Detailed information    

experimental Experimentally validated

Overview

Name   prx   Type   Regulator
Locus tag   SPYM3_RS07355 Genome accession   NC_004070
Coordinates   1410725..1410907 (-) Length   60 a.a.
NCBI ID   WP_011054856.1    Uniprot ID   -
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 1410725..1452229 1410725..1410907 within 0


Gene organization within MGE regions


Location: 1410725..1452229
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SPYM3_RS07355 (SpyM3_1408) prx 1410725..1410907 (-) 183 WP_011054856.1 hypothetical protein Regulator
  SPYM3_RS07360 (SpyM3_1409) - 1411140..1412126 (+) 987 WP_048901986.1 DNA/RNA non-specific endonuclease -
  SPYM3_RS07365 (SpyM3_1410) - 1412441..1412755 (-) 315 WP_228358673.1 hypothetical protein -
  SPYM3_RS07370 - 1413077..1414279 (-) 1203 Protein_1427 glucosaminidase domain-containing protein -
  SPYM3_RS07380 (SpyM3_1413) - 1414395..1414622 (-) 228 WP_003058873.1 phage holin -
  SPYM3_RS07385 (SpyM3_1414) - 1414619..1414891 (-) 273 WP_002986916.1 DUF7365 family protein -
  SPYM3_RS07390 (SpyM3_1415) - 1414901..1415518 (-) 618 WP_011054861.1 DUF1366 domain-containing protein -
  SPYM3_RS07395 (SpyM3_1416) - 1415515..1415952 (-) 438 WP_011054862.1 DUF1617 family protein -
  SPYM3_RS07400 (SpyM3_1417) - 1415964..1417979 (-) 2016 WP_011054863.1 gp58-like family protein -
  SPYM3_RS07405 (SpyM3_1418) - 1417989..1418996 (-) 1008 WP_011054441.1 hyaluronoglucosaminidase -
  SPYM3_RS07410 (SpyM3_1419) - 1418993..1420972 (-) 1980 WP_011054864.1 phage tail protein -
  SPYM3_RS07415 (SpyM3_1420) - 1420982..1421824 (-) 843 WP_011054865.1 phage tail family protein -
  SPYM3_RS07420 (SpyM3_1421) - 1421836..1426218 (-) 4383 WP_011054866.1 tape measure protein -
  SPYM3_RS07425 (SpyM3_1422) - 1426233..1426466 (-) 234 WP_011054867.1 hypothetical protein -
  SPYM3_RS07430 (SpyM3_1423) - 1426541..1426996 (-) 456 WP_011054868.1 tail assembly chaperone -
  SPYM3_RS07435 (SpyM3_1424) - 1427050..1427649 (-) 600 WP_011054869.1 phage major tail protein, TP901-1 family -
  SPYM3_RS07440 (SpyM3_1425) - 1427661..1428020 (-) 360 WP_011054870.1 hypothetical protein -
  SPYM3_RS07445 (SpyM3_1426) - 1428024..1428368 (-) 345 WP_011106640.1 HK97-gp10 family putative phage morphogenesis protein -
  SPYM3_RS07450 (SpyM3_1427) - 1428365..1428643 (-) 279 WP_011054872.1 hypothetical protein -
  SPYM3_RS07455 (SpyM3_1428) - 1428654..1429010 (-) 357 WP_011054873.1 phage head-tail connector protein -
  SPYM3_RS07460 (SpyM3_1429) - 1429022..1429909 (-) 888 WP_002983429.1 hypothetical protein -
  SPYM3_RS07465 (SpyM3_1430) - 1429922..1430491 (-) 570 WP_011054874.1 DUF4355 domain-containing protein -
  SPYM3_RS07470 (SpyM3_1431) - 1430659..1430925 (-) 267 WP_011054875.1 hypothetical protein -
  SPYM3_RS07475 (SpyM3_1432) - 1430930..1431118 (-) 189 WP_011054876.1 hypothetical protein -
  SPYM3_RS07480 (SpyM3_1433) - 1431146..1432594 (-) 1449 WP_011054877.1 minor capsid protein -
  SPYM3_RS07485 (SpyM3_1434) - 1432554..1434086 (-) 1533 WP_011106638.1 phage portal protein -
  SPYM3_RS07490 (SpyM3_1435) - 1434102..1435379 (-) 1278 WP_011054879.1 PBSX family phage terminase large subunit -
  SPYM3_RS07495 (SpyM3_1436) - 1435369..1435821 (-) 453 WP_011106637.1 terminase small subunit -
  SPYM3_RS07500 (SpyM3_1437) - 1435911..1436327 (-) 417 WP_011054881.1 transcriptional regulator -
  SPYM3_RS07505 (SpyM3_1438) - 1436460..1436732 (-) 273 WP_011054882.1 hypothetical protein -
  SPYM3_RS10410 (SpyM3_1439) - 1436725..1436895 (-) 171 WP_011054883.1 hypothetical protein -
  SPYM3_RS07510 (SpyM3_1440) - 1436896..1438218 (-) 1323 WP_011054884.1 SNF2-related protein -
  SPYM3_RS07515 (SpyM3_1441) - 1438215..1438490 (-) 276 WP_011054885.1 VRR-NUC domain-containing protein -
  SPYM3_RS07520 (SpyM3_1442) - 1438856..1441240 (-) 2385 WP_011054886.1 phage/plasmid primase, P4 family -
  SPYM3_RS07525 (SpyM3_1443) - 1441245..1443167 (-) 1923 WP_011054887.1 DNA polymerase -
  SPYM3_RS07530 (SpyM3_1444) - 1443210..1443773 (-) 564 WP_011054888.1 DUF2815 family protein -
  SPYM3_RS07535 (SpyM3_1445) - 1443787..1444944 (-) 1158 WP_011054889.1 DUF2800 domain-containing protein -
  SPYM3_RS07540 (SpyM3_1446) - 1444944..1445243 (-) 300 WP_000573833.1 hypothetical protein -
  SPYM3_RS07545 (SpyM3_1447) - 1445331..1445534 (-) 204 WP_011054890.1 hypothetical protein -
  SPYM3_RS07550 (SpyM3_1449) - 1445680..1446063 (-) 384 WP_011054892.1 hypothetical protein -
  SPYM3_RS07555 (SpyM3_1450) - 1446060..1446267 (-) 208 Protein_1464 hypothetical protein -
  SPYM3_RS10025 (SpyM3_1451) - 1446260..1446430 (-) 171 WP_011054894.1 hypothetical protein -
  SPYM3_RS07560 (SpyM3_1452) - 1446459..1446716 (-) 258 WP_011054895.1 hypothetical protein -
  SPYM3_RS07565 (SpyM3_1453) - 1446804..1447004 (-) 201 WP_011184050.1 hypothetical protein -
  SPYM3_RS07570 (SpyM3_1454) - 1447055..1447246 (-) 192 WP_001283052.1 hypothetical protein -
  SPYM3_RS07575 (SpyM3_1455) - 1447885..1448235 (+) 351 WP_011184049.1 helix-turn-helix domain-containing protein -
  SPYM3_RS07580 (SpyM3_1456) - 1448249..1448632 (+) 384 WP_011054898.1 ImmA/IrrE family metallo-endopeptidase -
  SPYM3_RS07585 (SpyM3_1457) - 1448643..1449194 (+) 552 WP_011054899.1 hypothetical protein -
  SPYM3_RS07590 (SpyM3_1458) - 1449370..1450458 (+) 1089 WP_011054900.1 site-specific integrase -
  SPYM3_RS07595 (SpyM3_1459) - 1450601..1452229 (-) 1629 WP_011054901.1 ABC transporter permease -

