Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100001 |
| Name | oriT_RP4  |
| 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
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 |
| oriT | oriT_RP4 |
| Relaxase | TraI_RP4 (MOBP) |
| Auxiliary protein | TraJ_RP4 , TraH_RP4 , TraK_RP4 |
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 |
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
MIAKHVPMRSIKKSDFAELVKYITDEQGKTERLGHVRVTNCEANTLPAVMAEVMATQHGNTRSEADKTYH
LLVSFRAGEKPDAETLRAIEDRICAGLGFAEHQRVSAVHHDTDNLHIHIAINKIHPTRNTIHEPYRAYRA
LADLCATLERDYGLERDNHETRQRVSENRANDMERHAGVESLVGWIKRECLPELQAAQSWEDLHRVLREN
GLKLRERGNGFIFEAGDGTTVKASTVSRDLSKPKLEARFGAFTPAEGGEAPRRREYRAKPLKTRIDTTEL
YARYQSERQEMGAVRKGELDTLRRRRDRLIEAAMRSNRLRRAAIKLLGEGRIAKRLMYAQAHKALRADLD
KINREYRQGRQAVQERTQRRAWADWLKAEAMKGDDKALAALRAREGRSDLKGNTIQGSGEAKPGHAAVTD
NITKKGTIIYRVGSSAVRDDGDRLQVSREATTDGLDAALRLAMERFGDRITVNGTAEFKERIAQAAAAGR
LAITFDDAALERRRQELLTKEQAHEQPERNDGRRDRGGDGGIRPAAARTTLNATGGDGDRRDARAVSAGG
TVALRKPNVGRIGRKPPPQSQNRLRALSQLGVVRIAGGAEMLLPRDVPGHVEQQGAEPAHALRRGVSGPG
RGLKPEQIAAAEKYVAEREQKRLNGFDIPKHARYTDYVGALSYAGTRNVEDQALALLRKENDEILVLPVD
KATVQRMKRLAIGDPVTVTPRGSLKTTRGRSR
Protein domains
Predicted by InterproScan.
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 |
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
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 |
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
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 |
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
MPKSYTDELAEWVESRAAKKRRRDEAAVAFLAVRADVEAALASGYALVTIWEHMRETGKVKFSYETFRSH
ARRHIKAKPADVPAPQAKAAEPAPAPKTPEPRRPKQGGKAEKPAPAAAPTGFTFNPTPDKKDLL
Protein domains
Predicted by InterproScan.
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 |
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
MKNRNNAVGPQIRAKKPKASKTVPILAGLSLGAGLQTATQYFAHSFQYQAGLGWNINHVYTPWSILQWAG
KWYGQYPDDFMRAASMGMVVSTVGLLGTAVTQMVKANTGKANDYLHGSARWADKKDIQAAGLLPRPRTVV
ELVSGKHPPTSSGVYVGGWQDKDGKFHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWAHSAVITDLKG
ELWALTAGWRKKHARNKVVRFEPASAQGSACWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLESHWQK
TSQALLVGVILHALYKAKNEGTPATLPSVDGMLADPNRDVGELWMEMTTYGHVDGQNHPAVGSAARDMMD
RPEEESGSVLSTAKSYLALYRDPVVARNVSKSDFRIKQLMHHDDPVSLFIVTQPNDKARLRPLVRVMVNM
IVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQDINQLKSRETG
YGHDESITSNCHVQNAYPPNRVETAEHLSKLTGTTTIVKEQITTSGRRTSALLGNVSRTFQEVQRPLLTP
DECLRMPGPKKSADGSIEEAGDMVVYVAGYPAIYGKQPLYFKDPIFQARAAVPAPKVSDKLIQTATVEEG
EGITI
Protein domains
Predicted by InterproScan.
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 |