Detailed information    

experimental Experimentally validated

Overview

Name   prx   Type   Regulator
Locus tag   SPYM3_RS06310 Genome accession   NC_004070
Coordinates   1230304..1230486 (-) Length   60 a.a.
NCBI ID   WP_011054726.1    Uniprot ID   A0A5S4TS04
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 1230304..1271815 1230304..1230486 within 0


Gene organization within MGE regions


Location: 1230304..1271815
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SPYM3_RS06310 (SpyM3_1203) prx 1230304..1230486 (-) 183 WP_011054726.1 hypothetical protein Regulator
  SPYM3_RS06320 (SpyM3_1204) - 1230832..1231407 (-) 576 WP_011054727.1 hypothetical protein -
  SPYM3_RS06325 (SpyM3_1205) spek 1231883..1232662 (-) 780 WP_011054728.1 streptococcal pyrogenic exotoxin SpeK -
  SPYM3_RS06330 (SpyM3_1206) - 1232966..1233832 (-) 867 WP_011054729.1 DUF334 domain-containing protein -
  SPYM3_RS06335 (SpyM3_1207) - 1233820..1234344 (-) 525 WP_011017840.1 Panacea domain-containing protein -
  SPYM3_RS06340 (SpyM3_1208) - 1234484..1235686 (-) 1203 WP_011054730.1 glucosaminidase domain-containing protein -
  SPYM3_RS06350 (SpyM3_1209) - 1235797..1235982 (-) 186 WP_011054731.1 holin -
  SPYM3_RS06355 (SpyM3_1210) - 1235979..1236275 (-) 297 WP_011054732.1 hypothetical protein -
  SPYM3_RS06360 (SpyM3_1211) - 1236286..1236897 (-) 612 WP_011054733.1 DUF1366 domain-containing protein -
  SPYM3_RS06365 (SpyM3_1212) - 1236900..1237331 (-) 432 WP_002987513.1 DUF1617 family protein -
  SPYM3_RS06370 (SpyM3_1213) - 1237343..1239226 (-) 1884 WP_011054734.1 gp58-like family protein -
  SPYM3_RS06375 (SpyM3_1214) hylP 1239241..1240254 (-) 1014 WP_011054735.1 hyaluronidase HylP -
  SPYM3_RS06380 (SpyM3_1215) - 1240251..1242395 (-) 2145 WP_011054736.1 phage tail spike protein -
  SPYM3_RS06385 (SpyM3_1216) - 1242392..1243108 (-) 717 WP_011054737.1 distal tail protein Dit -
  SPYM3_RS06390 (SpyM3_1217) - 1243105..1246365 (-) 3261 WP_011054738.1 tape measure protein -
  SPYM3_RS06395 (SpyM3_1218) - 1246355..1246936 (-) 582 WP_011054739.1 bacteriophage Gp15 family protein -
  SPYM3_RS06400 (SpyM3_1219) - 1246940..1247374 (-) 435 WP_011054740.1 hypothetical protein -
  SPYM3_RS06405 (SpyM3_1220) - 1247413..1247898 (-) 486 WP_011054741.1 phage tail tube protein -
  SPYM3_RS06410 (SpyM3_1221) - 1247898..1248296 (-) 399 WP_010922084.1 minor capsid protein -
  SPYM3_RS06415 (SpyM3_1222) - 1248293..1248649 (-) 357 WP_010922083.1 minor capsid protein -
  SPYM3_RS06420 (SpyM3_1223) - 1248649..1248981 (-) 333 WP_010922082.1 minor capsid protein -
  SPYM3_RS06425 (SpyM3_1224) - 1248971..1249387 (-) 417 WP_011054743.1 hypothetical protein -
  SPYM3_RS06430 (SpyM3_1225) - 1249441..1250259 (-) 819 WP_010922080.1 N4-gp56 family major capsid protein -
  SPYM3_RS06435 (SpyM3_1226) - 1250263..1250877 (-) 615 WP_011106689.1 hypothetical protein -
  SPYM3_RS06440 (SpyM3_1227) - 1251003..1251269 (-) 267 WP_011054745.1 hypothetical protein -
  SPYM3_RS06445 (SpyM3_1228) - 1251331..1251570 (-) 240 WP_002986829.1 hypothetical protein -
  SPYM3_RS06450 (SpyM3_1229) - 1251542..1253020 (-) 1479 WP_011054746.1 phage minor capsid protein -
  SPYM3_RS06455 (SpyM3_1230) - 1253025..1254527 (-) 1503 WP_002986832.1 phage portal protein -
  SPYM3_RS06460 (SpyM3_1231) - 1254541..1255832 (-) 1292 Protein_1245 PBSX family phage terminase large subunit -
  SPYM3_RS06465 (SpyM3_1232) - 1255835..1256308 (-) 474 WP_011054747.1 hypothetical protein -
  SPYM3_RS06470 (SpyM3_1233) - 1256359..1256736 (-) 378 WP_002986841.1 ASCH domain-containing protein -
  SPYM3_RS09960 (SpyM3_1234) - 1256797..1257273 (-) 477 WP_174132581.1 GNAT family N-acetyltransferase -
  SPYM3_RS06480 (SpyM3_1235) - 1257189..1257866 (-) 678 WP_002986850.1 ABC transporter ATP-binding protein -
  SPYM3_RS06485 (SpyM3_1236) - 1257845..1258363 (-) 519 WP_002986854.1 ParB N-terminal domain-containing protein -
  SPYM3_RS09965 (SpyM3_1237) - 1258444..1258701 (+) 258 WP_011054748.1 hypothetical protein -
