Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100001
Name   oriT_RP4 experimental
Organism   Pseudomonas aeruginosa
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   L27758 (51176..51274 [+], 99 nt)
oriT length   99 nt
IRs (inverted repeats)      13..31, 34..52  (GTGAAGAAGGAACACCCGC..GCGGGTGGGCCTACTTCAC)
Location of nic site      60..61
Conserved sequence flanking the
  nic site    		  TATCCTG|C
Note   minimal oriT sequence

  oriT sequence  


Download         Length: 99 nt

>oriT_RP4
GAATAAGGGACAGTGAAGAAGGAACACCCGCTCGCGGGTGGGCCTACTTCACCTATCCTGCCCGGCTGACGCCGTTGGATACACCAAGGAAAGTCTACA

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Dam B et al. (2009) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. Appl Environ Microbiol. 75(13):4362-73. [PMID:19411426]
[2] Pansegrau W et al. (1993) Relaxase (TraI) of IncP alpha plasmid RP4 catalyzes a site-specific cleaving-joining reaction of single-stranded DNA. Proc Natl Acad Sci U S A. 90(7):2925-9. [PMID:8385350]
[3] Cook DM et al. (1992) The oriT region of the Agrobacterium tumefaciens Ti plasmid pTiC58 shares DNA sequence identity with the transfer origins of RSF1010 and RK2/RP4 and with T-region borders. J Bacteriol. 174(19):6238-46. [PMID:1400174]
[4] Pansegrau W et al. (1990) In vitro assembly of relaxosomes at the transfer origin of plasmid RP4. Proc Natl Acad Sci U S A. 87(17):6555-9. [PMID:2168553]
[5] Fürste JP et al. (1989) Conjugative transfer of promiscuous IncP plasmids: interaction of plasmid-encoded products with the transfer origin. Proc Natl Acad Sci U S A. 86(6):1771-5. [PMID:2538813]
[6] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]


Relaxosome

This oriT is a component of a relaxosome.

Relaxosome name   RelaxosomeRP4 experimental
oriT   oriT_RP4 experimental
Relaxase   TraI_RP4 experimental (MOBP)
Auxiliary protein   TraJ_RP4 experimental, TraH_RP4 experimental, TraK_RP4 experimental

  Reference


[1] Dam B et al. (2009) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. Appl Environ Microbiol. 75(13):4362-73. [PMID:19411426]
[2] Grahn AM et al. (2000) Components of the RP4 Conjugative Transfer Apparatus Form an Envelope Structure Bridging Inner and Outer Membranes of Donor Cells: Implications for Related Macromolecule Transport Systems. J Bacteriol. 182(6):1564-74. [PMID:10692361]
[3] Pansegrau W et al. (1993) Relaxase (TraI) of IncP alpha plasmid RP4 catalyzes a site-specific cleaving-joining reaction of single-stranded DNA. Proc Natl Acad Sci U S A. 90(7):2925-9. [PMID:8385350]
[4] Cook DM et al. (1992) The oriT region of the Agrobacterium tumefaciens Ti plasmid pTiC58 shares DNA sequence identity with the transfer origins of RSF1010 and RK2/RP4 and with T-region borders. J Bacteriol. 174(19):6238-46. [PMID:1400174]
[5] G Ziegelin et al. (1992) TraK protein of conjugative plasmid RP4 forms a specialized nucleoprotein complex with the transfer origin. The Journal of biological chemistry. 267(24):17279-86. [PMID:1324929]
[6] Pansegrau W et al. (1990) In vitro assembly of relaxosomes at the transfer origin of plasmid RP4. Proc Natl Acad Sci U S A. 87(17):6555-9. [PMID:2168553]
[7] Fürste JP et al. (1989) Conjugative transfer of promiscuous IncP plasmids: interaction of plasmid-encoded products with the transfer origin. Proc Natl Acad Sci U S A. 86(6):1771-5. [PMID:2538813]
[8] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]


Relaxase

ID   1 GenBank   CAA38336
Name   TraI_RP4 experimental UniProt ID   Q00191
Length   732 a.a. PDB ID   
Note   relaxase; to recognize the conserved nick region sequence

  Relaxase protein sequence


Download         Length: 732 a.a.        Molecular weight: 81563.20 Da        Isoelectric Point: 10.5791

