357..1005770 (-) 414 WP_008087509.1 hypothetical protein -
  SPYM3_RS09920 (SpyM3_0957) - 1006032..1007039 (-) 1008 WP_228358681.1 phage/plasmid primase, P4 family -
  SPYM3_RS10790 (SpyM3_0958) - 1006952..1007506 (-) 555 WP_011054578.1 hypothetical protein -
  SPYM3_RS05140 (SpyM3_0959) - 1007496..1008308 (-) 813 WP_011106664.1 bifunctional DNA primase/polymerase -
  SPYM3_RS05145 (SpyM3_0960) - 1008311..1008769 (-) 459 WP_011054580.1 DUF669 domain-containing protein -
  SPYM3_RS05150 (SpyM3_0961) - 1008785..1010014 (-) 1230 WP_011054581.1 DEAD/DEAH box helicase -
  SPYM3_RS05155 (SpyM3_0962) - 1010116..1010796 (-) 681 WP_002995975.1 AAA family ATPase -
  SPYM3_RS05160 (SpyM3_0963) - 1010797..1011279 (-) 483 WP_011054582.1 siphovirus Gp157 family protein -
  SPYM3_RS05165 (SpyM3_0964) - 1011508..1011822 (-) 315 WP_011054583.1 helix-turn-helix transcriptional regulator -
  SPYM3_RS10635 (SpyM3_0965) - 1011838..1011972 (-) 135 WP_002995985.1 hypothetical protein -
  SPYM3_RS05170 (SpyM3_0966) - 1011969..1012265 (-) 297 WP_011054584.1 MerR family transcriptional regulator -
  SPYM3_RS05175 (SpyM3_0967) - 1012343..1012528 (-) 186 WP_011054585.1 helix-turn-helix domain-containing protein -
  SPYM3_RS05180 (SpyM3_0968) - 1012695..1012934 (+) 240 WP_011054586.1 hypothetical protein -
  SPYM3_RS05185 (SpyM3_0969) - 1013085..1013294 (+) 210 WP_002984292.1 hypothetical protein -
  SPYM3_RS05195 (SpyM3_0971) - 1013510..1013749 (-) 240 WP_011054588.1 helix-turn-helix domain-containing protein -
  SPYM3_RS05200 (SpyM3_0972) - 1013823..1014209 (+) 387 WP_011054589.1 hypothetical protein -
  SPYM3_RS05205 (SpyM3_0973) - 1014198..1014404 (-) 207 WP_011054590.1 hypothetical protein -
  SPYM3_RS05210 (SpyM3_0974) - 1014461..1015240 (+) 780 WP_011054591.1 hypothetical protein -
  SPYM3_RS09925 (SpyM3_0976) - 1015374..1015520 (-) 147 WP_011054593.1 hypothetical protein -
  SPYM3_RS05215 (SpyM3_0977) - 1015882..1016670 (+) 789 WP_011054594.1 LexA family transcriptional regulator -
  SPYM3_RS05220 - 1016680..1016985 (+) 306 WP_011106738.1 membrane protein -
  SPYM3_RS05225 (SpyM3_0978) - 1017105..1018193 (+) 1089 WP_011054595.1 site-specific integrase -
  SPYM3_RS05230 (SpyM3_0979) - 1018556..1019176 (+) 621 WP_011054596.1 DUF3862 domain-containing protein -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  prx comR negative effect
  comR comX/sigX/comX2/sigX2 positive effect
  comX/sigX/comX2/sigX2 late competence genes positive effect
  comX/sigX/comX1/sigX1 late competence genes positive effect
  comX/sigX/comX1/sigX1 late competence genes positive effect
  comR comX/sigX/comX1/sigX1 positive effect
  comS comX/sigX/comX1/sigX1 positive effect
  clpP comX/sigX/comX1/sigX1 negative effect
  comX/sigX/comX2/sigX2 late competence genes positive effect
  comS comX/sigX/comX2/sigX2 positive effect
  clpP comX/sigX/comX2/sigX2 negative effect

Sequence

Protein


Download         Length: 62 a.a.        Molecular weight: 7226.17 Da        Isoelectric Point: 3.9947

>NTDB_id=551 SPYM3_RS04945 WP_011054546.1 977437..977625(-) (prx) [Streptococcus pyogenes MGAS315]
MLTYDEFKQAIDDGYIVGDTVMIVRKNGQIFDYVLPHEEARNGEVVTEEKVEEVMVELDYIK

Nucleotide


Download         Length: 189 bp        

>NTDB_id=551 SPYM3_RS04945 WP_011054546.1 977437..977625(-) (prx) [Streptococcus pyogenes MGAS315]
ATGCTAACATACGACGAATTTAAGCAAGCTATTGATGACGGATATATCGTAGGAGACACAGTTATGATCGTGCGTAAAAA
CGGACAGATTTTTGATTATGTGTTGCCGCATGAGGAAGCGAGAAATGGAGAAGTTGTGACAGAGGAGAAGGTGGAAGAAG
TGATGGTGGAATTAGACTATATCAAATGA

Domains


No domain identified.



Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A5S4TJS4

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 (%) Ha-value
  prx Streptococcus pyogenes MGAS315

84.746

95.161

0.806
  prx Streptococcus pyogenes MGAS8232

84.483

93.548

0.79
  prx Streptococcus pyogenes MGAS315

82.759

93.548

0.774
  prx Streptococcus pyogenes MGAS315

77.966

95.161

0.742
  prx Streptococcus pyogenes MGAS315

87.805

68.333

0.6
  prx Streptococcus pyogenes MGAS315

76.19

70

0.533

Multiple sequence alignment    



References

[1] Lauren Mashburn-Warren et al. (2018) The conserved mosaic prophage protein paratox inhibits the natural competence regulator ComR in Streptococcus. Scientific Reports 8(1):16535. [PMID: 30409983]