oriTDB
The information of the oriT region
oriTDB accession number 100001
Name oriT_RP4  experimental
Sequence Completeness intact
oriT length 99 nt
oriT sequence GAATAAGGGACAGTGAAGAAGGAACACCCGCTCGCGGGTGGGCCTACTTCACCTATCCTG CCCGGCTGACGCCGTTGGATACACCAAGGAAAGTCTACA
IR (inverted repeat)[13-31] [34-52] nt  (GTGAAGAAGGAACACCCGC..GCGGGTGGGCCTACTTCAC)
Location of nic site [60-61] nt
Conserved sequence flanking the
  nic site 		TATCCTG|C
Note minimal oriT sequence
L:13-31;R:34-52;D:60-61
Visualization of oriT structure (The oriT was characterized experimentally)
Reference
[1] 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]
[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] 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] 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] 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]
I. Information of Relaxase
ID 1
Name TraI_RP4 experimental
GenBank accession number CAA38336
Family MOBP
Length 732 aa
UniProt ID Q00191
PDB ID _
Pfam Relaxase [PF03432.13], Evalue: 7.90E-67, Aligned region: 12..252
Note relaxase; to recognize the conserved nick region sequence
Protein sequence [Download] MIAKHVPMRSIKKSDFAELVKYITDEQGKTERLGHVRVTNCEANTLPAVMAEVMATQHGN
TRSEADKTYHLLVSFRAGEKPDAETLRAIEDRICAGLGFAEHQRVSAVHHDTDNLHIHIA
INKIHPTRNTIHEPYRAYRALADLCATLERDYGLERDNHETRQRVSENRANDMERHAGVE
SLVGWIKRECLPELQAAQSWEDLHRVLRENGLKLRERGNGFIFEAGDGTTVKASTVSRDL
SKPKLEARFGAFTPAEGGEAPRRREYRAKPLKTRIDTTELYARYQSERQEMGAVRKGELD
TLRRRRDRLIEAAMRSNRLRRAAIKLLGEGRIAKRLMYAQAHKALRADLDKINREYRQGR
QAVQERTQRRAWADWLKAEAMKGDDKALAALRAREGRSDLKGNTIQGSGEAKPGHAAVTD
NITKKGTIIYRVGSSAVRDDGDRLQVSREATTDGLDAALRLAMERFGDRITVNGTAEFKE
RIAQAAAAGRLAITFDDAALERRRQELLTKEQAHEQPERNDGRRDRGGDGGIRPAAARTT
LNATGGDGDRRDARAVSAGGTVALRKPNVGRIGRKPPPQSQNRLRALSQLGVVRIAGGAE
MLLPRDVPGHVEQQGAEPAHALRRGVSGPGRGLKPEQIAAAEKYVAEREQKRLNGFDIPK
HARYTDYVGALSYAGTRNVEDQALALLRKENDEILVLPVDKATVQRMKRLAIGDPVTVTP
RGSLKTTRGRSR
Reference
[1] 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]
[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] 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]
[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]


II. Auxiliary DNA-binding protein(s) of the relaxosome
# ID Name GenBank Length Note
1 1 TraJ_RP4 experimental CAA38338 123 aa to specifically bind to the nick site-proximal arm of the 19-bp inverted repeat sequence
2 2 TraH_RP4 experimental CAA38335 119 aa The role of TraH is to stabilize the initialcomplex of form I oriT DNA, TraJ, and TraI by specific protein-protein interactions
3 3 TraK_RP4 experimental CAA38339 134 aa TraK oriT binding protein
Information of T4CP
ID 1
Name TraG_RP4 experimental
SecReT4 accesion number _
GenBank accession number CAA38334
Family VirD4/TraG
Length 635
UniProt ID Q00185
PDB ID _
Pfam T4SS-DNA_transf [PF02534.13], Evalue: 2.20E-174, Aligned region: 120..624
TraG-D_C [PF12696.6], Evalue: 2.70E-31, Aligned region: 443..568
TrwB_AAD_bind [PF10412.8], Evalue: 1.80E-23, Aligned region: 175..575
Note conjugal transfer coupling protein TraG
Protein sequence [Download] MKNRNNAVGPQIRAKKPKASKTVPILAGLSLGAGLQTATQYFAHSFQYQAGLGWNINHVY
TPWSILQWAGKWYGQYPDDFMRAASMGMVVSTVGLLGTAVTQMVKANTGKANDYLHGSAR
WADKKDIQAAGLLPRPRTVVELVSGKHPPTSSGVYVGGWQDKDGKFHYLRHNGPEHVLTY
APTRSGKGVGLVVPTLLSWAHSAVITDLKGELWALTAGWRKKHARNKVVRFEPASAQGSA
CWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLESHWQKTSQALLVGVILHALYKAKNE
GTPATLPSVDGMLADPNRDVGELWMEMTTYGHVDGQNHPAVGSAARDMMDRPEEESGSVL
STAKSYLALYRDPVVARNVSKSDFRIKQLMHHDDPVSLFIVTQPNDKARLRPLVRVMVNM
IVRLLADKMDFENGRPVAHYKHRLLMMLDEFPSLGKLEILQESLAFVAGYGIKCYLICQD
INQLKSRETGYGHDESITSNCHVQNAYPPNRVETAEHLSKLTGTTTIVKEQITTSGRRTS
ALLGNVSRTFQEVQRPLLTPDECLRMPGPKKSADGSIEEAGDMVVYVAGYPAIYGKQPLY
FKDPIFQARAAVPAPKVSDKLIQTATVEEGEGITI

Reference
[1] Grahn AM et al (2000) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. J Bacteriol. 182(6):1564-74. [PMID:10692361]
[2] Cabezón E et al (1994) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. J Bacteriol. 176(14):4455-8. [PMID:8021231]
[3] Hamilton CM et al (2000) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. J Bacteriol. 182(6):1541-8. [PMID:10692358]
[4] Gomis-Rüth FX et al (2004) Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. Curr Pharm Des. 10(13):1551-65. [PMID:15134575]
Information of plasmid
ID 1
Plasmid name RP4
GenBank accession number X14165.1
Incompatibility group IncP1
Genome size 60099 bp
Coordinate of oriT  [Strand] _
Drug resistance experimental resistance to carbenicillin, kanamycin, ampicillin and tetracycline
Heavy-metal resistance _
Virulence factor _
Xenobiotic degradation experimental degradation of biphenyl and 4-chlorobiphenyl
Host bacterium [NCBI Taxonomy ID] Pseudomonas aeruginosa S8 [287]
Reference
[1] Saunders JR et al (1972) Properties of RP4, an R factor which originated in Pseudomonas aeruginosa S8.. J Bacteriol. 112(2):690-6. [PMID:4628745]
[2] Datta N et al (1971) Properties of an R factor from Pseudomonas aeruginosa. J Bacteriol. 108(3):1244-9. [PMID:4945193]
[3] Toussaint A et al (2003) The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. Appl Environ Microbiol. 69(8):4837-45. [PMID:12902278]
[4] Springael D et al (1993) Identification of a catabolic transposon, Tn4371, carrying biphenyl and 4-chlorobiphenyl degradation genes in ＿i>Alcaligenes eutrophus A5. J Bacteriol. 175(6):1674-81. [PMID:8383664]

Microbial Bioinformatics Group in MML, SJTU