>CAA38336.1 traI (plasmid) [Escherichia coli HB101]
MIAKHVPMRSIKKSDFAELVKYITDEQGKTERLGHVRVTNCEANTLPAVMAEVMATQHGNTRSEADKTYH
LLVSFRAGEKPDAETLRAIEDRICAGLGFAEHQRVSAVHHDTDNLHIHIAINKIHPTRNTIHEPYRAYRA
LADLCATLERDYGLERDNHETRQRVSENRANDMERHAGVESLVGWIKRECLPELQAAQSWEDLHRVLREN
GLKLRERGNGFIFEAGDGTTVKASTVSRDLSKPKLEARFGAFTPAEGGEAPRRREYRAKPLKTRIDTTEL
YARYQSERQEMGAVRKGELDTLRRRRDRLIEAAMRSNRLRRAAIKLLGEGRIAKRLMYAQAHKALRADLD
KINREYRQGRQAVQERTQRRAWADWLKAEAMKGDDKALAALRAREGRSDLKGNTIQGSGEAKPGHAAVTD
NITKKGTIIYRVGSSAVRDDGDRLQVSREATTDGLDAALRLAMERFGDRITVNGTAEFKERIAQAAAAGR
LAITFDDAALERRRQELLTKEQAHEQPERNDGRRDRGGDGGIRPAAARTTLNATGGDGDRRDARAVSAGG
TVALRKPNVGRIGRKPPPQSQNRLRALSQLGVVRIAGGAEMLLPRDVPGHVEQQGAEPAHALRRGVSGPG
RGLKPEQIAAAEKYVAEREQKRLNGFDIPKHARYTDYVGALSYAGTRNVEDQALALLRKENDEILVLPVD
KATVQRMKRLAIGDPVTVTPRGSLKTTRGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(417-507)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)


  Protein structure


Source ID Structure
AlphaFold DB Q00191

  Reference


[1] Grahn AM et al. (2000) Components of the RP4 Conjugative Transfer Apparatus Form an Envelope Structure Bridging Inner and Outer Membranes of Donor Cells: Implications for Related Macromolecule Transport Systems. J Bacteriol. 182(6):1564-74. [PMID:10692361]
[2] Pansegrau W et al. (1993) Relaxase (TraI) of IncP alpha plasmid RP4 catalyzes a site-specific cleaving-joining reaction of single-stranded DNA. Proc Natl Acad Sci U S A. 90(7):2925-9. [PMID:8385350]
[3] Pansegrau W et al. (1990) In vitro assembly of relaxosomes at the transfer origin of plasmid RP4. Proc Natl Acad Sci U S A. 87(17):6555-9. [PMID:2168553]
[4] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]


Auxiliary protein

ID   1 GenBank   CAA38338
Name   TraJ_RP4 experimental UniProt ID   P17909
Length   123 a.a. PDB ID   _
Note   to specifically bind to the nick site-proximal arm of the 19-bp inverted repeat sequence

  Auxiliary protein sequence


Download         Length: 123 a.a.        Molecular weight: 13463.65 Da        Isoelectric Point: 7.9867

>CAA38338.1 traJ (plasmid) [Escherichia coli HB101]
MADETKPTRKGSPPIKVYCLPDERRAIEEKAAAAGMSLSAYLLAVGQGYKITGVVDYEHVRELARINGDL
GRLGGLLKLWLTDDPRTARFGDATILALLAKIEEKQDELGKVMMGVVRPRAEP

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB P17909

  Reference


[1] Grahn AM et al. (2000) Components of the RP4 Conjugative Transfer Apparatus Form an Envelope Structure Bridging Inner and Outer Membranes of Donor Cells: Implications for Related Macromolecule Transport Systems. J Bacteriol. 182(6):1564-74. [PMID:10692361]
[2] Pansegrau W et al. (1990) In vitro assembly of relaxosomes at the transfer origin of plasmid RP4. Proc Natl Acad Sci U S A. 87(17):6555-9. [PMID:2168553]
[3] Fürste JP et al. (1989) Conjugative transfer of promiscuous IncP plasmids: interaction of plasmid-encoded products with the transfer origin. Proc Natl Acad Sci U S A. 86(6):1771-5. [PMID:2538813]
[4] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]

ID   2 GenBank   CAA38335
Name   TraH_RP4 experimental UniProt ID   Q00190
Length   119 a.a. PDB ID   _
Note   The role of TraH is to stabilize the initialcomplex of form I oriT DNA, TraJ, and TraI by specific protein-protein interactions

  Auxiliary protein sequence


Download         Length: 119 a.a.        Molecular weight: 12869.28 Da        Isoelectric Point: 4.1047

>CAA38335.1 traH (plasmid) [Escherichia coli HB101]
MSNPNEMTDEEIAAAMEAFDLPQPEPPSTPQAATATDGTLAPSAPAEPSHSASPTLDALDESRRPKAKTV
CERCPNSVWFASPAELKCYCRVMFLVTWSSKEPNQLTHCDGEFLGQEEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q00190

  Reference


[1] Grahn AM et al. (2000) Components of the RP4 Conjugative Transfer Apparatus Form an Envelope Structure Bridging Inner and Outer Membranes of Donor Cells: Implications for Related Macromolecule Transport Systems. J Bacteriol. 182(6):1564-74. [PMID:10692361]
[2] Pansegrau W et al. (1990) In vitro assembly of relaxosomes at the transfer origin of plasmid RP4. Proc Natl Acad Sci U S A. 87(17):6555-9. [PMID:2168553]
[3] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]

