Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101027
Name   oriT_pCW3 experimental
Organism   Clostridium perfringens
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_010937 (24697..24846 [+], 150 nt)
oriT length   150 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   

  oriT sequence  


Download         Length: 150 nt

>oriT_pCW3
AAGGAACTTTACAGGGAACTTTAAAAATTTAAATTGATATAAAAGTTCCCTGTATTAGTATAAGTATTTTAAAGGTATATATCATTATTAGTTCCTTATCGTATTATAGAGTATATATTATATATATAATATATACATATAATGTATTGG

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Jessica A Wisniewski et al. (2016) TcpM: a novel relaxase that mediates transfer of large conjugative plasmids from Clostridium perfringens. Molecular microbiology. 99(5):884-96. [PMID:26560080]


Relaxosome

This oriT is a component of a relaxosome.

Relaxosome name   RelaxosomepCW3 in_silico
oriT   oriT_pCW3 experimental
Relaxase   TcpM_pCW3 experimental (_)
Auxiliary protein   TcpK_pCW3 experimental

  Reference


[1] Daouda A K Traore et al. (2018) Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3. Nature communications. 9(1):3732. [PMID:30213934]
[2] Jessica A Wisniewski et al. (2016) TcpM: a novel relaxase that mediates transfer of large conjugative plasmids from Clostridium perfringens. Molecular microbiology. 99(5):884-96. [PMID:26560080]


Relaxase

ID   1085 GenBank   WP_003479716
Name   TcpM_pCW3 experimental UniProt ID   Q1PLI1
Length   266 a.a. PDB ID   
Note   

  Relaxase protein sequence


Download         Length: 266 a.a.        Molecular weight: 31237.01 Da        Isoelectric Point: 10.4048

>WP_003479716.1 MULTISPECIES: MobM family relaxase TcpM [Bacillota]
MNIFNLKKEMKNIIYSDSSLSKNSIRDRNSALNKIFENFNNLDDVSVITKDKILDNLNSIKFKTKLSAGV
NAIRFLKGQNLDVDFPSEDELKEIIKNKKKNNRKPTVEKNLIDIERKVNRVRKKNYRLAYKLMLESGLRV
HEVSALKKEDFSFDKNLITINLREAKGNKLCSIELENKYLSKNISEFVETKSEDERVFPHMRYLQEQATK
MGIKCHDLRRGFAKRTYKEELENDSPRSEALDKTRIKLRHTRSDTTKIYLNSKIKV

  Protein domains


Predicted by InterproScan.

Phage integrase family (Phage_integrase)

(121-226)


  Protein structure


Source ID Structure
AlphaFold DB Q1PLI1

  Reference


[1] Jessica A Wisniewski et al. (2016) TcpM: a novel relaxase that mediates transfer of large conjugative plasmids from Clostridium perfringens. Molecular microbiology. 99(5):884-96. [PMID:26560080]


Auxiliary protein

ID   389 GenBank   WP_003458874
Name   TcpK_pCW3 experimental UniProt ID   Q1PLI2
Length   102 a.a. PDB ID   5VFY
Note   

  Auxiliary protein sequence


Download         Length: 102 a.a.        Molecular weight: 12420.45 Da        Isoelectric Point: 9.1608

>WP_003458874.1 MULTISPECIES: hypothetical protein [Bacillota]
MKDLNLYAKELVDVVNYLMKKNQLVFSRNNKFIYVNTETIKSMLEKRNYDTVDGKLYLWRELEWIECAED
RFNKRIKIDGENMYAVVIKYSSYSILKRLYLE

  Protein domains


Predicted by InterproScan.

Cch helix turn helix domain (HTH_56)

(30-90)


  Protein structure


Source ID Structure
PDB 5VFY
AlphaFold DB Q1PLI2

  Reference


[1] Daouda A K Traore et al. (2018) Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3. Nature communications. 9(1):3732. [PMID:30213934]


Host bacterium

ID   1490 GenBank   NC_010937
Plasmid name   pCW3 Incompatibility group   -
Plasmid size   47263 bp Coordinate of oriT [Strand]   24697..24846 [+]
Host baterium   Clostridium perfringens

Cargo genes

Drug resistance gene   tetA(P), tetB(P)
Virulence gene   cna
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7