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: 60 a.a.        Molecular weight: 6927.67 Da        Isoelectric Point: 3.9286

>NTDB_id=549 SPYM3_RS07355 WP_011054856.1 1410725..1410907(-) (prx) [Streptococcus pyogenes MGAS315]
MLTYDEFKQAIDDGYITGDTVAIVRKNGQIFDYALPNEEVRNGEVVTYENVEEVLRELDK

Nucleotide


Download         Length: 183 bp        

>NTDB_id=549 SPYM3_RS07355 WP_011054856.1 1410725..1410907(-) (prx) [Streptococcus pyogenes MGAS315]
ATGCTAACATACGATGAGTTTAAGCAAGCTATTGATGACGGATATATCACAGGCGACACAGTGGCGATCGTGCGCAAAAA
CGGACAGATTTTTGATTATGCGTTGCCGAATGAAGAGGTAAGAAATGGGGAGGTTGTAACATACGAAAATGTGGAAGAAG
TGCTGAGGGAATTAGACAAATAA

Domains


No domain identified.



Secondary structure

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



3D structure

Source ID Structure

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

80

100

0.8
  prx Streptococcus pyogenes MGAS315

80

100

0.8
  prx Streptococcus pyogenes MGAS315

78.333

100

0.783
  prx Streptococcus pyogenes MGAS315

75

100

0.75
  prx Streptococcus pyogenes MGAS315

75

100

0.75

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]