ID   3 GenBank   CAA38339
Name   TraK_RP4 experimental UniProt ID   P17910
Length   134 a.a. PDB ID   _
Note   TraK oriT binding protein

  Auxiliary protein sequence


Download         Length: 134 a.a.        Molecular weight: 14716.82 Da        Isoelectric Point: 10.5082

>CAA38339.1 traK (plasmid) [Escherichia coli HB101]
MPKSYTDELAEWVESRAAKKRRRDEAAVAFLAVRADVEAALASGYALVTIWEHMRETGKVKFSYETFRSH
ARRHIKAKPADVPAPQAKAAEPAPAPKTPEPRRPKQGGKAEKPAPAAAPTGFTFNPTPDKKDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(7-74)


  Protein structure


Source ID Structure
AlphaFold DB P17910

  Reference


[1] Grahn AM et al. (2000) Components of the RP4 Conjugative Transfer Apparatus Form an Envelope Structure Bridging Inner and Outer Membranes of Donor Cells: Implications for Related Macromolecule Transport Systems. J Bacteriol. 182(6):1564-74. [PMID:10692361]
[2] Pansegrau W et al. (1990) In vitro assembly of relaxosomes at the transfer origin of plasmid RP4. Proc Natl Acad Sci U S A. 87(17):6555-9. [PMID:2168553]
[3] Pansegrau W et al. (1988) The origin of conjugative IncP plasmid transfer: interaction with plasmid-encoded products and the nucleotide sequence at the relaxation site. Biochim Biophys Acta. 951(2-3):365-74. [PMID:2850014]


T4CP

ID   1 GenBank   CAA38334
Name   TraG_RP4 experimental UniProt ID   Q00185
Length   635 a.a. PDB ID   _
Note   conjugal transfer coupling protein TraG

  T4CP protein sequence


Download         Length: 635 a.a.        Molecular weight: 69857.88 Da        Isoelectric Point: 9.1256

>CAA38334.1 traG (plasmid) [Escherichia coli HB101]
MKNRNNAVGPQIRAKKPKASKTVPILAGLSLGAGLQTATQYFAHSFQYQAGLGWNINHVYTPWSILQWAG
KWYGQYPDDFMRAASMGMVVSTVGLLGTAVTQMVKANTGKANDYLHGSARWADKKDIQAAGLLPRPRTVV
ELVSGKHPPTSSGVYVGGWQDKDGKFHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWAHSAVITDLKG
ELWALTAGWRKKHARNKVVRFEPASAQGSACWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLESHWQK
TSQALLVGVILHALYKAKNEGTPATLPSVDGMLADPNRDVGELWMEMTTYGHVDGQNHPAVGSAARDMMD
RPEEESGSVLSTAKSYLALYRDPVVARNVSKSDFRIKQLMHHDDPVSLFIVTQPNDKARLRPLVRVMVNM
IVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDINQLKSRETG
YGHDESITSNCHVQNAYPPNRVETAEHLSKLTGTTTIVKEQITTSGRRTSALLGNVSRTFQEVQRPLLTP
DECLRMPGPKKSADGSIEEAGDMVVYVAGYPAIYGKQPLYFKDPIFQARAAVPAPKVSDKLIQTATVEEG
EGITI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(120-621)

  Protein structure


Source ID Structure
AlphaFold DB Q00185

  Reference


[1] Gomis-Rüth FX et al. (2004) Coupling factors in macromolecular type-IV secretion machineries. Curr Pharm Des. 10(13):1551-65. [PMID:15134575]
[2] Grahn AM et al. (2000) Components of the RP4 Conjugative Transfer Apparatus Form an Envelope Structure Bridging Inner and Outer Membranes of Donor Cells: Implications for Related Macromolecule Transport Systems. J Bacteriol. 182(6):1564-74. [PMID:10692361]
[3] Hamilton CM et al. (2000) TraG from RP4 and TraG and VirD4 from Ti plasmids confer relaxosome specificity to the conjugal transfer system of pTiC58. J Bacteriol. 182(6):1541-8. [PMID:10692358]
[4] Cabezón E et al. (1994) Requirements for mobilization of plasmids RSF1010 and ColE1 by the IncW plasmid R388: trwB and RP4 traG are interchangeable. J Bacteriol. 176(14):4455-8. [PMID:8021231]


Host bacterium

ID   1 GenBank   L27758
Plasmid name   RP4 Incompatibility group   IncP1
Plasmid size   60099 bp Coordinate of oriT [Strand]   51176..51274 [+]
Host baterium   Pseudomonas aeruginosa

Cargo genes

Drug resistance gene   resistance to carbenicillin, kanamycin, ampicillin and tetracycline
Virulence gene   _
Metal resistance gene   _
Degradation gene   degradation of biphenyl and 4-chlorobiphenyl
Symbiosis gene   -
Anti-CRISPR   -