Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200003
Name   oriT_ICESt3 experimental
Organism   Streptococcus thermophilus site-specific integrative and potentially
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   AJ586568 (_)
oriT length   213 nt
IRs (inverted repeats)      1..8, 12..19  (GCCTGACC..GGTCAGGC)
  61..67, 80..86  (AACCCCC..GGGGGTT)
  154..159, 163..168  (AAAGTG..CACTTT)
  177..181, 185..189  (AAGTG..CACTT)
  155..167, 177..189  (AAGTGTGTCACTT..AAGTGTGTCACTT)
Location of nic site      22..23
Conserved sequence flanking the
  nic site    		  CT|AA
Note   (1) The intact IR5 region (155nt-189nt) of oriT_ICESt3 is an essential binding site for the relaxase Relst3 [PMID:35849337].
 (2) N-terminal HTH domain of Relst3 is required for oriT_ICESt3 binding in vitro and is essential for conjugation [PMID:35849337].
 (3) Tyrosine 252 (Y252) of Relst3 is involved in nicking-closing reactions [PMID:35849337].

  oriT sequence  


Download         Length: 213 nt

>oriT_ICESt3
GCCTGACCACAGGTCAGGCGCAGACCGTAGCCCGAAGTTCCTAGGCCATGATGAGACTTCAACCCCCGATTTCTAATAGGGGGGTTACATTTGGCCAAAGTGCCACGTCCACCCCTCCTCATTCCTTGTGGGAGTTGGGATTTCAAGATTTAGAAAGTGTGTCACTTTGGTCCAAAAAGTGTGTCACTTAGTCAAAAGGAGGTGTTCCCATGA

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Haifa Laroussi et al. (2022) Exploration of DNA processing features unravels novel properties of ICE conjugation in Gram-positive bacteria. Nucleic acids research. 50(14):8127-8142. [PMID:35849337]
[2] Pavlovic G et al. (2004) Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus. Microbiology. 150(Pt 4):759-74. [PMID:15073287]


Relaxase

ID   1080 GenBank   CAE52362
Name   RelSt3 experimental UniProt ID   Q70CA7
Length   410 a.a. PDB ID   
Note   

  Relaxase protein sequence


Download         Length: 410 a.a.        Molecular weight: 48429.03 Da        Isoelectric Point: 7.2206

>CAE52362.1 putative transfer protein [Streptococcus thermophilus]
MTKISPFQIKNFRKQTGLSQKAFAQAVNLPIRTYRSYESGERGLTIDKFRKLKEKLGYYQECHKNNLRAH
IDYLRLTFPSLRDLETFCENFLFCHLSEFTDQETRLMNYTHLWQRGNIWIFDFFDKSATNNYQTCLQLSG
QGCREMELLLEHKGISWQTFLQNILYAYQDVRVKRLDIALDELYKGYGHEEEHIQIPKLIDKLYAKEIVL
DTIRKWNITGGGSFTDNDNMEANHGLSLYFGSRQSQLYFNFYEKRYEIARMENISLEESLEIFGIWNRYE
LRFSDQKAQGVVEEYINGVDLGEIARGIVNKEIQVYDGVTRFGSYKPYEKWQRLFGGVEPLKLSTSPQPY
SIERTIRWLTYQVANSLALVSEADKIMQTEYMKMIQNSGEITDRGEAILRLLKTNKHYEH

  Protein domains


Predicted by InterproScan.

Helix-turn-helix (HTH_3)

(9-57)

Replication initiation factor (Rep_trans)

(172-384)

Rolling Circle replication initiation protein N-terminal domain (Rol_Rep_N)

(69-162)


  Protein structure


Source ID Structure
AlphaFold DB Q70CA7

  Reference


[1] Haifa Laroussi et al. (2022) Exploration of DNA processing features unravels novel properties of ICE conjugation in Gram-positive bacteria. Nucleic acids research. 50(14):8127-8142. [PMID:35849337]


Host bacterium

ID   8 Element type   ICE (Integrative and conjugative element)
Element name   ICESt3 GenBank   AJ586568
Element size   28372 bp Coordinate of oriT [Strand]   16955..17103 [+]
Host bacterium   Streptococcus thermophilus site-specific integrative and potentially

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -