Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100209
Name   oriT_R1 experimental
Organism   E.coli
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   X00783 (299..369 [+], 71 nt)
oriT length   71 nt
IRs (inverted repeats)      10..17, 20..27  (GCAAAAAC..GTTTTTGC)
Location of nic site      36..37
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   (1) The T4CP TraD_R1 and auxiliary protein TraM_R1 stimulate relaxosomeR1 activity in vitro [PMID:19114496].
 (2) oriT_R1, auxiliary protein TraY and TraM are important to the activation of protein secretion through T4SS [PMID:22248924].

  oriT sequence  


Download         Length: 71 nt

>oriT_R1
AGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGA

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Csitkovits VC et al. (2004) Concomitant reconstitution of TraI-catalyzed DNA transesterase and DNA helicase activity in vitro. J Biol Chem. 279(44):45477-84. [PMID:15322083]


Relaxosome

This oriT is a component of a relaxosome.

Relaxosome name   RelaxosomeR1 experimental
oriT   oriT_R1 experimental
Relaxase   TraI_R1 experimental (MOBF)
Auxiliary protein   TraM_R1 experimental, TraY_R1 experimental, IHF_R1 experimental

  Reference


[1] Silvia Lang et al. (2014) Common requirement for the relaxosome of plasmid R1 in multiple activities of the conjugative type IV secretion system. Journal of bacteriology. 196(11):2108-21. [PMID:24682328]
[2] Sanja Mihajlovic et al. (2009) Plasmid r1 conjugative DNA processing is regulated at the coupling protein interface. Journal of bacteriology. 191(22):6877-87. [PMID:19767437]
[3] Csitkovits VC et al. (2004) Concomitant reconstitution of TraI-catalyzed DNA transesterase and DNA helicase activity in vitro. J Biol Chem. 279(44):45477-84. [PMID:15322083]
[4] Schwab M et al. (1991) The TraM protein of plasmid R1 is a DNA-binding protein. Mol Microbiol. 5(2):439-46. [PMID:2041477]


Relaxase

ID   202 GenBank   AAQ98619
Name   TraI_R1 experimental UniProt ID   Q6TDU5
Length   1756 a.a. PDB ID   
Note   TraI; relaxase; oriT nicking and unwinding

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191754.64 Da        Isoelectric Point: 5.9593

>AAQ98619.1 DNA helicase I (plasmid) [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRTEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTEMARAYALIAAGGGRAVASGDTDQLQAIAPGQSFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(968-1156)

TrwC relaxase (TrwC)

(10-283)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)


  Protein structure


Source ID Structure
PDB 4L0J

  Reference


[1] Csitkovits VC et al. (2004) Concomitant reconstitution of TraI-catalyzed DNA transesterase and DNA helicase activity in vitro. J Biol Chem. 279(44):45477-84. [PMID:15322083]
[2] Schwab M et al. (1991) The TraM protein of plasmid R1 is a DNA-binding protein. Mol Microbiol. 5(2):439-46. [PMID:2041477]


Auxiliary protein

ID   283 GenBank   P07294
Name   TraM_R1 experimental UniProt ID   P07294
Length   127 a.a. PDB ID   1DP3
Note   (1) The T4CP TraD_R1 and auxiliary protein TraM_R1 stimulate relaxosomeR1 activity in vitro [PMID:19114496].
 (2) oriT_R1, auxiliary protein TraY and TraM are important to the activation of protein secretion through T4SS [PMID:22248924].

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: Da        Isoelectric Point:

>sp|P07294.1|TRAM2_ECOLX RecName: Full=Relaxosome protein TraM
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
PDB 1DP3
AlphaFold DB P07294

  Reference


[1] Csitkovits VC et al. (2004) Concomitant reconstitution of TraI-catalyzed DNA transesterase and DNA helicase activity in vitro. J Biol Chem. 279(44):45477-84. [PMID:15322083]
[2] Schwab M et al. (1991) The TraM protein of plasmid R1 is a DNA-binding protein. Mol Microbiol. 5(2):439-46. [PMID:2041477]

ID   284 GenBank   CAA31972
Name   TraY_R1 experimental UniProt ID   P10512
Length   75 a.a. PDB ID   _
Note   oriT_R1, auxiliary protein TraY and TraM are important to the activation of protein secretion through T4SS [PMID:22248924].

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9072.20 Da        Isoelectric Point: 10.2071

>CAA31972.1 traY peptide (AA 1-75) (plasmid) [Escherichia coli]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB P10512

  Reference


[1] Csitkovits VC et al. (2004) Concomitant reconstitution of TraI-catalyzed DNA transesterase and DNA helicase activity in vitro. J Biol Chem. 279(44):45477-84. [PMID:15322083]
[2] Schwab M et al. (1991) The TraM protein of plasmid R1 is a DNA-binding protein. Mol Microbiol. 5(2):439-46. [PMID:2041477]


T4CP

ID   202 GenBank   AAT85682
Name   TraD_R1 experimental UniProt ID   Q6B3Y6
Length   735 a.a. PDB ID   _
Note   The T4CP TraD_R1 and auxiliary protein TraM_R1 stimulate relaxosomeR1 activity in vitro [PMID:19114496].

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83647.44 Da        Isoelectric Point: 5.1048

>AAT85682.1 TraD (plasmid) [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRAFFRSPSHQIA
EFAAGEIGEKEHLKASLQYSYGADPVRDGISTGKEMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNIPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

  Protein structure


Source ID Structure
AlphaFold DB Q6B3Y6

  Reference


[1] Csitkovits VC et al. (2004) Concomitant reconstitution of TraI-catalyzed DNA transesterase and DNA helicase activity in vitro. J Biol Chem. 279(44):45477-84. [PMID:15322083]


Host bacterium

ID   202 GenBank   X00783
Plasmid name   R1 Incompatibility group   -
Plasmid size   450 bp Coordinate of oriT [Strand]   299..369 [+]
Host baterium   E.coli

Cargo genes

Drug resistance gene   resistance to chloramphenicol, kanamycin, ampicillin, streptomycin and spectinomycinand sulphonamides
Virulence gene   _
Metal resistance gene   _
Degradation gene   _
Symbiosis gene   -
Anti-CRISPR   -