  SPYM3_RS06490 (SpyM3_1240) - 1259340..1259780 (-) 441 WP_011017866.1 ArpU family phage packaging/lysis transcriptional regulator -
  SPYM3_RS10365 - 1260054..1260224 (-) 171 WP_164997036.1 hypothetical protein -
  SPYM3_RS06495 (SpyM3_1241) - 1260221..1260727 (-) 507 WP_011054751.1 DUF1642 domain-containing protein -
  SPYM3_RS10370 (SpyM3_1242) - 1260724..1260894 (-) 171 WP_011054752.1 hypothetical protein -
  SPYM3_RS06500 (SpyM3_1243) - 1260891..1261295 (-) 405 WP_011054753.1 YopX family protein -
  SPYM3_RS06505 (SpyM3_1244) - 1261305..1261574 (-) 270 WP_011054754.1 hypothetical protein -
  SPYM3_RS06510 (SpyM3_1245) - 1261571..1261855 (-) 285 WP_011054755.1 DUF3310 domain-containing protein -
  SPYM3_RS06515 (SpyM3_1246) - 1261849..1262100 (-) 252 WP_011054756.1 hypothetical protein -
  SPYM3_RS06520 (SpyM3_1247) - 1262097..1262453 (-) 357 WP_011054757.1 hypothetical protein -
  SPYM3_RS06525 (SpyM3_1248) - 1262450..1262890 (-) 441 WP_011054758.1 RusA family crossover junction endodeoxyribonuclease -
  SPYM3_RS06530 - 1262890..1263093 (-) 204 WP_011106686.1 hypothetical protein -
  SPYM3_RS06535 (SpyM3_1249) ssbA 1263099..1263518 (-) 420 WP_011054759.1 single-stranded DNA-binding protein Machinery gene
  SPYM3_RS06540 (SpyM3_1250) - 1263511..1264185 (-) 675 WP_011054760.1 ERF family protein -
  SPYM3_RS06545 (SpyM3_1251) - 1264186..1264668 (-) 483 WP_011018142.1 siphovirus Gp157 family protein -
  SPYM3_RS06550 (SpyM3_1252) - 1264690..1264944 (-) 255 WP_011054761.1 hypothetical protein -
  SPYM3_RS10250 - 1264955..1265095 (-) 141 WP_011284979.1 hypothetical protein -
  SPYM3_RS06555 (SpyM3_1253) - 1265092..1265325 (-) 234 WP_011054762.1 hypothetical protein -
  SPYM3_RS06560 (SpyM3_1254) - 1265306..1265719 (-) 414 WP_011054763.1 DnaD domain protein -
  SPYM3_RS06565 (SpyM3_1255) - 1265841..1266098 (-) 258 WP_011106684.1 hypothetical protein -
  SPYM3_RS06570 (SpyM3_1256) - 1266192..1266377 (-) 186 WP_011054765.1 hypothetical protein -
  SPYM3_RS06575 (SpyM3_1257) - 1266406..1266663 (-) 258 WP_002988339.1 hypothetical protein -
  SPYM3_RS09985 (SpyM3_1258) - 1266909..1267076 (-) 168 WP_002986885.1 hypothetical protein -
  SPYM3_RS06585 (SpyM3_1259) - 1267152..1267352 (+) 201 WP_002986887.1 KTSC domain-containing protein -
  SPYM3_RS10375 (SpyM3_1260) - 1267349..1267498 (-) 150 WP_002986888.1 hypothetical protein -
  SPYM3_RS06590 (SpyM3_1261) - 1267531..1268259 (-) 729 WP_011054767.1 phage antirepressor KilAC domain-containing protein -
  SPYM3_RS06595 (SpyM3_1262) - 1268270..1268461 (-) 192 WP_002986891.1 hypothetical protein -
  SPYM3_RS06600 (SpyM3_1263) - 1269257..1269616 (+) 360 WP_011054768.1 helix-turn-helix domain-containing protein -
  SPYM3_RS06605 (SpyM3_1264) - 1269630..1270010 (+) 381 WP_002986894.1 ImmA/IrrE family metallo-endopeptidase -
  SPYM3_RS06610 (SpyM3_1265) - 1270021..1270542 (+) 522 WP_002986895.1 hypothetical protein -
  SPYM3_RS06615 (SpyM3_1266) - 1270718..1271815 (+) 1098 WP_015967409.1 site-specific integrase -

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: 6771.70 Da        Isoelectric Point: 3.9944

>NTDB_id=550 SPYM3_RS06310 WP_011054726.1 1230304..1230486(-) (prx) [Streptococcus pyogenes MGAS315]
MLTYDEFKQAIDNGYIVGDTVAIVRKNGQIFDYVLPGEKVRPSEVVAEEIVEEVVVELDK

Nucleotide


Download         Length: 183 bp        

>NTDB_id=550 SPYM3_RS06310 WP_011054726.1 1230304..1230486(-) (prx) [Streptococcus pyogenes MGAS315]
ATGCTAACATACGACGAGTTTAAGCAAGCGATTGACAATGGATATATCGTAGGAGACACAGTAGCGATTGTGCGTAAAAA
CGGACAGATTTTTGATTATGTGTTGCCTGGCGAAAAAGTCAGACCGTCGGAGGTTGTGGCTGAGGAAATAGTGGAAGAGG
TGGTGGTGGAATTAGACAAATAA

Domains


No domain identified.



Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A5S4TS04

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 MGAS8232

80

100

0.8
  prx Streptococcus pyogenes MGAS315

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

73.333

100

0.733
  prx Streptococcus pyogenes MGAS315

87.805

68.333

0.6

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]